From 95787ecf9438328069346b47d583ff038c1367c7 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 16 Sep 2021 16:52:25 -0400
Subject: [PATCH 001/347] Initial commit adding Microscopy related files

---
 README.md                                     |   1 +
 mkdocs.yml                                    |   1 +
 src/02-common-principles.md                   |   1 +
 .../10-microscopy.md                          | 361 ++++++++++++++++++
 .../images/microscopy_chunks.png              | Bin 0 -> 136682 bytes
 .../images/microscopy_sem_overview.jpg        | Bin 0 -> 169378 bytes
 src/99-appendices/04-entity-table.md          |   4 +
 src/schema/datatypes/microscopy.yaml          |  45 +++
 src/schema/entities.yaml                      |  20 +
 9 files changed, 433 insertions(+)
 create mode 100644 src/04-modality-specific-files/10-microscopy.md
 create mode 100644 src/04-modality-specific-files/images/microscopy_chunks.png
 create mode 100644 src/04-modality-specific-files/images/microscopy_sem_overview.jpg
 create mode 100644 src/schema/datatypes/microscopy.yaml

diff --git a/README.md b/README.md
index 41136e0fd3..69fe0beb5f 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - behavioral
 - physiological
 - PET
+- Microscopy
 
 # Formatting your data with BIDS
 
diff --git a/mkdocs.yml b/mkdocs.yml
index 59c29c098a..7927fd923d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -37,6 +37,7 @@ nav:
         - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
         - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
         - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
+        - Microscopy: 04-modality-specific-files/10-microscopy.md
       - Derivatives:
         - BIDS Derivatives: 05-derivatives/01-introduction.md
         - Common data types and metadata: 05-derivatives/02-common-data-types.md
diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index c8c5b306c6..4da3cad0b1 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -56,6 +56,7 @@ misunderstanding we clarify them here.
     1.  `ieeg` (intracranial electroencephalography)
     1.  `beh` (behavioral)
     1.  `pet` (positron emission tomography)
+    1.  `microscopy`
 
     Data files are contained in a directory named for the data type.
     In raw datasets, the data type directory is nested inside subject and
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
new file mode 100644
index 0000000000..d2572cc6ec
--- /dev/null
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -0,0 +1,361 @@
+# Microscopy
+
+Support for Microscopy was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
+
+<!---
+The following link is temporary and points to the bep031 branch of bids-examples,
+update to 'https://github.com/bids-standard/bids-examples' when examples are merged.
+-->
+Microscopy datasets formatted using this specification are available on the
+[BIDS examples repository](https://github.com/neuropoly/bids-examples/tree/bep031)
+(`microscopy_SEM001` and `microscopy_SPIM001`) and can be used for practical
+guidance when curating a new dataset.
+
+Further Microscopy datasets are available:
+
+-   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
+-   In OME-TIFF format: [link to the dataset - pending]
+
+## Microscopy recording data
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+-->
+Template:
+```
+sub-<label>/
+    [ses-<label>/]
+        microscopy/
+            sub-<label>[_ses-<label>]_sample-<label>[_chunk-<index>][_acq-<label>][_stain-<label>][_run-<index>]_<suffix>.<extension>
+            sub-<label>[_ses-<label>]_sample-<label>[_chunk-<index>][_acq-<label>][_stain-<label>][_run-<index>]_<suffix>.json
+```
+Microscopy data MUST be stored in the `microscopy` directory.
+
+### File formats
+The Microscopy community uses a variety of formats for storing raw data, and there is no single
+standard that all researchers agree on. However, a standardized file structure has been developed
+by the [Open Microscopy Environment](https://www.openmicroscopy.org/) for whole-slide imaging with
+the [OME-TIFF file specifications](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/file-structure.html).
+The OME-TIFF file allows for multi-pages TIFF file to store multiple image planes and supports
+multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
+file’s header.
+
+In Microscopy-BIDS, we accept different file formats to accommodate datasets stored in 2D image
+formats and whole-slide imaging formats, to accommodate lossless and lossy compression,
+and to avoid unnecessary conversions of the original data from a non-tiled to a tiled format,
+or vice-versa.
+
+For BIDS, Microscopy raw data MUST be stored in one of the following formats:
+
+- [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
+- [Tag Image File Format](https://www.adobe.io/open/standards/TIFF.html) (`.tif`)
+- [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
+(`.ome.tif` for standard TIFF files or `.ome.btf` for
+[BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
+
+If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the native format MAY be
+stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+
+Future versions of Microscopy-BIDS may extend this list of supported file formats.
+For example with the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) format currently
+developed by OME as a successor to OME-TIFF for better remote sharing of large datasets.
+
+### Modality suffixes
+Microscopy data currently support the following imaging modalities:
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+-->
+| **Name**                                         | `suffix` |
+| ------------------------------------------------ | -------- |
+| Transmission electron microscopy                 | TEM      |
+| Scanning electron microscopy                     | SEM      |
+| Micro-CT                                         | CT       |
+| Bright-field microscopy                          | BF       |
+| Dark-field microscopy                            | DF       |
+| Phase-contrast microscopy                        | PC       |
+| Differential interference contrast microscopy    | DIC      |
+| Fluorescence                                     | FLUO     |
+| Confocal microscopy                              | CONF     |
+| Polarized-light microscopy                       | PLI      |
+| Coherent anti-Stokes Raman spectroscopy          | CARS     |
+| 2-photon excitation microscopy                   | 2PE      |
+| Multi-photon excitation microscopy               | MPE      |
+| Super-resolution microscopy                      | SR       |
+| Nonlinear optical microscopy                     | NLO      |
+| Optical coherence tomography                     | OCT      |
+| Selective plane illumination microscopy          | SPIM     |
+
+### Filename entities
+
+In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))
+can refer to all the acquisitions between the start and the end of an imaging experiment
+for ex vivo imaging or a subject lab visit for biopsy procedure and/or in vivo imaging.
+
+The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRED for
+Microscopy data and is used to distinguish between different samples from the same subject.
+The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
+
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`.
+```Text
+sub-01/
+    microscopy/
+        sub-01_sample-01_<modality_suffix>.<ext>
+        sub-01_sample-02_<modality_suffix>.<ext>
+        sub-01_sample-03_<modality_suffix>.<ext>
+        sub-01_<modality_suffix>.json
+```
+In this example, JSON metadata is common for all samples of `sub-01`.
+JSON metadata may be defined per subject or per sample as appropriate, per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+
+The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when multiples
+regions (2D images or 3D volumes files) of the same physical sample are imaged with different
+fields of view, regardless if they overlap or not.
+
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`) of subject `sub-01`.
+```Text
+sub-01/
+    microscopy/
+        sub-01_sample-01_chunk-01_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-01_<modality_suffix>.json
+        sub-01_sample-01_chunk-02_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-02_<modality_suffix>.json
+        sub-01_sample-01_chunk-03_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-03_<modality_suffix>.json
+        sub-01_sample-01_chunk-04_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-04_<modality_suffix>.json
+```
+In this example, JSON metadata is different for each chunk of `sub-01_sample-01`.
+JSON metadata may be defined per sample or per chunk as appropriate, per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+
+In some cases, the chunks can be "ordered" and correspond to the displacement of the
+microscope stage for example.
+In others cases, the chunks can be different images of the same sample with no explicit
+spatial relation between them.
+
+Examples of different chunks configurations can be seen in Figure 1.
+![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
+
+Figure 1: Examples of chunks configurations. a) ordered 2D chunks without overlap,
+b) ordered 2D chunks with overlap, c) unordered 2D chunks with and without overlap,
+d) and e) ordered 2D chunks on different 3D planes, f) ordered 3D chunks
+
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
+MAY be used to distinguish a different set of parameters used for acquiring the same modality.
+For example, two images of the same sample acquired with different magnification of 40x and 60x.
+In such case two files could have the following names:
+`sub-01_sample-01_acq-40x_<modality_suffix>.<ext>` and
+`sub-01_sample-01_acq-60x_<modality_suffix>.<ext>`, however the user is free to choose any other
+label as long as they are consistent across subjects and sessions.
+
+The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity can be used to distinguish
+image files from the same sample using different stains or antibodies for contrast enhancement.
+
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+Brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three stains
+(`stain-01`, `stain-02`, `stain-03`) in three separate files.
+In this example, the entity stain is used to distinguish images with different
+stains in separate files from the same sample.
+```Text
+sub-01/
+    microscopy/
+        sub-01_sample-01_stain-01_<modality_suffix>.<ext>
+        sub-01_sample-01_stain-01_<modality_suffix>.json
+        sub-01_sample-01_stain-02_<modality_suffix>.<ext>
+        sub-01_sample-01_stain-02_<modality_suffix>.json
+        sub-01_sample-01_stain-03_<modality_suffix>.<ext>
+        sub-01_sample-01_stain-03_<modality_suffix>.json
+```
+In this example, the entity stain is used to distinguish images with different
+stains in separate files from the same sample.
+In the case where a single file contains different staining in each channel, the
+`stain-<label>` is omitted.
+
+Stains or antibodies SHOULD be indicated as appropriate in the `"SampleStaining"`,
+`"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` keys in the sidecar JSON file,
+although the label may be different.
+
+If more than one run of the same sample, chunk, acquisition and stain are acquired during
+the same session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
+`_run-1`, `_run-2`, `_run-3`, and so on.
+If only one run was acquired the `run-<index>` can be omitted.
+
+In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
+In the case where a multiple resolutions file format is converted to single resolution file format,
+only the higher resolution file is present in the raw data.
+Lower resolutions files MUST be placed under the `derivatives` folder and use the
+[`res-<label>`](../99-appendices/09-entities.md#res) entity.
+See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes).
+
+### Microscopy metadata (Sidecar JSON)
+
+Microscopy data MUST be described by metadata fields, stored in sidecar JSON files.
+
+#### Device Hardware
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+
+Note: For `StationName`, we removed "Corresponds to DICOM Tag 0008, 1010 `Station Name`." from the description.
+It will require changes to `src/schema/metatata/StationName.yaml` and `src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md`.
+-->
+| **Key name**              | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
+| ------------------------- | --------------------- | ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Manufacturer              | RECOMMENDED           | string    | Manufacturer of the equipment that produced the measurements. |
+| ManufacturersModelName    | RECOMMENDED           | string    | Manufacturer’s model name of the equipment that produced the measurements. |
+| DeviceSerialNumber        | RECOMMENDED           | string    | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset. |
+| StationName               | RECOMMENDED           | string    | Institution defined name of the machine that produced the measurements. |
+| SoftwareVersions          | RECOMMENDED           | string    | Manufacturer’s designation of software version of the equipment that produced the measurements. |
+| InstitutionName           | RECOMMENDED           | string    | The name of the institution in charge of the equipment that produced the measurements. |
+| InstitutionAddress        | RECOMMENDED           | string    | The address of the institution in charge of the equipment that produced the measurements. |
+| InstitutionDepartmentName | RECOMMENDED           | string    | The department in the institution in charge of the equipment that produced the measurements. |
+
+
+#### Image Acquisition
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+-->
+| **Key name**               | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
+| -------------------------- | --------------------- | ------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| PixelSize                  | REQUIRED              | array of numbers    | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
+| PixelSizeUnits             | REQUIRED              | string              | Unit format of the specified PixelSize. MUST be micrometer (`"um"`). |
+| Immersion                  | OPTIONAL              | string              | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field. |
+| NumericalAperture          | OPTIONAL              | number              | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field. |
+| Magnification              | OPTIONAL              | number              | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.|
+| ImageAcquisitionProtocol   | OPTIONAL              | string or URI       | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/). |
+| OtherAcquisitionParameters | OPTIONAL              | string              | Description of other relevant image acquisition parameters. |
+
+#### Sample
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+
+Note: For `BodyPart`, we removed: "Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. For example: `"BRAIN"`."
+from the description, and replace with
+"from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN".`)".
+It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modality-specific-files/09-positron-emission-tomography.md`.
+-->
+| **Key name**                | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
+| --------------------------- | --------------------- | -------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| BodyPart                    | RECOMMENDED           | string                     | Body part of the organ / body region scanned. from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)". |
+| BodyPartDetails             | OPTIONAL              | string                     | If needed, additional details about body part or location (for example: `"corpus callosum"`). |
+| BodyPartDetailsOntology     | OPTIONAL              | string                     | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`). |
+| Environment                 | RECOMMENDED           | string                     | RECOMMENDED. Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`. |
+| SampleEmbedding             | OPTIONAL              | string                     | Description of the tissue sample embedding (for example: `"Epoxy resin"`). |
+| SampleFixation              | OPTIONAL              | string                     | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`). |
+| SampleStaining              | RECOMMENDED           | string or array of strings | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`). |
+| SamplePrimaryAntibody       | RECOMMENDED           | string or array of strings | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
+| SampleSecondaryAntibody     | RECOMMENDED           | string or array of strings | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
+| SliceThickness              | OPTIONAL              | number                     | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`). |
+| ShrinkageFactor             | OPTIONAL              | number                     | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`). |
+| SampleExtractionProtocol    | OPTIONAL              | string or URI              | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/). |
+| SampleExtractionInstitution | OPTIONAL              | string                     | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image. |
+
+#### Chunk transformations
+
+Chunk transformations metadata describes the spatial relation between chunks
+of the same sample in an implicit coordinate system.
+
+- The source frame of reference is the frame of reference of the associated image.
+- The target frame of reference is the implicit coordinate system of the transform.
+- The target frame of reference has the same units as the `PixelSizeUnits` metadata.
+- The chunk transform is described by 2 metadata fields: a transformation matrix and a
+description of the axis of the matrix.
+- Other transformations should be described in derivatives.
+<!---
+The following table will be generated automatically with macros after community review.
+A "manual" table is provided to facilitate the review process.
+-->
+| **Key name**                  | **Requirement level**                                            | **Data type**              | **Description**                                                                                                                                                                        |
+| ----------------------------- | ---------------------------------------------------------------- | -------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ChunkTransformationMatrix     | OPTIONAL                                                         | array of arrays of numbers | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
+| ChunkTransformationMatrixAxis | OPTIONAL, but REQUIRED if `ChunkTransformationMatrix` is present | arrays of strings          | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`) |
+
+#### Example (`*_<suffix>.json`)
+```JSON
+{
+        "Manufacturer": "Hamamatsu",
+        "ManufacturersModelName": "C9600-12",
+        "PixelSize": [0.23, 0.23],
+        "PixelSizeUnits": "um",
+        "Magnification": 40,
+        "BodyPart": "BRAIN",
+        "BodyPartDetails": "corpus callosum",
+        "Environment": "exvivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "LFB",
+        "SliceThickness": 5,
+        "ShrinkageFactor": 3
+}
+```
+
+## Required Samples file (`samples.tsv`)
+
+For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file) is REQUIRED.
+
+Additional optional columns in `samples.tsv` MAY be used to describe other samples' attributes.
+
+## Recommended participant data (`participants.tsv`)
+<!---
+This section may be removed or modified depending if it is included in the "general"
+participants.tsv file in PR #816.
+(https://github.com/bids-standard/bids-specification/pull/816#issuecomment-909343123)
+-->
+In addition to the species column in the [Participants file](../03-modality-agnostic-files.md#participants-file),
+the following data SHOULD be included for species different from `homo sapiens`:
+
+-   `strain`: string value indicating the strain of the species, for example: `C57BL/6J`.
+-   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
+    of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
+
+For example:
+```Text
+participant_id species strain strain_rrid
+sub-01 mus musculus C57BL/6J RRID:IMSR_JAX:000664
+sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
+```
+
+## Photos of the samples (`*_photo.<extension>`)
+Photos of the tissue sample, overview microscopy scans or blockface images from cutting
+MAY be included for visualization of large samples or to indicate the location of chunks
+in a sample.
+<!--- The following example will be generated automatically with macros after community review. -->
+```Text
+sub-<label>/
+    [ses-<label>/]
+        microscopy/
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.<extension>
+```
+The file `<extension>` for photos can be either `.jpg`, `.png` or `.tif`.
+
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to indicate
+acquisition of different photos of the same sample.
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+```Text
+sub-01/
+    microscopy/
+        sub-01_sample-01_acq-1_photo.jpg
+        sub-01_sample-01_acq-2_photo.jpg
+```
+Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2018.
+[doi:10.1038/s41598-018-22181-4](https://doi.org/10.1038/s41598-018-22181-4).
+```Text
+    sub-01_sample-01_photo.jpg
+```
+![SEM overview](images/microscopy_sem_overview.jpg "SEM overview")
+
+<!-- Link Definitions -->
diff --git a/src/04-modality-specific-files/images/microscopy_chunks.png b/src/04-modality-specific-files/images/microscopy_chunks.png
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literal 0
HcmV?d00001

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 0151c08738..92ae16c1e0 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -36,3 +36,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 ## Behavioral Data
 
 {{ MACROS___make_entity_table(datatypes=["beh"], auxdatatypes=[]) }}
+
+## Microscopy
+
+{{ MACROS___make_entity_table(datatypes=["microscopy"], auxdatatypes=[]) }}
diff --git a/src/schema/datatypes/microscopy.yaml b/src/schema/datatypes/microscopy.yaml
new file mode 100644
index 0000000000..20e1547875
--- /dev/null
+++ b/src/schema/datatypes/microscopy.yaml
@@ -0,0 +1,45 @@
+---
+# Microscopy
+- suffixes:
+    - TEM
+    - SEM
+    - CT
+    - BF
+    - DF
+    - PC
+    - DIC
+    - FLUO
+    - CONF
+    - PLI
+    - CARS
+    - 2PE
+    - MPE
+    - SR
+    - NLO
+    - OCT
+    - SPIM
+  extensions:
+    - .ome.tif
+    - .ome.btf
+    - .png
+    - .tiff
+    - .json
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    chunk: optional
+    acquisition: optional
+    stain: optional
+    run: optional
+- suffixes:
+    - photo
+  extensions:
+    - .jpg
+    - .png
+    - .tif
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    acquisition: optional
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 8bcd1a16c1..42db8eab05 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -38,6 +38,15 @@ sample:
     The label MUST be unique per subject and is RECOMMENDED to be unique
     throughout the dataset.
   format: label
+chunk:
+  name: Chunk
+  entity: chunk
+  description: |
+    The `chunk-<index>` key/value pair is used to distinguish between different
+    regions, 2D images or 3D volumes files, of the same physical sample with
+    different fields of view acquired in the same imaging experiment.
+  type: string
+  format: index
 task:
   name: Task
   entity: task
@@ -91,6 +100,17 @@ tracer:
     although the label may be different.
   type: string
   format: label
+stain:
+  name: Stain
+  entity: stain
+  description: |
+    The `stain-<label>` key/pair values can be used to distinguish image files
+    from the same sample using different stains or antibodies for contrast enhancement.
+    Stains or antibodies SHOULD be indicated as appropriate in the `SampleStaining`,
+    `SamplePrimaryAntibodies` and/or `SampleSecondaryAntobodies` keys in the JSON file,
+    although the label may be different.
+  type: string
+  format: label
 reconstruction:
   name: Reconstruction
   entity: rec

From b83a72d271914d8cd970ab6b9dbdce1ef9961298 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 16 Sep 2021 19:36:38 -0400
Subject: [PATCH 002/347] Add Link descriptions and fix md formatting

---
 .../10-microscopy.md                          | 156 ++++++++++--------
 1 file changed, 86 insertions(+), 70 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index d2572cc6ec..7deebaa50c 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -19,6 +19,7 @@ guidance when curating a new dataset.
 Further Microscopy datasets are available:
 
 -   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
+
 -   In OME-TIFF format: [link to the dataset - pending]
 
 ## Microscopy recording data
@@ -27,7 +28,7 @@ The following table will be generated automatically with macros after community
 A "manual" table is provided to facilitate the review process.
 -->
 Template:
-```
+```Text
 sub-<label>/
     [ses-<label>/]
         microscopy/
@@ -52,11 +53,13 @@ or vice-versa.
 
 For BIDS, Microscopy raw data MUST be stored in one of the following formats:
 
-- [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
-- [Tag Image File Format](https://www.adobe.io/open/standards/TIFF.html) (`.tif`)
-- [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
-(`.ome.tif` for standard TIFF files or `.ome.btf` for
-[BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
+-   [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
+
+-   [Tag Image File Format](https://www.adobe.io/open/standards/TIFF.html) (`.tif`)
+
+-   [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
+    (`.ome.tif` for standard TIFF files or `.ome.btf` for
+    [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
 
 If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the native format MAY be
 stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
@@ -71,25 +74,25 @@ Microscopy data currently support the following imaging modalities:
 The following table will be generated automatically with macros after community review.
 A "manual" table is provided to facilitate the review process.
 -->
-| **Name**                                         | `suffix` |
-| ------------------------------------------------ | -------- |
-| Transmission electron microscopy                 | TEM      |
-| Scanning electron microscopy                     | SEM      |
-| Micro-CT                                         | CT       |
-| Bright-field microscopy                          | BF       |
-| Dark-field microscopy                            | DF       |
-| Phase-contrast microscopy                        | PC       |
-| Differential interference contrast microscopy    | DIC      |
-| Fluorescence                                     | FLUO     |
-| Confocal microscopy                              | CONF     |
-| Polarized-light microscopy                       | PLI      |
-| Coherent anti-Stokes Raman spectroscopy          | CARS     |
-| 2-photon excitation microscopy                   | 2PE      |
-| Multi-photon excitation microscopy               | MPE      |
-| Super-resolution microscopy                      | SR       |
-| Nonlinear optical microscopy                     | NLO      |
-| Optical coherence tomography                     | OCT      |
-| Selective plane illumination microscopy          | SPIM     |
+| **Name**                                      | `suffix` |
+| --------------------------------------------- | -------- |
+| Transmission electron microscopy              | TEM      |
+| Scanning electron microscopy                  | SEM      |
+| Micro-CT                                      | CT       |
+| Bright-field microscopy                       | BF       |
+| Dark-field microscopy                         | DF       |
+| Phase-contrast microscopy                     | PC       |
+| Differential interference contrast microscopy | DIC      |
+| Fluorescence                                  | FLUO     |
+| Confocal microscopy                           | CONF     |
+| Polarized-light microscopy                    | PLI      |
+| Coherent anti-Stokes Raman spectroscopy       | CARS     |
+| 2-photon excitation microscopy                | 2PE      |
+| Multi-photon excitation microscopy            | MPE      |
+| Super-resolution microscopy                   | SR       |
+| Nonlinear optical microscopy                  | NLO      |
+| Optical coherence tomography                  | OCT      |
+| Selective plane illumination microscopy       | SPIM     |
 
 ### Filename entities
 
@@ -211,32 +214,31 @@ A "manual" table is provided to facilitate the review process.
 Note: For `StationName`, we removed "Corresponds to DICOM Tag 0008, 1010 `Station Name`." from the description.
 It will require changes to `src/schema/metatata/StationName.yaml` and `src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md`.
 -->
-| **Key name**              | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
-| ------------------------- | --------------------- | ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Manufacturer              | RECOMMENDED           | string    | Manufacturer of the equipment that produced the measurements. |
-| ManufacturersModelName    | RECOMMENDED           | string    | Manufacturer’s model name of the equipment that produced the measurements. |
-| DeviceSerialNumber        | RECOMMENDED           | string    | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset. |
-| StationName               | RECOMMENDED           | string    | Institution defined name of the machine that produced the measurements. |
-| SoftwareVersions          | RECOMMENDED           | string    | Manufacturer’s designation of software version of the equipment that produced the measurements. |
-| InstitutionName           | RECOMMENDED           | string    | The name of the institution in charge of the equipment that produced the measurements. |
-| InstitutionAddress        | RECOMMENDED           | string    | The address of the institution in charge of the equipment that produced the measurements. |
-| InstitutionDepartmentName | RECOMMENDED           | string    | The department in the institution in charge of the equipment that produced the measurements. |
-
+| **Key name**              | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                           |
+| ------------------------- | --------------------- | ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Manufacturer              | RECOMMENDED           | [string][]    | Manufacturer of the equipment that produced the measurements.                                                                                                                                             |
+| ManufacturersModelName    | RECOMMENDED           | [string][]    | Manufacturer’s model name of the equipment that produced the measurements.                                                                                                                                |
+| DeviceSerialNumber        | RECOMMENDED           | [string][]    | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset. |
+| StationName               | RECOMMENDED           | [string][]    | Institution defined name of the machine that produced the measurements.                                                                                                                                   |
+| SoftwareVersions          | RECOMMENDED           | [string][]    | Manufacturer’s designation of software version of the equipment that produced the measurements.                                                                                                           |
+| InstitutionName           | RECOMMENDED           | [string][]    | The name of the institution in charge of the equipment that produced the measurements.                                                                                                                    |
+| InstitutionAddress        | RECOMMENDED           | [string][]    | The address of the institution in charge of the equipment that produced the measurements.                                                                                                                 |
+| InstitutionDepartmentName | RECOMMENDED           | [string][]    | The department in the institution in charge of the equipment that produced the measurements.                                                                                                              |
 
 #### Image Acquisition
 <!---
 The following table will be generated automatically with macros after community review.
 A "manual" table is provided to facilitate the review process.
 -->
-| **Key name**               | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
-| -------------------------- | --------------------- | ------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| PixelSize                  | REQUIRED              | array of numbers    | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
-| PixelSizeUnits             | REQUIRED              | string              | Unit format of the specified PixelSize. MUST be micrometer (`"um"`). |
-| Immersion                  | OPTIONAL              | string              | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field. |
-| NumericalAperture          | OPTIONAL              | number              | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field. |
-| Magnification              | OPTIONAL              | number              | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.|
-| ImageAcquisitionProtocol   | OPTIONAL              | string or URI       | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/). |
-| OtherAcquisitionParameters | OPTIONAL              | string              | Description of other relevant image acquisition parameters. |
+| **Key name**               | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
+| -------------------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| PixelSize                  | REQUIRED              | [array][] of [numbers][] | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
+| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be micrometer (`"um"`).                                                                                                                                                                                                                                                                                                                                                                                                     |
+| Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
+| NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
+| Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
+| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][]    | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                     |
+| OtherAcquisitionParameters | OPTIONAL              | [string][]               | Description of other relevant image acquisition parameters.                                                                                                                                                                                                                                                                                                                                                                                                              |
 
 #### Sample
 <!---
@@ -248,41 +250,46 @@ from the description, and replace with
 "from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN".`)".
 It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modality-specific-files/09-positron-emission-tomography.md`.
 -->
-| **Key name**                | **Requirement level** | **Data type** | **Description**                                                                                                                                                                        |
-| --------------------------- | --------------------- | -------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| BodyPart                    | RECOMMENDED           | string                     | Body part of the organ / body region scanned. from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)". |
-| BodyPartDetails             | OPTIONAL              | string                     | If needed, additional details about body part or location (for example: `"corpus callosum"`). |
-| BodyPartDetailsOntology     | OPTIONAL              | string                     | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`). |
-| Environment                 | RECOMMENDED           | string                     | RECOMMENDED. Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`. |
-| SampleEmbedding             | OPTIONAL              | string                     | Description of the tissue sample embedding (for example: `"Epoxy resin"`). |
-| SampleFixation              | OPTIONAL              | string                     | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`). |
-| SampleStaining              | RECOMMENDED           | string or array of strings | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`). |
-| SamplePrimaryAntibody       | RECOMMENDED           | string or array of strings | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
-| SampleSecondaryAntibody     | RECOMMENDED           | string or array of strings | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
-| SliceThickness              | OPTIONAL              | number                     | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`). |
-| ShrinkageFactor             | OPTIONAL              | number                     | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`). |
-| SampleExtractionProtocol    | OPTIONAL              | string or URI              | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/). |
-| SampleExtractionInstitution | OPTIONAL              | string                     | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image. |
+| **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
+| --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
+| BodyPartDetails             | OPTIONAL              | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
+| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`).                                                                                                                                                                                                                                                                                                                                                                 |
+| Environment                 | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| SampleStaining              | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`).                                                                                                                                                                                                                                                                                                                                  |
+| SamplePrimaryAntibody       | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
+| SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
+| SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| ShrinkageFactor             | OPTIONAL              | [number][]                             | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`).                                                                                                                                                                                                                                                                                                                                                                                      |
+| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][]                  | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
 #### Chunk transformations
 
 Chunk transformations metadata describes the spatial relation between chunks
 of the same sample in an implicit coordinate system.
 
-- The source frame of reference is the frame of reference of the associated image.
-- The target frame of reference is the implicit coordinate system of the transform.
-- The target frame of reference has the same units as the `PixelSizeUnits` metadata.
-- The chunk transform is described by 2 metadata fields: a transformation matrix and a
-description of the axis of the matrix.
-- Other transformations should be described in derivatives.
+-   The source frame of reference is the frame of reference of the associated image.
+
+-   The target frame of reference is the implicit coordinate system of the transform.
+
+-   The target frame of reference has the same units as the `PixelSizeUnits` metadata.
+
+-   The chunk transform is described by 2 metadata fields: a transformation matrix and a
+    description of the axis of the matrix.
+
+-   Other transformations should be described in derivatives.
+
 <!---
 The following table will be generated automatically with macros after community review.
 A "manual" table is provided to facilitate the review process.
 -->
-| **Key name**                  | **Requirement level**                                            | **Data type**              | **Description**                                                                                                                                                                        |
-| ----------------------------- | ---------------------------------------------------------------- | -------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ChunkTransformationMatrix     | OPTIONAL                                                         | array of arrays of numbers | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
-| ChunkTransformationMatrixAxis | OPTIONAL, but REQUIRED if `ChunkTransformationMatrix` is present | arrays of strings          | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`) |
+| **Key name**                  | **Requirement level**                                            | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| ----------------------------- | ---------------------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ChunkTransformationMatrix     | OPTIONAL                                                         | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
+| ChunkTransformationMatrixAxis | OPTIONAL, but REQUIRED if `ChunkTransformationMatrix` is present | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`)                                                                                                                                                                                                                                                                                                                                                             |
 
 #### Example (`*_<suffix>.json`)
 ```JSON
@@ -318,6 +325,7 @@ In addition to the species column in the [Participants file](../03-modality-agno
 the following data SHOULD be included for species different from `homo sapiens`:
 
 -   `strain`: string value indicating the strain of the species, for example: `C57BL/6J`.
+
 -   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
     of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
 
@@ -359,3 +367,11 @@ Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2
 ![SEM overview](images/microscopy_sem_overview.jpg "SEM overview")
 
 <!-- Link Definitions -->
+
+[strings]: https://www.w3schools.com/js/js_json_datatypes.asp
+[string]: https://www.w3schools.com/js/js_json_datatypes.asp
+[numbers]: https://www.w3schools.com/js/js_json_datatypes.asp
+[number]: https://www.w3schools.com/js/js_json_datatypes.asp
+[arrays]: https://www.w3schools.com/js/js_json_arrays.asp
+[array]: https://www.w3schools.com/js/js_json_arrays.asp
+[URI]: ../02-common-principles.md#uniform-resource-indicator

From 8e29cd84f64e09431aa5b4173f981c146a8d84b9 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 20 Sep 2021 11:06:03 -0400
Subject: [PATCH 003/347] Fix md formatting

---
 src/04-modality-specific-files/10-microscopy.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 7deebaa50c..5808cd1e8c 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -19,8 +19,7 @@ guidance when curating a new dataset.
 Further Microscopy datasets are available:
 
 -   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
-
--   In OME-TIFF format: [link to the dataset - pending]
+-   In OME-TIFF format: (link to the dataset - pending)
 
 ## Microscopy recording data
 <!---
@@ -237,7 +236,7 @@ A "manual" table is provided to facilitate the review process.
 | Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
 | NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
 | Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
-| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][]    | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                     |
+| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][uri] | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                     |
 | OtherAcquisitionParameters | OPTIONAL              | [string][]               | Description of other relevant image acquisition parameters.                                                                                                                                                                                                                                                                                                                                                                                                              |
 
 #### Sample
@@ -263,7 +262,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
 | SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ShrinkageFactor             | OPTIONAL              | [number][]                             | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`).                                                                                                                                                                                                                                                                                                                                                                                      |
-| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][]                  | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
 #### Chunk transformations
@@ -374,4 +373,4 @@ Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2
 [number]: https://www.w3schools.com/js/js_json_datatypes.asp
 [arrays]: https://www.w3schools.com/js/js_json_arrays.asp
 [array]: https://www.w3schools.com/js/js_json_arrays.asp
-[URI]: ../02-common-principles.md#uniform-resource-indicator
+[uri]: ../02-common-principles.md#uniform-resource-indicator

From ec29dcd8ac7ae78dde06095901d5f75519df35fc Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 28 Sep 2021 11:02:20 -0400
Subject: [PATCH 004/347] Move "chunk" entity at the end of filename before
 modality_suffix

---
 .../10-microscopy.md                          | 80 +++++++++----------
 src/schema/datatypes/microscopy.yaml          |  2 +-
 src/schema/entities.yaml                      | 18 ++---
 3 files changed, 50 insertions(+), 50 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 5808cd1e8c..43401820e4 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -31,8 +31,8 @@ Template:
 sub-<label>/
     [ses-<label>/]
         microscopy/
-            sub-<label>[_ses-<label>]_sample-<label>[_chunk-<index>][_acq-<label>][_stain-<label>][_run-<index>]_<suffix>.<extension>
-            sub-<label>[_ses-<label>]_sample-<label>[_chunk-<index>][_acq-<label>][_stain-<label>][_run-<index>]_<suffix>.json
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.<extension>
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.json
 ```
 Microscopy data MUST be stored in the `microscopy` directory.
 
@@ -118,41 +118,6 @@ In this example, JSON metadata is common for all samples of `sub-01`.
 JSON metadata may be defined per subject or per sample as appropriate, per the
 [inheritance principle](../02-common-principles.md#the-inheritance-principle).
 
-The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when multiples
-regions (2D images or 3D volumes files) of the same physical sample are imaged with different
-fields of view, regardless if they overlap or not.
-
-<!--- The following example will be generated automatically with macros after community review. -->
-For example:
-Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`) of subject `sub-01`.
-```Text
-sub-01/
-    microscopy/
-        sub-01_sample-01_chunk-01_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-01_<modality_suffix>.json
-        sub-01_sample-01_chunk-02_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-02_<modality_suffix>.json
-        sub-01_sample-01_chunk-03_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-03_<modality_suffix>.json
-        sub-01_sample-01_chunk-04_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-04_<modality_suffix>.json
-```
-In this example, JSON metadata is different for each chunk of `sub-01_sample-01`.
-JSON metadata may be defined per sample or per chunk as appropriate, per the
-[inheritance principle](../02-common-principles.md#the-inheritance-principle).
-
-In some cases, the chunks can be "ordered" and correspond to the displacement of the
-microscope stage for example.
-In others cases, the chunks can be different images of the same sample with no explicit
-spatial relation between them.
-
-Examples of different chunks configurations can be seen in Figure 1.
-![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
-
-Figure 1: Examples of chunks configurations. a) ordered 2D chunks without overlap,
-b) ordered 2D chunks with overlap, c) unordered 2D chunks with and without overlap,
-d) and e) ordered 2D chunks on different 3D planes, f) ordered 3D chunks
-
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
 MAY be used to distinguish a different set of parameters used for acquiring the same modality.
 For example, two images of the same sample acquired with different magnification of 40x and 60x.
@@ -189,11 +154,46 @@ Stains or antibodies SHOULD be indicated as appropriate in the `"SampleStaining"
 `"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` keys in the sidecar JSON file,
 although the label may be different.
 
-If more than one run of the same sample, chunk, acquisition and stain are acquired during
-the same session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
+If more than one run of the same sample, acquisition and stain are acquired during the same
+session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
 `_run-1`, `_run-2`, `_run-3`, and so on.
 If only one run was acquired the `run-<index>` can be omitted.
 
+The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when multiples
+regions (2D images or 3D volumes files) of the same physical sample are imaged with different
+fields of view, regardless if they overlap or not.
+
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`) of subject `sub-01`.
+```Text
+sub-01/
+    microscopy/
+        sub-01_sample-01_chunk-01_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-01_<modality_suffix>.json
+        sub-01_sample-01_chunk-02_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-02_<modality_suffix>.json
+        sub-01_sample-01_chunk-03_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-03_<modality_suffix>.json
+        sub-01_sample-01_chunk-04_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-04_<modality_suffix>.json
+```
+In this example, JSON metadata is different for each chunk of `sub-01_sample-01`.
+JSON metadata may be defined per sample or per chunk as appropriate, per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+
+In some cases, the chunks can be "ordered" and correspond to the displacement of the
+microscope stage for example.
+In others cases, the chunks can be different images of the same sample with no explicit
+spatial relation between them.
+
+Examples of different chunks configurations can be seen in Figure 1.
+![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
+
+Figure 1: Examples of chunks configurations. a) ordered 2D chunks without overlap,
+b) ordered 2D chunks with overlap, c) unordered 2D chunks with and without overlap,
+d) and e) ordered 2D chunks on different 3D planes, f) ordered 3D chunks
+
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,
 only the higher resolution file is present in the raw data.
@@ -251,7 +251,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 -->
 | **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 | --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
+| BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
 | BodyPartDetails             | OPTIONAL              | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
 | BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`).                                                                                                                                                                                                                                                                                                                                                                 |
 | Environment                 | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
diff --git a/src/schema/datatypes/microscopy.yaml b/src/schema/datatypes/microscopy.yaml
index 20e1547875..0d14474d3d 100644
--- a/src/schema/datatypes/microscopy.yaml
+++ b/src/schema/datatypes/microscopy.yaml
@@ -28,10 +28,10 @@
     subject: required
     session: optional
     sample: required
-    chunk: optional
     acquisition: optional
     stain: optional
     run: optional
+    chunk: optional
 - suffixes:
     - photo
   extensions:
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 42db8eab05..33cf47ad17 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -38,15 +38,6 @@ sample:
     The label MUST be unique per subject and is RECOMMENDED to be unique
     throughout the dataset.
   format: label
-chunk:
-  name: Chunk
-  entity: chunk
-  description: |
-    The `chunk-<index>` key/value pair is used to distinguish between different
-    regions, 2D images or 3D volumes files, of the same physical sample with
-    different fields of view acquired in the same imaging experiment.
-  type: string
-  format: index
 task:
   name: Task
   entity: task
@@ -293,6 +284,15 @@ split:
     [Scans file](../03-modality-agnostic-files.md#scans-file).
   type: string
   format: index
+chunk:
+  name: Chunk
+  entity: chunk
+  description: |
+    The `chunk-<index>` key/value pair is used to distinguish between different
+    regions, 2D images or 3D volumes files, of the same physical sample with
+    different fields of view acquired in the same imaging experiment.
+  type: string
+  format: index
 resolution:
   name: Resolution
   entity: res

From 5e092ca55b8f9061a5b98915e512979ffe79a7db Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 30 Sep 2021 16:44:35 -0400
Subject: [PATCH 005/347] Add link to OME-TIFF dataset

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 43401820e4..6a5a00eb84 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -19,7 +19,7 @@ guidance when curating a new dataset.
 Further Microscopy datasets are available:
 
 -   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
--   In OME-TIFF format: (link to the dataset - pending)
+-   In OME-TIFF format: [`Broca's Area Light-Sheet Microscopy`](https://doi.org/10.5281/zenodo.5517223)
 
 ## Microscopy recording data
 <!---

From d4449af2b9e64d79ac0540eda5fd62775c00faff Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Thu, 30 Sep 2021 16:53:10 -0400
Subject: [PATCH 006/347] Update
 src/04-modality-specific-files/10-microscopy.md

Typo

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 6a5a00eb84..074f7ab6be 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -41,7 +41,7 @@ The Microscopy community uses a variety of formats for storing raw data, and the
 standard that all researchers agree on. However, a standardized file structure has been developed
 by the [Open Microscopy Environment](https://www.openmicroscopy.org/) for whole-slide imaging with
 the [OME-TIFF file specifications](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/file-structure.html).
-The OME-TIFF file allows for multi-pages TIFF file to store multiple image planes and supports
+The OME-TIFF file allows for multi-page TIFF files to store multiple image planes and supports
 multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
 file’s header.
 

From b8ad76685824b68aef686041a1248b2187b8adcd Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Fri, 1 Oct 2021 15:02:34 -0400
Subject: [PATCH 007/347] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 074f7ab6be..61138a26e5 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -77,7 +77,7 @@ A "manual" table is provided to facilitate the review process.
 | --------------------------------------------- | -------- |
 | Transmission electron microscopy              | TEM      |
 | Scanning electron microscopy                  | SEM      |
-| Micro-CT                                      | CT       |
+| Micro-CT                                      | uCT      |
 | Bright-field microscopy                       | BF       |
 | Dark-field microscopy                         | DF       |
 | Phase-contrast microscopy                     | PC       |
@@ -254,7 +254,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
 | BodyPartDetails             | OPTIONAL              | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
 | BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`).                                                                                                                                                                                                                                                                                                                                                                 |
-| Environment                 | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| SampleEnvironment           | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 | SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | SampleStaining              | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`).                                                                                                                                                                                                                                                                                                                                  |

From 2a5cf259fedc8e0816cf0dde90c6a27fe0e32c61 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 1 Oct 2021 15:18:56 -0400
Subject: [PATCH 008/347] Update "TissueDeformationScaling" field and JSON
 example

---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 61138a26e5..bede26a495 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -261,7 +261,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SamplePrimaryAntibody       | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
 | SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
 | SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| ShrinkageFactor             | OPTIONAL              | [number][]                             | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`).                                                                                                                                                                                                                                                                                                                                                                                      |
+| TissueDeformationScaling    | OPTIONAL              | [number][]                             | Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is `97`; and for an expansion of 100%, the value is `200`).                                                                                                                                                                                                                                                                                                                         |
 | SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
@@ -300,11 +300,11 @@ A "manual" table is provided to facilitate the review process.
         "Magnification": 40,
         "BodyPart": "BRAIN",
         "BodyPartDetails": "corpus callosum",
-        "Environment": "exvivo",
+        "SampleEnvironment": "exvivo",
         "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
         "SampleStaining": "LFB",
         "SliceThickness": 5,
-        "ShrinkageFactor": 3
+        "TissueDeformationScaling": 97
 }
 ```
 

From a133357c84e013127f42fb5cbd328e76c5312a31 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 1 Oct 2021 15:21:44 -0400
Subject: [PATCH 009/347] Update "uCT" suffix in
 schema/datatypes/microscopy.yaml

---
 src/schema/datatypes/microscopy.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/datatypes/microscopy.yaml b/src/schema/datatypes/microscopy.yaml
index 0d14474d3d..f3f8bdf1df 100644
--- a/src/schema/datatypes/microscopy.yaml
+++ b/src/schema/datatypes/microscopy.yaml
@@ -3,7 +3,7 @@
 - suffixes:
     - TEM
     - SEM
-    - CT
+    - uCT
     - BF
     - DF
     - PC

From 7f39d4c1f0cb3df34cd168d71abea19ea4157f70 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 1 Oct 2021 15:45:32 -0400
Subject: [PATCH 010/347] Add res-label example

---
 .../10-microscopy.md                           | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index bede26a495..5bb409e24e 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -199,7 +199,23 @@ In the case where a multiple resolutions file format is converted to single reso
 only the higher resolution file is present in the raw data.
 Lower resolutions files MUST be placed under the `derivatives` folder and use the
 [`res-<label>`](../99-appendices/09-entities.md#res) entity.
-See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes).
+
+<!--- The following example will be generated automatically with macros after community review. -->
+For example:
+```Text
+my_dataset/
+    derivatives/
+        downsampled/
+            sub-01/
+                microscopy/
+                    sub-01_sample-01_res-4x_TEM.png
+                    sub-01_sample-01_res-4x.json
+    sub-01/
+        microscopy/
+            sub-01_sample-01_TEM.png
+```
+See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes)
+for details.
 
 ### Microscopy metadata (Sidecar JSON)
 

From b5e745ef46b5e19046c93036bd8461eb3b09e307 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 Oct 2021 13:35:49 -0400
Subject: [PATCH 011/347] Start reorganizing.

---
 tools/schemacode/MANIFEST.in                  |    1 +
 tools/schemacode/README.md                    |    3 +
 tools/schemacode/pyproject.toml               |   29 +
 tools/schemacode/{ => schemacode}/__init__.py |    0
 tools/schemacode/schemacode/_version.py       |  554 +++++
 tools/schemacode/schemacode/info.py           |   84 +
 tools/schemacode/{ => schemacode}/schema.py   |   10 +-
 tools/schemacode/schemacode/tests/__init__.py |    0
 .../schemacode/tests/test_schema.py           |    1 +
 tools/schemacode/{ => schemacode}/utils.py    |    3 +-
 tools/schemacode/setup.cfg                    |   22 +
 tools/schemacode/setup.py                     |   57 +
 tools/schemacode/versioneer.py                | 1885 +++++++++++++++++
 13 files changed, 2643 insertions(+), 6 deletions(-)
 create mode 100644 tools/schemacode/MANIFEST.in
 create mode 100644 tools/schemacode/README.md
 create mode 100644 tools/schemacode/pyproject.toml
 rename tools/schemacode/{ => schemacode}/__init__.py (100%)
 create mode 100644 tools/schemacode/schemacode/_version.py
 create mode 100644 tools/schemacode/schemacode/info.py
 rename tools/schemacode/{ => schemacode}/schema.py (99%)
 create mode 100644 tools/schemacode/schemacode/tests/__init__.py
 create mode 100644 tools/schemacode/schemacode/tests/test_schema.py
 rename tools/schemacode/{ => schemacode}/utils.py (98%)
 create mode 100644 tools/schemacode/setup.cfg
 create mode 100644 tools/schemacode/setup.py
 create mode 100644 tools/schemacode/versioneer.py

diff --git a/tools/schemacode/MANIFEST.in b/tools/schemacode/MANIFEST.in
new file mode 100644
index 0000000000..a24694ff41
--- /dev/null
+++ b/tools/schemacode/MANIFEST.in
@@ -0,0 +1 @@
+include versioneer.py
diff --git a/tools/schemacode/README.md b/tools/schemacode/README.md
new file mode 100644
index 0000000000..e2b682a800
--- /dev/null
+++ b/tools/schemacode/README.md
@@ -0,0 +1,3 @@
+# schemacode
+
+A Python library for working with the BIDS schema.
diff --git a/tools/schemacode/pyproject.toml b/tools/schemacode/pyproject.toml
new file mode 100644
index 0000000000..d362784a8c
--- /dev/null
+++ b/tools/schemacode/pyproject.toml
@@ -0,0 +1,29 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+
+[tool.black]
+line-length = 99
+target-version = ['py37']
+include = '\.pyi?$'
+exclude = '''
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.github
+    | \.hg
+    | \.pytest_cache
+    | _build
+    | build
+    | dist
+  )/
+  | get_version.py
+  | versioneer.py
+  | schemacode/info.py
+  | schemacode/_version.py
+)
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
diff --git a/tools/schemacode/__init__.py b/tools/schemacode/schemacode/__init__.py
similarity index 100%
rename from tools/schemacode/__init__.py
rename to tools/schemacode/schemacode/__init__.py
diff --git a/tools/schemacode/schemacode/_version.py b/tools/schemacode/schemacode/_version.py
new file mode 100644
index 0000000000..bac97d022e
--- /dev/null
+++ b/tools/schemacode/schemacode/_version.py
@@ -0,0 +1,554 @@
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "$Format:%d$"
+    git_full = "$Format:%H$"
+    git_date = "$Format:%ci$"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "pep440"
+    cfg.tag_prefix = ""
+    cfg.parentdir_prefix = ""
+    cfg.versionfile_source = "schemacode/_version.py"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r"\d", r)])
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix) :]
+            if verbose:
+                print("picking %s" % r)
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(
+        GITS,
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s*" % tag_prefix,
+        ],
+        cwd=root,
+    )
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+                full_tag,
+                tag_prefix,
+            )
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for i in cfg.versionfile_source.split("/"):
+            root = os.path.dirname(root)
+    except NameError:
+        return {
+            "version": "0+unknown",
+            "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to find root of source tree",
+            "date": None,
+        }
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
diff --git a/tools/schemacode/schemacode/info.py b/tools/schemacode/schemacode/info.py
new file mode 100644
index 0000000000..d696c427b7
--- /dev/null
+++ b/tools/schemacode/schemacode/info.py
@@ -0,0 +1,84 @@
+"""Base module variables."""
+import importlib.util
+import os.path as op
+from pathlib import Path
+
+# Get version
+spec = importlib.util.spec_from_file_location(
+    "_version", op.join(op.dirname(__file__), "schemacode/_version.py")
+)
+_version = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(_version)
+
+VERSION = _version.get_versions()["version"]
+del _version
+
+# Get package description from README
+# Since this file is executed from ../setup.py, the path to the README is determined by the
+# location of setup.py.
+readme_path = Path(__file__).parent.joinpath("README.md")
+longdesc = readme_path.open().read()
+
+# Fields
+AUTHOR = "bids-standard developers"
+COPYRIGHT = "Copyright 2021, bids-standard developers"
+CREDITS = "bids-standard developers"
+LICENSE = "LGPL 2.1"
+MAINTAINER = ""
+EMAIL = ""
+STATUS = "Prototype"
+URL = "https://github.com/bids-standard/schemacode"
+PACKAGENAME = "schemacode"
+DESCRIPTION = ""
+LONGDESC = longdesc
+
+DOWNLOAD_URL = "https://github.com/bids-standard/{name}/archive/{ver}.tar.gz".format(
+    name=PACKAGENAME, ver=VERSION
+)
+
+REQUIRES = [
+    "numpy",
+    "pandas",
+    "tabulate",
+    "pyyaml",
+]
+
+TESTS_REQUIRES = [
+    "codecov",
+    "coverage<5.0",
+    "flake8>=3.7",
+    "flake8-black",
+    "flake8-isort",
+    "pytest",
+    "pytest-cov",
+]
+
+EXTRA_REQUIRES = {
+    "dev": ["versioneer"],
+    "doc": [
+        "sphinx>=1.5.3",
+        "sphinx_rtd_theme",
+    ],
+    "tests": TESTS_REQUIRES,
+}
+
+ENTRY_POINTS = {}
+
+# Enable a handle to install all extra dependencies at once
+EXTRA_REQUIRES["all"] = list(set([v for deps in EXTRA_REQUIRES.values() for v in deps]))
+
+# Supported Python versions using PEP 440 version specifiers
+# Should match the same set of Python versions as classifiers
+PYTHON_REQUIRES = ">=3.6"
+
+# Package classifiers
+CLASSIFIERS = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+]
diff --git a/tools/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
similarity index 99%
rename from tools/schemacode/schema.py
rename to tools/schemacode/schemacode/schema.py
index 472efc0df3..d813d3535c 100644
--- a/tools/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -1,11 +1,10 @@
-"""Schema loading- and processing-related functions.
-"""
+"""Schema loading- and processing-related functions."""
 import logging
 import os
 from copy import deepcopy
 from pathlib import Path
-from warnings import warn
 from pprint import pprint
+from warnings import warn
 
 import pandas as pd
 import yaml
@@ -20,7 +19,10 @@
 )
 logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
 
-BIDS_SCHEMA = Path(__file__).parent.parent / "src" / "schema"
+
+def get_schema_dir():
+    schema_dir = Path(__file__).parent.parent.parent / "src" / "schema"
+    return schema_dir
 
 
 def _get_entry_name(path):
diff --git a/tools/schemacode/schemacode/tests/__init__.py b/tools/schemacode/schemacode/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
new file mode 100644
index 0000000000..91d7de897b
--- /dev/null
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -0,0 +1 @@
+"""Tests for the schemacode package."""
\ No newline at end of file
diff --git a/tools/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
similarity index 98%
rename from tools/schemacode/utils.py
rename to tools/schemacode/schemacode/utils.py
index 36f449ee90..1a0051a609 100644
--- a/tools/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -1,5 +1,4 @@
-"""Utility functions for the bids-specification schema.
-"""
+"""Utility functions for the bids-specification schema."""
 import logging
 import os.path as op
 
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
new file mode 100644
index 0000000000..ae6de3aed3
--- /dev/null
+++ b/tools/schemacode/setup.cfg
@@ -0,0 +1,22 @@
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = schemacode/_version.py
+versionfile_build = schemacode/_version.py
+tag_prefix =
+parentdir_prefix =
+
+[flake8]
+max-line-length = 99
+exclude=*build/
+ignore = E203,E402,W503
+per-file-ignores =
+    */__init__.py:F401
+
+[tool:pytest]
+log_cli = true
+
+[options.package_data]
+* =
+    resources/*
+    tests/data/*
diff --git a/tools/schemacode/setup.py b/tools/schemacode/setup.py
new file mode 100644
index 0000000000..413a51cf28
--- /dev/null
+++ b/tools/schemacode/setup.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+""" schemacode setup script """
+
+
+def main():
+    """ Install entry-point """
+    import os.path as op
+    from inspect import currentframe, getfile
+    from io import open
+
+    from setuptools import find_packages, setup
+
+    import versioneer
+
+    ver_file = op.join("schemacode", "info.py")
+    with open(ver_file) as f:
+        exec(f.read())
+    vars = locals()
+
+    root_dir = op.dirname(op.abspath(getfile(currentframe())))
+    cmdclass = versioneer.get_cmdclass()
+
+    pkg_data = {
+        "schemacode": [
+            "tests/data/*",
+        ]
+    }
+
+    setup(
+        name=vars["PACKAGENAME"],
+        version=vars["VERSION"],
+        description=vars["DESCRIPTION"],
+        long_description=vars["LONGDESC"],
+        long_description_content_type="text/markdown",
+        author=vars["AUTHOR"],
+        author_email=vars["EMAIL"],
+        maintainer=vars["MAINTAINER"],
+        maintainer_email=vars["EMAIL"],
+        url=vars["URL"],
+        license=vars["LICENSE"],
+        classifiers=vars["CLASSIFIERS"],
+        download_url=vars["DOWNLOAD_URL"],
+        # Dependencies handling
+        python_requires=vars["PYTHON_REQUIRES"],
+        install_requires=vars["REQUIRES"],
+        tests_require=vars["TESTS_REQUIRES"],
+        extras_require=vars["EXTRA_REQUIRES"],
+        entry_points=vars["ENTRY_POINTS"],
+        packages=find_packages(exclude=("tests",)),
+        zip_safe=False,
+        cmdclass=cmdclass,
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tools/schemacode/versioneer.py b/tools/schemacode/versioneer.py
new file mode 100644
index 0000000000..2b54540510
--- /dev/null
+++ b/tools/schemacode/versioneer.py
@@ -0,0 +1,1885 @@
+# Version: 0.18
+
+"""The Versioneer - like a rocketeer, but for versions.
+
+The Versioneer
+==============
+
+* like a rocketeer, but for versions!
+* https://github.com/warner/python-versioneer
+* Brian Warner
+* License: Public Domain
+* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
+* [![Latest Version]
+(https://pypip.in/version/versioneer/badge.svg?style=flat)
+](https://pypi.python.org/pypi/versioneer/)
+* [![Build Status]
+(https://travis-ci.org/warner/python-versioneer.png?branch=master)
+](https://travis-ci.org/warner/python-versioneer)
+
+This is a tool for managing a recorded version number in distutils-based
+python projects. The goal is to remove the tedious and error-prone "update
+the embedded version string" step from your release process. Making a new
+release should be as easy as recording a new tag in your version-control
+system, and maybe making new tarballs.
+
+
+## Quick Install
+
+* `pip install versioneer` to somewhere to your $PATH
+* add a `[versioneer]` section to your setup.cfg (see below)
+* run `versioneer install` in your source tree, commit the results
+
+## Version Identifiers
+
+Source trees come from a variety of places:
+
+* a version-control system checkout (mostly used by developers)
+* a nightly tarball, produced by build automation
+* a snapshot tarball, produced by a web-based VCS browser, like github's
+  "tarball from tag" feature
+* a release tarball, produced by "setup.py sdist", distributed through PyPI
+
+Within each source tree, the version identifier (either a string or a number,
+this tool is format-agnostic) can come from a variety of places:
+
+* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows
+  about recent "tags" and an absolute revision-id
+* the name of the directory into which the tarball was unpacked
+* an expanded VCS keyword ($Id$, etc)
+* a `_version.py` created by some earlier build step
+
+For released software, the version identifier is closely related to a VCS
+tag. Some projects use tag names that include more than just the version
+string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool
+needs to strip the tag prefix to extract the version identifier. For
+unreleased software (between tags), the version identifier should provide
+enough information to help developers recreate the same tree, while also
+giving them an idea of roughly how old the tree is (after version 1.2, before
+version 1.3). Many VCS systems can report a description that captures this,
+for example `git describe --tags --dirty --always` reports things like
+"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
+0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
+uncommitted changes.
+
+The version identifier is used for multiple purposes:
+
+* to allow the module to self-identify its version: `myproject.__version__`
+* to choose a name and prefix for a 'setup.py sdist' tarball
+
+## Theory of Operation
+
+Versioneer works by adding a special `_version.py` file into your source
+tree, where your `__init__.py` can import it. This `_version.py` knows how to
+dynamically ask the VCS tool for version information at import time.
+
+`_version.py` also contains `$Revision$` markers, and the installation
+process marks `_version.py` to have this marker rewritten with a tag name
+during the `git archive` command. As a result, generated tarballs will
+contain enough information to get the proper version.
+
+To allow `setup.py` to compute a version too, a `versioneer.py` is added to
+the top level of your source tree, next to `setup.py` and the `setup.cfg`
+that configures it. This overrides several distutils/setuptools commands to
+compute the version when invoked, and changes `setup.py build` and `setup.py
+sdist` to replace `_version.py` with a small static file that contains just
+the generated version data.
+
+## Installation
+
+See [INSTALL.md](./INSTALL.md) for detailed installation instructions.
+
+## Version-String Flavors
+
+Code which uses Versioneer can learn about its version string at runtime by
+importing `_version` from your main `__init__.py` file and running the
+`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can
+import the top-level `versioneer.py` and run `get_versions()`.
+
+Both functions return a dictionary with different flavors of version
+information:
+
+* `['version']`: A condensed version string, rendered using the selected
+  style. This is the most commonly used value for the project's version
+  string. The default "pep440" style yields strings like `0.11`,
+  `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section
+  below for alternative styles.
+
+* `['full-revisionid']`: detailed revision identifier. For Git, this is the
+  full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac".
+
+* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the
+  commit date in ISO 8601 format. This will be None if the date is not
+  available.
+
+* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that
+  this is only accurate if run in a VCS checkout, otherwise it is likely to
+  be False or None
+
+* `['error']`: if the version string could not be computed, this will be set
+  to a string describing the problem, otherwise it will be None. It may be
+  useful to throw an exception in setup.py if this is set, to avoid e.g.
+  creating tarballs with a version string of "unknown".
+
+Some variants are more useful than others. Including `full-revisionid` in a
+bug report should allow developers to reconstruct the exact code being tested
+(or indicate the presence of local changes that should be shared with the
+developers). `version` is suitable for display in an "about" box or a CLI
+`--version` output: it can be easily compared against release notes and lists
+of bugs fixed in various releases.
+
+The installer adds the following text to your `__init__.py` to place a basic
+version in `YOURPROJECT.__version__`:
+
+    from ._version import get_versions
+    __version__ = get_versions()['version']
+    del get_versions
+
+## Styles
+
+The setup.cfg `style=` configuration controls how the VCS information is
+rendered into a version string.
+
+The default style, "pep440", produces a PEP440-compliant string, equal to the
+un-prefixed tag name for actual releases, and containing an additional "local
+version" section with more detail for in-between builds. For Git, this is
+TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags
+--dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the
+tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and
+that this commit is two revisions ("+2") beyond the "0.11" tag. For released
+software (exactly equal to a known tag), the identifier will only contain the
+stripped tag, e.g. "0.11".
+
+Other styles are available. See [details.md](details.md) in the Versioneer
+source tree for descriptions.
+
+## Debugging
+
+Versioneer tries to avoid fatal errors: if something goes wrong, it will tend
+to return a version of "0+unknown". To investigate the problem, run `setup.py
+version`, which will run the version-lookup code in a verbose mode, and will
+display the full contents of `get_versions()` (including the `error` string,
+which may help identify what went wrong).
+
+## Known Limitations
+
+Some situations are known to cause problems for Versioneer. This details the
+most significant ones. More can be found on Github
+[issues page](https://github.com/warner/python-versioneer/issues).
+
+### Subprojects
+
+Versioneer has limited support for source trees in which `setup.py` is not in
+the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are
+two common reasons why `setup.py` might not be in the root:
+
+* Source trees which contain multiple subprojects, such as
+  [Buildbot](https://github.com/buildbot/buildbot), which contains both
+  "master" and "slave" subprojects, each with their own `setup.py`,
+  `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
+  distributions (and upload multiple independently-installable tarballs).
+* Source trees whose main purpose is to contain a C library, but which also
+  provide bindings to Python (and perhaps other langauges) in subdirectories.
+
+Versioneer will look for `.git` in parent directories, and most operations
+should get the right version string. However `pip` and `setuptools` have bugs
+and implementation details which frequently cause `pip install .` from a
+subproject directory to fail to find a correct version string (so it usually
+defaults to `0+unknown`).
+
+`pip install --editable .` should work correctly. `setup.py install` might
+work too.
+
+Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
+some later version.
+
+[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
+this issue. The discussion in
+[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
+issue from the Versioneer side in more detail.
+[pip PR#3176](https://github.com/pypa/pip/pull/3176) and
+[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
+pip to let Versioneer work correctly.
+
+Versioneer-0.16 and earlier only looked for a `.git` directory next to the
+`setup.cfg`, so subprojects were completely unsupported with those releases.
+
+### Editable installs with setuptools <= 18.5
+
+`setup.py develop` and `pip install --editable .` allow you to install a
+project into a virtualenv once, then continue editing the source code (and
+test) without re-installing after every change.
+
+"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a
+convenient way to specify executable scripts that should be installed along
+with the python package.
+
+These both work as expected when using modern setuptools. When using
+setuptools-18.5 or earlier, however, certain operations will cause
+`pkg_resources.DistributionNotFound` errors when running the entrypoint
+script, which must be resolved by re-installing the package. This happens
+when the install happens with one version, then the egg_info data is
+regenerated while a different version is checked out. Many setup.py commands
+cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
+a different virtualenv), so this can be surprising.
+
+[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
+this one, but upgrading to a newer version of setuptools should probably
+resolve it.
+
+### Unicode version strings
+
+While Versioneer works (and is continually tested) with both Python 2 and
+Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
+Newer releases probably generate unicode version strings on py2. It's not
+clear that this is wrong, but it may be surprising for applications when then
+write these strings to a network connection or include them in bytes-oriented
+APIs like cryptographic checksums.
+
+[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
+this question.
+
+
+## Updating Versioneer
+
+To upgrade your project to a new release of Versioneer, do the following:
+
+* install the new Versioneer (`pip install -U versioneer` or equivalent)
+* edit `setup.cfg`, if necessary, to include any new configuration settings
+  indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details.
+* re-run `versioneer install` in your source tree, to replace
+  `SRC/_version.py`
+* commit any changed files
+
+## Future Directions
+
+This tool is designed to make it easily extended to other version-control
+systems: all VCS-specific components are in separate directories like
+src/git/ . The top-level `versioneer.py` script is assembled from these
+components by running make-versioneer.py . In the future, make-versioneer.py
+will take a VCS name as an argument, and will construct a version of
+`versioneer.py` that is specific to the given VCS. It might also take the
+configuration arguments that are currently provided manually during
+installation by editing setup.py . Alternatively, it might go the other
+direction and include code from all supported VCS systems, reducing the
+number of intermediate scripts.
+
+
+## License
+
+To make Versioneer easier to embed, all its code is dedicated to the public
+domain. The `_version.py` that it creates is also in the public domain.
+Specifically, both are released under the Creative Commons "Public Domain
+Dedication" license (CC0-1.0), as described in
+https://creativecommons.org/publicdomain/zero/1.0/ .
+
+"""
+
+from __future__ import print_function
+
+try:
+    import configparser
+except ImportError:
+    import ConfigParser as configparser
+import errno
+import json
+import os
+import re
+import subprocess
+import sys
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_root():
+    """Get the project root directory.
+
+    We require that all commands are run from the project root, i.e. the
+    directory that contains setup.py, setup.cfg, and versioneer.py .
+    """
+    root = os.path.realpath(os.path.abspath(os.getcwd()))
+    setup_py = os.path.join(root, "setup.py")
+    versioneer_py = os.path.join(root, "versioneer.py")
+    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+        # allow 'python path/to/setup.py COMMAND'
+        root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
+        setup_py = os.path.join(root, "setup.py")
+        versioneer_py = os.path.join(root, "versioneer.py")
+    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+        err = (
+            "Versioneer was unable to run the project root directory. "
+            "Versioneer requires setup.py to be executed from "
+            "its immediate directory (like 'python setup.py COMMAND'), "
+            "or in a way that lets it use sys.argv[0] to find the root "
+            "(like 'python path/to/setup.py COMMAND')."
+        )
+        raise VersioneerBadRootError(err)
+    try:
+        # Certain runtime workflows (setup.py install/develop in a setuptools
+        # tree) execute all dependencies in a single python process, so
+        # "versioneer" may be imported multiple times, and python's shared
+        # module-import table will cache the first one. So we can't use
+        # os.path.dirname(__file__), as that will find whichever
+        # versioneer.py was first imported, even in later projects.
+        me = os.path.realpath(os.path.abspath(__file__))
+        me_dir = os.path.normcase(os.path.splitext(me)[0])
+        vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
+        if me_dir != vsr_dir:
+            print(
+                "Warning: build in %s is using versioneer.py from %s"
+                % (os.path.dirname(me), versioneer_py)
+            )
+    except NameError:
+        pass
+    return root
+
+
+def get_config_from_root(root):
+    """Read the project setup.cfg file to determine Versioneer config."""
+    # This might raise EnvironmentError (if setup.cfg is missing), or
+    # configparser.NoSectionError (if it lacks a [versioneer] section), or
+    # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+    # the top of versioneer.py for instructions on writing your setup.cfg .
+    setup_cfg = os.path.join(root, "setup.cfg")
+    parser = configparser.SafeConfigParser()
+    with open(setup_cfg, "r") as f:
+        parser.readfp(f)
+    VCS = parser.get("versioneer", "VCS")  # mandatory
+
+    def get(parser, name):
+        if parser.has_option("versioneer", name):
+            return parser.get("versioneer", name)
+        return None
+
+    cfg = VersioneerConfig()
+    cfg.VCS = VCS
+    cfg.style = get(parser, "style") or ""
+    cfg.versionfile_source = get(parser, "versionfile_source")
+    cfg.versionfile_build = get(parser, "versionfile_build")
+    cfg.tag_prefix = get(parser, "tag_prefix")
+    if cfg.tag_prefix in ("''", '""'):
+        cfg.tag_prefix = ""
+    cfg.parentdir_prefix = get(parser, "parentdir_prefix")
+    cfg.verbose = get(parser, "verbose")
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+# these dictionaries contain VCS-specific tools
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+LONG_VERSION_PY[
+    "git"
+] = '''
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
+    git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
+    git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "%(STYLE)s"
+    cfg.tag_prefix = "%(TAG_PREFIX)s"
+    cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s"
+    cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %%s" %% dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %%s" %% (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %%s (error)" %% dispcmd)
+            print("stdout was %%s" %% stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %%s but none started with prefix %%s" %%
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %%d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r'\d', r)])
+        if verbose:
+            print("discarding '%%s', no digits" %% ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %%s" %% ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            if verbose:
+                print("picking %%s" %% r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %%s not under git control" %% root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
+                                          "--always", "--long",
+                                          "--match", "%%s*" %% tag_prefix],
+                                   cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%%s'"
+                               %% describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%%s' doesn't start with prefix '%%s'"
+                print(fmt %% (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'"
+                               %% (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%%d" %% pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%%d" %% pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%%s" %% pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%%s" %% pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%%s'" %% style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for i in cfg.versionfile_source.split('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}
+'''
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r"\d", r)])
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix) :]
+            if verbose:
+                print("picking %s" % r)
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(
+        GITS,
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s*" % tag_prefix,
+        ],
+        cwd=root,
+    )
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+                full_tag,
+                tag_prefix,
+            )
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
+        0
+    ].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def do_vcs_install(manifest_in, versionfile_source, ipy):
+    """Git-specific installation logic for Versioneer.
+
+    For Git, this means creating/changing .gitattributes to mark _version.py
+    for export-subst keyword substitution.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+    files = [manifest_in, versionfile_source]
+    if ipy:
+        files.append(ipy)
+    try:
+        me = __file__
+        if me.endswith(".pyc") or me.endswith(".pyo"):
+            me = os.path.splitext(me)[0] + ".py"
+        versioneer_file = os.path.relpath(me)
+    except NameError:
+        versioneer_file = "versioneer.py"
+    files.append(versioneer_file)
+    present = False
+    try:
+        f = open(".gitattributes", "r")
+        for line in f.readlines():
+            if line.strip().startswith(versionfile_source):
+                if "export-subst" in line.strip().split()[1:]:
+                    present = True
+        f.close()
+    except EnvironmentError:
+        pass
+    if not present:
+        f = open(".gitattributes", "a+")
+        f.write("%s export-subst\n" % versionfile_source)
+        f.close()
+        files.append(".gitattributes")
+    run_command(GITS, ["add", "--"] + files)
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+SHORT_VERSION_PY = """
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+%s
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)
+"""
+
+
+def versions_from_file(filename):
+    """Try to determine the version from _version.py if present."""
+    try:
+        with open(filename) as f:
+            contents = f.read()
+    except EnvironmentError:
+        raise NotThisMethod("unable to read _version.py")
+    mo = re.search(
+        r"version_json = '''\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
+    )
+    if not mo:
+        mo = re.search(
+            r"version_json = '''\r\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
+        )
+    if not mo:
+        raise NotThisMethod("no version_json in _version.py")
+    return json.loads(mo.group(1))
+
+
+def write_to_version_file(filename, versions):
+    """Write the given version number to the given _version.py file."""
+    os.unlink(filename)
+    contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": "))
+    with open(filename, "w") as f:
+        f.write(SHORT_VERSION_PY % contents)
+
+    print("set %s to '%s'" % (filename, versions["version"]))
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
+
+
+class VersioneerBadRootError(Exception):
+    """The project root directory is unknown or missing key files."""
+
+
+def get_versions(verbose=False):
+    """Get the project version from whatever source is available.
+
+    Returns dict with two keys: 'version' and 'full'.
+    """
+    if "versioneer" in sys.modules:
+        # see the discussion in cmdclass.py:get_cmdclass()
+        del sys.modules["versioneer"]
+
+    root = get_root()
+    cfg = get_config_from_root(root)
+
+    assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
+    handlers = HANDLERS.get(cfg.VCS)
+    assert handlers, "unrecognized VCS '%s'" % cfg.VCS
+    verbose = verbose or cfg.verbose
+    assert (
+        cfg.versionfile_source is not None
+    ), "please set versioneer.versionfile_source"
+    assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
+
+    versionfile_abs = os.path.join(root, cfg.versionfile_source)
+
+    # extract version from first of: _version.py, VCS command (e.g. 'git
+    # describe'), parentdir. This is meant to work for developers using a
+    # source checkout, for users of a tarball created by 'setup.py sdist',
+    # and for users of a tarball/zipball created by 'git archive' or github's
+    # download-from-tag feature or the equivalent in other VCSes.
+
+    get_keywords_f = handlers.get("get_keywords")
+    from_keywords_f = handlers.get("keywords")
+    if get_keywords_f and from_keywords_f:
+        try:
+            keywords = get_keywords_f(versionfile_abs)
+            ver = from_keywords_f(keywords, cfg.tag_prefix, verbose)
+            if verbose:
+                print("got version from expanded keyword %s" % ver)
+            return ver
+        except NotThisMethod:
+            pass
+
+    try:
+        ver = versions_from_file(versionfile_abs)
+        if verbose:
+            print("got version from file %s %s" % (versionfile_abs, ver))
+        return ver
+    except NotThisMethod:
+        pass
+
+    from_vcs_f = handlers.get("pieces_from_vcs")
+    if from_vcs_f:
+        try:
+            pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
+            ver = render(pieces, cfg.style)
+            if verbose:
+                print("got version from VCS %s" % ver)
+            return ver
+        except NotThisMethod:
+            pass
+
+    try:
+        if cfg.parentdir_prefix:
+            ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+            if verbose:
+                print("got version from parentdir %s" % ver)
+            return ver
+    except NotThisMethod:
+        pass
+
+    if verbose:
+        print("unable to compute version")
+
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
+
+
+def get_version():
+    """Get the short version string for this project."""
+    return get_versions()["version"]
+
+
+def get_cmdclass():
+    """Get the custom setuptools/distutils subclasses used by Versioneer."""
+    if "versioneer" in sys.modules:
+        del sys.modules["versioneer"]
+        # this fixes the "python setup.py develop" case (also 'install' and
+        # 'easy_install .'), in which subdependencies of the main project are
+        # built (using setup.py bdist_egg) in the same python process. Assume
+        # a main project A and a dependency B, which use different versions
+        # of Versioneer. A's setup.py imports A's Versioneer, leaving it in
+        # sys.modules by the time B's setup.py is executed, causing B to run
+        # with the wrong versioneer. Setuptools wraps the sub-dep builds in a
+        # sandbox that restores sys.modules to it's pre-build state, so the
+        # parent is protected against the child's "import versioneer". By
+        # removing ourselves from sys.modules here, before the child build
+        # happens, we protect the child from the parent's versioneer too.
+        # Also see https://github.com/warner/python-versioneer/issues/52
+
+    cmds = {}
+
+    # we add "version" to both distutils and setuptools
+    from distutils.core import Command
+
+    class cmd_version(Command):
+        description = "report generated version string"
+        user_options = []
+        boolean_options = []
+
+        def initialize_options(self):
+            pass
+
+        def finalize_options(self):
+            pass
+
+        def run(self):
+            vers = get_versions(verbose=True)
+            print("Version: %s" % vers["version"])
+            print(" full-revisionid: %s" % vers.get("full-revisionid"))
+            print(" dirty: %s" % vers.get("dirty"))
+            print(" date: %s" % vers.get("date"))
+            if vers["error"]:
+                print(" error: %s" % vers["error"])
+
+    cmds["version"] = cmd_version
+
+    # we override "build_py" in both distutils and setuptools
+    #
+    # most invocation pathways end up running build_py:
+    #  distutils/build -> build_py
+    #  distutils/install -> distutils/build ->..
+    #  setuptools/bdist_wheel -> distutils/install ->..
+    #  setuptools/bdist_egg -> distutils/install_lib -> build_py
+    #  setuptools/install -> bdist_egg ->..
+    #  setuptools/develop -> ?
+    #  pip install:
+    #   copies source tree to a tempdir before running egg_info/etc
+    #   if .git isn't copied too, 'git describe' will fail
+    #   then does setup.py bdist_wheel, or sometimes setup.py install
+    #  setup.py egg_info -> ?
+
+    # we override different "build_py" commands for both environments
+    if "setuptools" in sys.modules:
+        from setuptools.command.build_py import build_py as _build_py
+    else:
+        from distutils.command.build_py import build_py as _build_py
+
+    class cmd_build_py(_build_py):
+        def run(self):
+            root = get_root()
+            cfg = get_config_from_root(root)
+            versions = get_versions()
+            _build_py.run(self)
+            # now locate _version.py in the new build/ directory and replace
+            # it with an updated value
+            if cfg.versionfile_build:
+                target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+
+    cmds["build_py"] = cmd_build_py
+
+    if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
+        from cx_Freeze.dist import build_exe as _build_exe
+
+        # nczeczulin reports that py2exe won't like the pep440-style string
+        # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
+        # setup(console=[{
+        #   "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION
+        #   "product_version": versioneer.get_version(),
+        #   ...
+
+        class cmd_build_exe(_build_exe):
+            def run(self):
+                root = get_root()
+                cfg = get_config_from_root(root)
+                versions = get_versions()
+                target_versionfile = cfg.versionfile_source
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+
+                _build_exe.run(self)
+                os.unlink(target_versionfile)
+                with open(cfg.versionfile_source, "w") as f:
+                    LONG = LONG_VERSION_PY[cfg.VCS]
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
+        cmds["build_exe"] = cmd_build_exe
+        del cmds["build_py"]
+
+    if "py2exe" in sys.modules:  # py2exe enabled?
+        try:
+            from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
+        except ImportError:
+            from py2exe.build_exe import py2exe as _py2exe  # py2
+
+        class cmd_py2exe(_py2exe):
+            def run(self):
+                root = get_root()
+                cfg = get_config_from_root(root)
+                versions = get_versions()
+                target_versionfile = cfg.versionfile_source
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+
+                _py2exe.run(self)
+                os.unlink(target_versionfile)
+                with open(cfg.versionfile_source, "w") as f:
+                    LONG = LONG_VERSION_PY[cfg.VCS]
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
+        cmds["py2exe"] = cmd_py2exe
+
+    # we override different "sdist" commands for both environments
+    if "setuptools" in sys.modules:
+        from setuptools.command.sdist import sdist as _sdist
+    else:
+        from distutils.command.sdist import sdist as _sdist
+
+    class cmd_sdist(_sdist):
+        def run(self):
+            versions = get_versions()
+            self._versioneer_generated_versions = versions
+            # unless we update this, the command will keep using the old
+            # version
+            self.distribution.metadata.version = versions["version"]
+            return _sdist.run(self)
+
+        def make_release_tree(self, base_dir, files):
+            root = get_root()
+            cfg = get_config_from_root(root)
+            _sdist.make_release_tree(self, base_dir, files)
+            # now locate _version.py in the new base_dir directory
+            # (remembering that it may be a hardlink) and replace it with an
+            # updated value
+            target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
+            print("UPDATING %s" % target_versionfile)
+            write_to_version_file(
+                target_versionfile, self._versioneer_generated_versions
+            )
+
+    cmds["sdist"] = cmd_sdist
+
+    return cmds
+
+
+CONFIG_ERROR = """
+setup.cfg is missing the necessary Versioneer configuration. You need
+a section like:
+
+ [versioneer]
+ VCS = git
+ style = pep440
+ versionfile_source = src/myproject/_version.py
+ versionfile_build = myproject/_version.py
+ tag_prefix =
+ parentdir_prefix = myproject-
+
+You will also need to edit your setup.py to use the results:
+
+ import versioneer
+ setup(version=versioneer.get_version(),
+       cmdclass=versioneer.get_cmdclass(), ...)
+
+Please read the docstring in ./versioneer.py for configuration instructions,
+edit setup.cfg, and re-run the installer or 'python versioneer.py setup'.
+"""
+
+SAMPLE_CONFIG = """
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+
+[versioneer]
+#VCS = git
+#style = pep440
+#versionfile_source =
+#versionfile_build =
+#tag_prefix =
+#parentdir_prefix =
+
+"""
+
+INIT_PY_SNIPPET = """
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions
+"""
+
+
+def do_setup():
+    """Main VCS-independent setup function for installing Versioneer."""
+    root = get_root()
+    try:
+        cfg = get_config_from_root(root)
+    except (
+        EnvironmentError,
+        configparser.NoSectionError,
+        configparser.NoOptionError,
+    ) as e:
+        if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
+            print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
+            with open(os.path.join(root, "setup.cfg"), "a") as f:
+                f.write(SAMPLE_CONFIG)
+        print(CONFIG_ERROR, file=sys.stderr)
+        return 1
+
+    print(" creating %s" % cfg.versionfile_source)
+    with open(cfg.versionfile_source, "w") as f:
+        LONG = LONG_VERSION_PY[cfg.VCS]
+        f.write(
+            LONG
+            % {
+                "DOLLAR": "$",
+                "STYLE": cfg.style,
+                "TAG_PREFIX": cfg.tag_prefix,
+                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                "VERSIONFILE_SOURCE": cfg.versionfile_source,
+            }
+        )
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
+    if os.path.exists(ipy):
+        try:
+            with open(ipy, "r") as f:
+                old = f.read()
+        except EnvironmentError:
+            old = ""
+        if INIT_PY_SNIPPET not in old:
+            print(" appending to %s" % ipy)
+            with open(ipy, "a") as f:
+                f.write(INIT_PY_SNIPPET)
+        else:
+            print(" %s unmodified" % ipy)
+    else:
+        print(" %s doesn't exist, ok" % ipy)
+        ipy = None
+
+    # Make sure both the top-level "versioneer.py" and versionfile_source
+    # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
+    # they'll be copied into source distributions. Pip won't be able to
+    # install the package without this.
+    manifest_in = os.path.join(root, "MANIFEST.in")
+    simple_includes = set()
+    try:
+        with open(manifest_in, "r") as f:
+            for line in f:
+                if line.startswith("include "):
+                    for include in line.split()[1:]:
+                        simple_includes.add(include)
+    except EnvironmentError:
+        pass
+    # That doesn't cover everything MANIFEST.in can do
+    # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
+    # it might give some false negatives. Appending redundant 'include'
+    # lines is safe, though.
+    if "versioneer.py" not in simple_includes:
+        print(" appending 'versioneer.py' to MANIFEST.in")
+        with open(manifest_in, "a") as f:
+            f.write("include versioneer.py\n")
+    else:
+        print(" 'versioneer.py' already in MANIFEST.in")
+    if cfg.versionfile_source not in simple_includes:
+        print(
+            " appending versionfile_source ('%s') to MANIFEST.in"
+            % cfg.versionfile_source
+        )
+        with open(manifest_in, "a") as f:
+            f.write("include %s\n" % cfg.versionfile_source)
+    else:
+        print(" versionfile_source already in MANIFEST.in")
+
+    # Make VCS-specific changes. For git, this means creating/changing
+    # .gitattributes to mark _version.py for export-subst keyword
+    # substitution.
+    do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
+    return 0
+
+
+def scan_setup_py():
+    """Validate the contents of setup.py against Versioneer's expectations."""
+    found = set()
+    setters = False
+    errors = 0
+    with open("setup.py", "r") as f:
+        for line in f.readlines():
+            if "import versioneer" in line:
+                found.add("import")
+            if "versioneer.get_cmdclass()" in line:
+                found.add("cmdclass")
+            if "versioneer.get_version()" in line:
+                found.add("get_version")
+            if "versioneer.VCS" in line:
+                setters = True
+            if "versioneer.versionfile_source" in line:
+                setters = True
+    if len(found) != 3:
+        print("")
+        print("Your setup.py appears to be missing some important items")
+        print("(but I might be wrong). Please make sure it has something")
+        print("roughly like the following:")
+        print("")
+        print(" import versioneer")
+        print(" setup( version=versioneer.get_version(),")
+        print("        cmdclass=versioneer.get_cmdclass(),  ...)")
+        print("")
+        errors += 1
+    if setters:
+        print("You should remove lines like 'versioneer.VCS = ' and")
+        print("'versioneer.versionfile_source = ' . This configuration")
+        print("now lives in setup.cfg, and should be removed from setup.py")
+        print("")
+        errors += 1
+    return errors
+
+
+if __name__ == "__main__":
+    cmd = sys.argv[1]
+    if cmd == "setup":
+        errors = do_setup()
+        errors += scan_setup_py()
+        if errors:
+            sys.exit(1)

From 2cbcffc2ce85b63f003191e9ef634af6d26c2397 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 Oct 2021 15:46:26 -0400
Subject: [PATCH 012/347] Clean up docstrings.

---
 tools/schemacode/schemacode/schema.py | 11 ++---------
 tools/schemacode/schemacode/utils.py  |  1 +
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 0036acb526..e3352dc555 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -20,11 +20,6 @@
 logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
 
 
-def get_schema_dir():
-    schema_dir = Path(__file__).parent.parent.parent / "src" / "schema"
-    return schema_dir
-
-
 def _get_entry_name(path):
     if path.suffix == ".yaml":
         return path.name[:-5]  # no .yaml
@@ -168,8 +163,7 @@ def filter_schema(schema, **kwargs):
 
 
 def make_entity_definitions(schema):
-    """Generate definitions and other relevant information for entities in the
-    specification.
+    """Generate definitions and other relevant information for entities in the specification.
 
     Each entity gets its own heading.
 
@@ -211,8 +205,7 @@ def make_entity_definitions(schema):
 
 
 def make_filename_template(schema, **kwargs):
-    """Create codeblocks containing example filename patterns for a given
-    datatype.
+    """Create codeblocks containing example filename patterns for a given datatype.
 
     Parameters
     ----------
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 1532437aa5..7a7e204d90 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -89,6 +89,7 @@ def set_logger_level(lgr, level):
 
 def drop_unused_entities(df):
     """Remove columns from a dataframe where all values in the column are NaNs.
+
     For entity tables, this limits each table to only entities that are used
     within the modality.
 

From 3ca5bcac7ec89f969c3fb17c6cabd445dd267f46 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 8 Oct 2021 14:21:48 -0400
Subject: [PATCH 013/347] Add "mm" and "nm" to PixelSizeUnits

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 5bb409e24e..a7eb189108 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -248,7 +248,7 @@ A "manual" table is provided to facilitate the review process.
 | **Key name**               | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
 | -------------------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | PixelSize                  | REQUIRED              | [array][] of [numbers][] | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
-| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be micrometer (`"um"`).                                                                                                                                                                                                                                                                                                                                                                                                     |
+| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be millimeter (`"mm"`), micrometer (`"um"`) or nanometer (`"nm"`).                                                                                                                                                                                                                                                                                                                                                          |
 | Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
 | NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
 | Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |

From 94112b61d898aeb1642ad61d0817821ffed24104 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 11 Oct 2021 11:56:01 -0400
Subject: [PATCH 014/347] BF: typo + added trailing period

---
 src/03-modality-agnostic-files.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index d0d58e24d0..7833f96b60 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -64,8 +64,8 @@ Example:
 #### Derived dataset and pipeline description
 
 As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
-top level of the a derived dataset:
-`<dataset>/derivatives/<pipeline_name>/dataset_description.json`
+top level of every derived dataset:
+`<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
 
 In addition to the keys for raw BIDS datasets,
 derived BIDS datasets include the following REQUIRED and RECOMMENDED

From 13044ba07c26ad9554ee727c8f7add51490dd555 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:10:39 -0400
Subject: [PATCH 015/347] Change license to MIT.

---
 tools/schemacode/schemacode/info.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/schemacode/schemacode/info.py b/tools/schemacode/schemacode/info.py
index d696c427b7..6ed687c144 100644
--- a/tools/schemacode/schemacode/info.py
+++ b/tools/schemacode/schemacode/info.py
@@ -23,13 +23,13 @@
 AUTHOR = "bids-standard developers"
 COPYRIGHT = "Copyright 2021, bids-standard developers"
 CREDITS = "bids-standard developers"
-LICENSE = "LGPL 2.1"
+LICENSE = "MIT"
 MAINTAINER = ""
 EMAIL = ""
 STATUS = "Prototype"
 URL = "https://github.com/bids-standard/schemacode"
 PACKAGENAME = "schemacode"
-DESCRIPTION = ""
+DESCRIPTION = "Python tools for working with the BIDS schema."
 LONGDESC = longdesc
 
 DOWNLOAD_URL = "https://github.com/bids-standard/{name}/archive/{ver}.tar.gz".format(
@@ -76,7 +76,7 @@
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Information Analysis",
-    "License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)",
+    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",

From 73e89c54d7b44f66604f8086e1521424e3389ae4 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:14:08 -0400
Subject: [PATCH 016/347] Fix spelling in versioneer files.

---
 tools/schemacode/schemacode/_version.py | 2 +-
 tools/schemacode/versioneer.py          | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/schemacode/schemacode/_version.py b/tools/schemacode/schemacode/_version.py
index bac97d022e..8c0102e67f 100644
--- a/tools/schemacode/schemacode/_version.py
+++ b/tools/schemacode/schemacode/_version.py
@@ -292,7 +292,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
diff --git a/tools/schemacode/versioneer.py b/tools/schemacode/versioneer.py
index 2b54540510..323046a244 100644
--- a/tools/schemacode/versioneer.py
+++ b/tools/schemacode/versioneer.py
@@ -179,7 +179,7 @@
   `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
   distributions (and upload multiple independently-installable tarballs).
 * Source trees whose main purpose is to contain a C library, but which also
-  provide bindings to Python (and perhaps other langauges) in subdirectories.
+  provide bindings to Python (and perhaps other languages) in subdirectories.
 
 Versioneer will look for `.git` in parent directories, and most operations
 should get the right version string. However `pip` and `setuptools` have bugs
@@ -281,6 +281,7 @@
     import configparser
 except ImportError:
     import ConfigParser as configparser
+
 import errno
 import json
 import os
@@ -699,7 +700,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%%s'"
                                %% describe_out)
             return pieces
@@ -1106,7 +1107,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 

From 4b59f93269954fb08d61dd3dfa38e954c4051313 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:16:55 -0400
Subject: [PATCH 017/347] Install schemacode in config file.

---
 .circleci/config.yml               | 1 +
 tools/mkdocs_macros_bids/macros.py | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 70f6abe904..c8b40b9eaf 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -11,6 +11,7 @@ jobs:
           command: |
             python -m pip install --upgrade pip
             pip install -r requirements.txt
+            pip install -e ~/project/tools/schemacode/
       - run:
           name: generate docs
           command: mkdocs build --clean --strict --verbose
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index 9a3cf15cc2..55d69c8fea 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -2,10 +2,11 @@
 import os
 import sys
 
+from schemacode import schema, utils
+
 code_path = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 sys.path.append(code_path)
 
-from schemacode import schema, utils
 from examplecode import example
 
 

From 5df0354e8ba75dcc57ecb7d30313e761b027e7d1 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:20:25 -0400
Subject: [PATCH 018/347] Update config.yml

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index c8b40b9eaf..bd7b0fde07 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -11,7 +11,7 @@ jobs:
           command: |
             python -m pip install --upgrade pip
             pip install -r requirements.txt
-            pip install -e ~/project/tools/schemacode/
+            pip install ~/project/tools/schemacode/
       - run:
           name: generate docs
           command: mkdocs build --clean --strict --verbose

From 53839481d55d65ae4d02dbb8a61440a39cc4955a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:40:50 -0400
Subject: [PATCH 019/347] Fix path to schema.

I don't like this. We need something less dependent on folder locations.
---
 tools/schemacode/schemacode/utils.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 7a7e204d90..a2a033bf3b 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -14,9 +14,10 @@ def get_schema_path():
     str
         Absolute path to the folder containing schema-related files.
     """
-    return op.abspath(
-        op.join(op.dirname(op.dirname(op.dirname(__file__))), "src", "schema") + op.sep
+    schema_dir = op.abspath(
+        op.join(op.dirname(op.dirname(op.dirname(op.dirname(__file__)))), "src", "schema") + op.sep
     )
+    return schema_dir
 
 
 def combine_extensions(lst):

From f2492f8b45ea157a746383480f5a4f2d79f8c435 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:47:43 -0400
Subject: [PATCH 020/347] Log.

---
 tools/schemacode/schemacode/schema.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index e3352dc555..72dfb4388a 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -80,6 +80,7 @@ def load_schema(schema_path):
     object_group_files = sorted(glob(str(objects_dir / "*.yaml")))
     for object_group_file in object_group_files:
         group_name = op.splitext(op.basename(object_group_file))[0]
+        lgr.info(f"Loading {group_name} objects.")
         with open(object_group_file, "r") as fo:
             dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
             dict_ = dereference_yaml(dict_, dict_)
@@ -91,6 +92,7 @@ def load_schema(schema_path):
     rule_group_folders = [f for f in rule_group_folders if op.isdir(f)]
     for rule_group_file in rule_group_files:
         group_name = op.splitext(op.basename(rule_group_file))[0]
+        lgr.info(f"Loading {group_name} rules.")
         with open(rule_group_file, "r") as fo:
             dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
             dict_ = dereference_yaml(dict_, dict_)
@@ -103,6 +105,7 @@ def load_schema(schema_path):
         schema["rules"][group_name] = {}
         for rule_subgroup_file in rule_subgroup_files:
             subgroup_name = op.splitext(op.basename(rule_subgroup_file))[0]
+            lgr.info(f"Loading {subgroup_name} rules.")
             with open(rule_subgroup_file, "r") as fo:
                 dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
                 dict_ = dereference_yaml(dict_, dict_)

From 4d594f4c1676d6d7ada6736277f9e5a5c965e239 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 13:51:23 -0400
Subject: [PATCH 021/347] Why isn't CircleCI working?

It works locally...
---
 tools/schemacode/schemacode/utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index a2a033bf3b..328e8dd316 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -17,6 +17,7 @@ def get_schema_path():
     schema_dir = op.abspath(
         op.join(op.dirname(op.dirname(op.dirname(op.dirname(__file__)))), "src", "schema") + op.sep
     )
+    raise Exception(schema_dir)
     return schema_dir
 
 

From 2c7db1a22dfe5e206975db6241126d01948ba0bd Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 14:01:44 -0400
Subject: [PATCH 022/347] Make loading function more restrictive.

---
 tools/schemacode/schemacode/schema.py | 5 +++++
 tools/schemacode/schemacode/utils.py  | 1 -
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 72dfb4388a..8b38781fc1 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -72,6 +72,11 @@ def load_schema(schema_path):
     objects_dir = schema_path / "objects/"
     rules_dir = schema_path / "rules/"
 
+    if not objects_dir.is_dir() or not rules_dir.is_dir():
+        raise ValueError(
+            f"Schema path or paths do not exist:\n\t{str(objects_dir)}\n\t{str(rules_dir)}"
+        )
+
     schema = {}
     schema["objects"] = {}
     schema["rules"] = {}
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 328e8dd316..a2a033bf3b 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -17,7 +17,6 @@ def get_schema_path():
     schema_dir = op.abspath(
         op.join(op.dirname(op.dirname(op.dirname(op.dirname(__file__)))), "src", "schema") + op.sep
     )
-    raise Exception(schema_dir)
     return schema_dir
 
 

From a3e7dfec3480f82488d986b9849e587d68a829b0 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 11 Oct 2021 15:01:43 -0400
Subject: [PATCH 023/347] Move rendering functions into a new module.

---
 tools/mkdocs_macros_bids/macros.py            |  12 +-
 tools/schemacode/schemacode/__init__.py       |   3 +-
 tools/schemacode/schemacode/render.py         | 371 ++++++++++++++++++
 tools/schemacode/schemacode/schema.py         | 363 +----------------
 tools/schemacode/schemacode/tests/conftest.py |  10 +
 .../schemacode/tests/test_schema.py           |  14 +-
 6 files changed, 405 insertions(+), 368 deletions(-)
 create mode 100644 tools/schemacode/schemacode/render.py
 create mode 100644 tools/schemacode/schemacode/tests/conftest.py

diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index 55d69c8fea..a6ea5c2a73 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -2,7 +2,7 @@
 import os
 import sys
 
-from schemacode import schema, utils
+from schemacode import render, schema, utils
 
 code_path = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 sys.path.append(code_path)
@@ -29,7 +29,7 @@ def make_filename_template(**kwargs):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    codeblock = schema.make_filename_template(schema_obj, **kwargs)
+    codeblock = render.make_filename_template(schema_obj, **kwargs)
     return codeblock
 
 
@@ -51,7 +51,7 @@ def make_entity_table(**kwargs):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_entity_table(schema_obj, **kwargs)
+    table = render.make_entity_table(schema_obj, **kwargs)
     return table
 
 
@@ -67,7 +67,7 @@ def make_entity_definitions():
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    text = schema.make_entity_definitions(schema_obj)
+    text = render.make_entity_definitions(schema_obj)
     return text
 
 
@@ -87,7 +87,7 @@ def make_suffix_table(suffixes):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_suffix_table(schema_obj, suffixes)
+    table = render.make_suffix_table(schema_obj, suffixes)
     return table
 
 
@@ -112,7 +112,7 @@ def make_metadata_table(field_info):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_metadata_table(schema_obj, field_info)
+    table = render.make_metadata_table(schema_obj, field_info)
     return table
 
 
diff --git a/tools/schemacode/schemacode/__init__.py b/tools/schemacode/schemacode/__init__.py
index 3f492a4087..d01d8a33d3 100644
--- a/tools/schemacode/schemacode/__init__.py
+++ b/tools/schemacode/schemacode/__init__.py
@@ -1,7 +1,8 @@
 """A Python package for working with the BIDS schema."""
-from . import schema, utils
+from . import render, schema, utils
 
 __all__ = [
+    "render",
     "schema",
     "utils",
 ]
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
new file mode 100644
index 0000000000..f3dfaaa7b9
--- /dev/null
+++ b/tools/schemacode/schemacode/render.py
@@ -0,0 +1,371 @@
+"""Functions for rendering portions of the schema as text."""
+import logging
+import os
+
+import pandas as pd
+from tabulate import tabulate
+
+from . import utils
+from .schema import filter_schema
+
+lgr = utils.get_logger()
+# Basic settings for output, for now just basic
+utils.set_logger_level(
+    lgr, os.environ.get("BIDS_SCHEMA_LOG_LEVEL", logging.INFO)
+)
+logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
+
+
+def make_entity_definitions(schema):
+    """Generate definitions and other relevant information for entities in the specification.
+
+    Each entity gets its own heading.
+
+    Parameters
+    ----------
+    schema : dict
+        The schema object, which is a dictionary with nested dictionaries and
+        lists stored within it.
+
+    Returns
+    -------
+    text : str
+        A string containing descriptions and some formatting
+        information about the entities in the schema.
+    """
+    entity_order = schema["rules"]["entities"]
+    entity_definitions = schema["objects"]["entities"]
+
+    text = ""
+    for entity in entity_order:
+        entity_info = entity_definitions[entity]
+        entity_shorthand = entity_info["entity"]
+        text += "\n"
+        text += "## {}".format(entity_shorthand)
+        text += "\n\n"
+        text += "Full name: {}".format(entity_info["name"])
+        text += "\n\n"
+        text += "Format: `{}-<{}>`".format(
+            entity_info["entity"],
+            entity_info.get("format", "label"),
+        )
+        text += "\n\n"
+        if "enum" in entity_info.keys():
+            text += "Allowed values: `{}`".format("`, `".join(entity_info["enum"]))
+            text += "\n\n"
+
+        text += "Definition: {}".format(entity_info["description"])
+    return text
+
+
+def make_filename_template(schema, **kwargs):
+    """Create codeblocks containing example filename patterns for a given datatype.
+
+    Parameters
+    ----------
+    schema : dict
+        The schema object, which is a dictionary with nested dictionaries and
+        lists stored within it.
+    kwargs : dict
+        Keyword arguments used to filter the schema.
+        Example kwargs that may be used include: "suffixes", "datatypes",
+        "extensions".
+
+    Returns
+    -------
+    codeblock : str
+        A multiline string containing the filename templates for file types
+        in the schema, after filtering.
+    """
+    schema = filter_schema(schema, **kwargs)
+
+    entity_order = schema["rules"]["entities"]
+
+    paragraph = ""
+    # Parent folders
+    paragraph += "{}-<{}>/\n\t[{}-<{}>/]\n".format(
+        schema["objects"]["entities"]["subject"]["entity"],
+        schema["objects"]["entities"]["subject"]["format"],
+        schema["objects"]["entities"]["session"]["entity"],
+        schema["objects"]["entities"]["session"]["format"],
+    )
+
+    for datatype in schema["rules"]["datatypes"].keys():
+        paragraph += "\t\t{}/\n".format(datatype)
+
+        # Unique filename patterns
+        for group in schema["rules"]["datatypes"][datatype]:
+            string = "\t\t\t"
+            for ent in entity_order:
+                ent_format = "{}-<{}>".format(
+                    schema["objects"]["entities"][ent]["entity"],
+                    schema["objects"]["entities"][ent].get("format", "label")
+                )
+                if ent in group["entities"]:
+                    if group["entities"][ent] == "required":
+                        if len(string.strip()):
+                            string += "_" + ent_format
+                        else:
+                            # Only the first entity doesn't need an underscore
+                            string += ent_format
+                    else:
+                        if len(string.strip()):
+                            string += "[_" + ent_format + "]"
+                        else:
+                            # Only the first entity doesn't need an underscore
+                            string += "[" + ent_format + "]"
+
+            # In cases of large numbers of suffixes,
+            # we use the "suffix" variable and expect a table later in the spec
+            if len(group["suffixes"]) > 5:
+                suffix = "_<suffix>"
+                string += suffix
+                strings = [string]
+            else:
+                strings = [
+                    string + "_" + suffix for suffix in group["suffixes"]
+                ]
+
+            # Add extensions
+            full_strings = []
+            extensions = group["extensions"]
+            extensions = [
+                ext if ext != "*" else ".<extension>" for ext in extensions
+            ]
+            extensions = utils.combine_extensions(extensions)
+            if len(extensions) > 5:
+                # Combine exts when there are many, but keep JSON separate
+                if ".json" in extensions:
+                    extensions = [".<extension>", ".json"]
+                else:
+                    extensions = [".<extension>"]
+
+            for extension in extensions:
+                for string in strings:
+                    new_string = string + extension
+                    full_strings.append(new_string)
+
+            full_strings = sorted(full_strings)
+            if full_strings:
+                paragraph += "\n".join(full_strings) + "\n"
+
+    paragraph = paragraph.rstrip()
+    codeblock = "Template:\n```Text\n" + paragraph + "\n```"
+    codeblock = codeblock.expandtabs(4)
+    return codeblock
+
+
+def make_entity_table(schema, tablefmt="github", **kwargs):
+    """Produce entity table (markdown) based on schema.
+
+    Parameters
+    ----------
+    schema_path : str
+        Folder containing schema, which is stored in yaml files.
+    entities_file : str, optional
+        File in which entities are described.
+        This is used for hyperlinks in the table, so the path to the file
+        should be considered from the location of out_file.
+        Default is '09-entities.md'.
+
+    Returns
+    -------
+    table_str : str
+        Markdown string containing the table.
+    """
+    schema = filter_schema(schema, **kwargs)
+
+    ENTITIES_FILE = "09-entities.md"
+
+    # prepare the table based on the schema
+    # import pdb; pdb.set_trace()
+    header = ["Entity", "DataType"]
+    formats = ["Format", "DataType"]
+    entity_to_col = {}
+    table = [formats]
+
+    # Compose header and formats first
+    for i, (entity, spec) in enumerate(schema["objects"]["entities"].items()):
+        entity_shorthand = schema["objects"]["entities"][entity]["entity"]
+        header.append(spec["name"])
+        formats.append(
+            f'[`{entity_shorthand}-<{spec.get("format", "label")}>`]'
+            f"({ENTITIES_FILE}#{entity_shorthand})"
+        )
+        entity_to_col[entity] = i + 1
+
+    # Go through data types
+    for dtype, dtype_specs in schema["rules"]["datatypes"].items():
+        dtype_rows = {}
+
+        # each dtype could have multiple specs
+        for spec in dtype_specs:
+            suffixes = spec.get("suffixes")
+
+            # Skip this part of the schema if no suffixes are found.
+            # This is a hack to work around filter_schema's limitations.
+            if not len(suffixes):
+                continue
+
+            # TODO: <br> is specific for html form
+            suffixes_str = " ".join(suffixes) if suffixes else ""
+            dtype_row = [dtype] + ([""] * len(entity_to_col))
+            for ent, req in spec.get("entities", []).items():
+                dtype_row[entity_to_col[ent]] = req.upper()
+
+            # Merge specs within dtypes if they share all of the same entities
+            if dtype_row in dtype_rows.values():
+                for k, v in dtype_rows.items():
+                    if dtype_row == v:
+                        dtype_rows.pop(k)
+                        new_k = k + " " + suffixes_str
+                        new_k = new_k.strip()
+                        dtype_rows[new_k] = v
+                        break
+            else:
+                dtype_rows[suffixes_str] = dtype_row
+
+        # Reformat first column
+        dtype_rows = {
+            dtype + "<br>({})".format(k): v for k, v in dtype_rows.items()
+        }
+        dtype_rows = [[k] + v for k, v in dtype_rows.items()]
+        table += dtype_rows
+
+    # Create multi-level index because first two rows are headers
+    cols = list(zip(header, table[0]))
+    cols = pd.MultiIndex.from_tuples(cols)
+    table = pd.DataFrame(data=table[1:], columns=cols)
+    table = table.set_index(("Entity", "Format"))
+
+    # Remove unnecessary columns
+    table = utils.drop_unused_entities(table)
+    table = utils.flatten_multiindexed_columns(table)
+
+    # Print it as markdown
+    table_str = tabulate(table, headers="keys", tablefmt=tablefmt)
+    return table_str
+
+
+def make_suffix_table(schema, suffixes, tablefmt="github"):
+    """Produce suffix table (markdown) based on requested suffixes.
+
+    Parameters
+    ----------
+    schema : dict
+    suffixes : list of str
+    tablefmt : str
+
+    Returns
+    -------
+    table_str : str
+        Tabulated table as a string.
+    """
+    # The filter function doesn't work here.
+    suffix_schema = schema["objects"]["suffixes"]
+
+    suffixes_found = [f for f in suffixes if f in suffix_schema.keys()]
+    suffixes_not_found = [f for f in suffixes if f not in suffix_schema.keys()]
+    if suffixes_not_found:
+        raise Exception(
+            "Warning: Missing suffixes: {}".format(
+                ", ".join(suffixes_not_found)
+            )
+        )
+
+    df = pd.DataFrame(
+        index=suffixes_found,
+        columns=["**Name**", "**Description**"],
+    )
+    # Index by suffix because name cannot be assumed to be unique
+    df.index.name = "`suffix`"
+    for suffix in suffixes_found:
+        suffix_info = suffix_schema[suffix]
+        description = suffix_info["description"]
+        # A backslash before a newline means continue a string
+        description = description.replace("\\\n", "")
+        # Two newlines should be respected
+        description = description.replace("\n\n", "<br>")
+        # Otherwise a newline corresponds to a space
+        description = description.replace("\n", " ")
+
+        df.loc[suffix] = [suffix_info["name"], description]
+
+    df = df.reset_index(drop=False)
+    df = df.set_index("**Name**")
+    df = df[["`suffix`", "**Description**"]]
+
+    # Print it as markdown
+    table_str = tabulate(df, headers="keys", tablefmt=tablefmt)
+    return table_str
+
+
+def make_metadata_table(schema, field_info, tablefmt="github"):
+    """Produce metadata table (markdown) based on requested fields.
+
+    Parameters
+    ----------
+    schema : dict
+        The BIDS schema.
+    field_info : dict of strings or tuples
+        A dictionary mapping metadata keys to requirement levels in the
+        rendered metadata table.
+        The dictionary values may be strings, in which case the string
+        is the requirement level information, or two-item tuples of strings,
+        in which case the first string is the requirement level information
+        and the second string is additional table-specific information
+        about the metadata field that will be appended to the field's base
+        definition from the schema.
+    tablefmt : string, optional
+        The target table format. The default is "github" (GitHub format).
+
+    Returns
+    -------
+    table_str : str
+        The tabulated table as a Markdown string.
+    """
+    fields = list(field_info.keys())
+    # The filter function doesn't work here.
+    metadata_schema = schema["objects"]["metadata"]
+
+    retained_fields = [f for f in fields if f in metadata_schema.keys()]
+    dropped_fields = [f for f in fields if f not in metadata_schema.keys()]
+    if dropped_fields:
+        print("Warning: Missing fields: {}".format(", ".join(dropped_fields)))
+
+    # Use the "name" field in the table, to allow for filenames to not match
+    # "names".
+    df = pd.DataFrame(
+        index=[metadata_schema[f]["name"] for f in retained_fields],
+        columns=["**Requirement Level**", "**Data type**", "**Description**"],
+    )
+    df.index.name = "**Key name**"
+    for field in retained_fields:
+        field_name = metadata_schema[field]["name"]
+        requirement_info = field_info[field]
+        description_addendum = ""
+        if isinstance(requirement_info, tuple):
+            requirement_info, description_addendum = requirement_info
+
+        requirement_info = requirement_info.replace(
+            "DEPRECATED",
+            "[DEPRECATED](/02-common-principles.html#definitions)",
+        )
+
+        type_string = utils.resolve_metadata_type(metadata_schema[field])
+
+        description = (
+            metadata_schema[field]["description"] + " " + description_addendum
+        )
+        # A backslash before a newline means continue a string
+        description = description.replace("\\\n", "")
+        # Two newlines should be respected
+        description = description.replace("\n\n", "<br>")
+        # Otherwise a newline corresponds to a space
+        description = description.replace("\n", " ")
+
+        df.loc[field_name] = [requirement_info, type_string, description]
+
+    # Print it as markdown
+    table_str = tabulate(df, headers="keys", tablefmt=tablefmt)
+    return table_str
diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 8b38781fc1..efb976e491 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -6,9 +6,7 @@
 from glob import glob
 from pathlib import Path
 
-import pandas as pd
 import yaml
-from tabulate import tabulate
 
 from . import utils
 
@@ -85,7 +83,7 @@ def load_schema(schema_path):
     object_group_files = sorted(glob(str(objects_dir / "*.yaml")))
     for object_group_file in object_group_files:
         group_name = op.splitext(op.basename(object_group_file))[0]
-        lgr.info(f"Loading {group_name} objects.")
+        lgr.debug(f"Loading {group_name} objects.")
         with open(object_group_file, "r") as fo:
             dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
             dict_ = dereference_yaml(dict_, dict_)
@@ -97,7 +95,7 @@ def load_schema(schema_path):
     rule_group_folders = [f for f in rule_group_folders if op.isdir(f)]
     for rule_group_file in rule_group_files:
         group_name = op.splitext(op.basename(rule_group_file))[0]
-        lgr.info(f"Loading {group_name} rules.")
+        lgr.debug(f"Loading {group_name} rules.")
         with open(rule_group_file, "r") as fo:
             dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
             dict_ = dereference_yaml(dict_, dict_)
@@ -110,7 +108,7 @@ def load_schema(schema_path):
         schema["rules"][group_name] = {}
         for rule_subgroup_file in rule_subgroup_files:
             subgroup_name = op.splitext(op.basename(rule_subgroup_file))[0]
-            lgr.info(f"Loading {subgroup_name} rules.")
+            lgr.debug(f"Loading {subgroup_name} rules.")
             with open(rule_subgroup_file, "r") as fo:
                 dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
                 dict_ = dereference_yaml(dict_, dict_)
@@ -168,358 +166,3 @@ def filter_schema(schema, **kwargs):
             if isinstance(item, dict):
                 new_schema[i] = filter_schema(item, **kwargs)
     return new_schema
-
-
-def make_entity_definitions(schema):
-    """Generate definitions and other relevant information for entities in the specification.
-
-    Each entity gets its own heading.
-
-    Parameters
-    ----------
-    schema : dict
-        The schema object, which is a dictionary with nested dictionaries and
-        lists stored within it.
-
-    Returns
-    -------
-    text : str
-        A string containing descriptions and some formatting
-        information about the entities in the schema.
-    """
-    entity_order = schema["rules"]["entities"]
-    entity_definitions = schema["objects"]["entities"]
-
-    text = ""
-    for entity in entity_order:
-        entity_info = entity_definitions[entity]
-        entity_shorthand = entity_info["entity"]
-        text += "\n"
-        text += "## {}".format(entity_shorthand)
-        text += "\n\n"
-        text += "Full name: {}".format(entity_info["name"])
-        text += "\n\n"
-        text += "Format: `{}-<{}>`".format(
-            entity_info["entity"],
-            entity_info.get("format", "label"),
-        )
-        text += "\n\n"
-        if "enum" in entity_info.keys():
-            text += "Allowed values: `{}`".format("`, `".join(entity_info["enum"]))
-            text += "\n\n"
-
-        text += "Definition: {}".format(entity_info["description"])
-    return text
-
-
-def make_filename_template(schema, **kwargs):
-    """Create codeblocks containing example filename patterns for a given datatype.
-
-    Parameters
-    ----------
-    schema : dict
-        The schema object, which is a dictionary with nested dictionaries and
-        lists stored within it.
-    kwargs : dict
-        Keyword arguments used to filter the schema.
-        Example kwargs that may be used include: "suffixes", "datatypes",
-        "extensions".
-
-    Returns
-    -------
-    codeblock : str
-        A multiline string containing the filename templates for file types
-        in the schema, after filtering.
-    """
-    schema = filter_schema(schema, **kwargs)
-
-    entity_order = schema["rules"]["entities"]
-
-    paragraph = ""
-    # Parent folders
-    paragraph += "{}-<{}>/\n\t[{}-<{}>/]\n".format(
-        schema["objects"]["entities"]["subject"]["entity"],
-        schema["objects"]["entities"]["subject"]["format"],
-        schema["objects"]["entities"]["session"]["entity"],
-        schema["objects"]["entities"]["session"]["format"],
-    )
-
-    for datatype in schema["rules"]["datatypes"].keys():
-        paragraph += "\t\t{}/\n".format(datatype)
-
-        # Unique filename patterns
-        for group in schema["rules"]["datatypes"][datatype]:
-            string = "\t\t\t"
-            for ent in entity_order:
-                ent_format = "{}-<{}>".format(
-                    schema["objects"]["entities"][ent]["entity"],
-                    schema["objects"]["entities"][ent].get("format", "label")
-                )
-                if ent in group["entities"]:
-                    if group["entities"][ent] == "required":
-                        if len(string.strip()):
-                            string += "_" + ent_format
-                        else:
-                            # Only the first entity doesn't need an underscore
-                            string += ent_format
-                    else:
-                        if len(string.strip()):
-                            string += "[_" + ent_format + "]"
-                        else:
-                            # Only the first entity doesn't need an underscore
-                            string += "[" + ent_format + "]"
-
-            # In cases of large numbers of suffixes,
-            # we use the "suffix" variable and expect a table later in the spec
-            if len(group["suffixes"]) > 5:
-                suffix = "_<suffix>"
-                string += suffix
-                strings = [string]
-            else:
-                strings = [
-                    string + "_" + suffix for suffix in group["suffixes"]
-                ]
-
-            # Add extensions
-            full_strings = []
-            extensions = group["extensions"]
-            extensions = [
-                ext if ext != "*" else ".<extension>" for ext in extensions
-            ]
-            extensions = utils.combine_extensions(extensions)
-            if len(extensions) > 5:
-                # Combine exts when there are many, but keep JSON separate
-                if ".json" in extensions:
-                    extensions = [".<extension>", ".json"]
-                else:
-                    extensions = [".<extension>"]
-
-            for extension in extensions:
-                for string in strings:
-                    new_string = string + extension
-                    full_strings.append(new_string)
-
-            full_strings = sorted(full_strings)
-            if full_strings:
-                paragraph += "\n".join(full_strings) + "\n"
-
-    paragraph = paragraph.rstrip()
-    codeblock = "Template:\n```Text\n" + paragraph + "\n```"
-    codeblock = codeblock.expandtabs(4)
-    return codeblock
-
-
-def make_entity_table(schema, tablefmt="github", **kwargs):
-    """Produce entity table (markdown) based on schema.
-
-    Parameters
-    ----------
-    schema_path : str
-        Folder containing schema, which is stored in yaml files.
-    entities_file : str, optional
-        File in which entities are described.
-        This is used for hyperlinks in the table, so the path to the file
-        should be considered from the location of out_file.
-        Default is '09-entities.md'.
-
-    Returns
-    -------
-    table_str : str
-        Markdown string containing the table.
-    """
-    schema = filter_schema(schema, **kwargs)
-
-    ENTITIES_FILE = "09-entities.md"
-
-    # prepare the table based on the schema
-    # import pdb; pdb.set_trace()
-    header = ["Entity", "DataType"]
-    formats = ["Format", "DataType"]
-    entity_to_col = {}
-    table = [formats]
-
-    # Compose header and formats first
-    for i, (entity, spec) in enumerate(schema["objects"]["entities"].items()):
-        entity_shorthand = schema["objects"]["entities"][entity]["entity"]
-        header.append(spec["name"])
-        formats.append(
-            f'[`{entity_shorthand}-<{spec.get("format", "label")}>`]'
-            f"({ENTITIES_FILE}#{entity_shorthand})"
-        )
-        entity_to_col[entity] = i + 1
-
-    # Go through data types
-    for dtype, dtype_specs in schema["rules"]["datatypes"].items():
-        dtype_rows = {}
-
-        # each dtype could have multiple specs
-        for spec in dtype_specs:
-            suffixes = spec.get("suffixes")
-
-            # Skip this part of the schema if no suffixes are found.
-            # This is a hack to work around filter_schema's limitations.
-            if not len(suffixes):
-                continue
-
-            # TODO: <br> is specific for html form
-            suffixes_str = " ".join(suffixes) if suffixes else ""
-            dtype_row = [dtype] + ([""] * len(entity_to_col))
-            for ent, req in spec.get("entities", []).items():
-                dtype_row[entity_to_col[ent]] = req.upper()
-
-            # Merge specs within dtypes if they share all of the same entities
-            if dtype_row in dtype_rows.values():
-                for k, v in dtype_rows.items():
-                    if dtype_row == v:
-                        dtype_rows.pop(k)
-                        new_k = k + " " + suffixes_str
-                        new_k = new_k.strip()
-                        dtype_rows[new_k] = v
-                        break
-            else:
-                dtype_rows[suffixes_str] = dtype_row
-
-        # Reformat first column
-        dtype_rows = {
-            dtype + "<br>({})".format(k): v for k, v in dtype_rows.items()
-        }
-        dtype_rows = [[k] + v for k, v in dtype_rows.items()]
-        table += dtype_rows
-
-    # Create multi-level index because first two rows are headers
-    cols = list(zip(header, table[0]))
-    cols = pd.MultiIndex.from_tuples(cols)
-    table = pd.DataFrame(data=table[1:], columns=cols)
-    table = table.set_index(("Entity", "Format"))
-
-    # Remove unnecessary columns
-    table = utils.drop_unused_entities(table)
-    table = utils.flatten_multiindexed_columns(table)
-
-    # Print it as markdown
-    table_str = tabulate(table, headers="keys", tablefmt=tablefmt)
-    return table_str
-
-
-def make_suffix_table(schema, suffixes, tablefmt="github"):
-    """Produce suffix table (markdown) based on requested suffixes.
-
-    Parameters
-    ----------
-    schema : dict
-    suffixes : list of str
-    tablefmt : str
-
-    Returns
-    -------
-    table_str : str
-        Tabulated table as a string.
-    """
-    # The filter function doesn't work here.
-    suffix_schema = schema["objects"]["suffixes"]
-
-    suffixes_found = [f for f in suffixes if f in suffix_schema.keys()]
-    suffixes_not_found = [f for f in suffixes if f not in suffix_schema.keys()]
-    if suffixes_not_found:
-        raise Exception(
-            "Warning: Missing suffixes: {}".format(
-                ", ".join(suffixes_not_found)
-            )
-        )
-
-    df = pd.DataFrame(
-        index=suffixes_found,
-        columns=["**Name**", "**Description**"],
-    )
-    # Index by suffix because name cannot be assumed to be unique
-    df.index.name = "`suffix`"
-    for suffix in suffixes_found:
-        suffix_info = suffix_schema[suffix]
-        description = suffix_info["description"]
-        # A backslash before a newline means continue a string
-        description = description.replace("\\\n", "")
-        # Two newlines should be respected
-        description = description.replace("\n\n", "<br>")
-        # Otherwise a newline corresponds to a space
-        description = description.replace("\n", " ")
-
-        df.loc[suffix] = [suffix_info["name"], description]
-
-    df = df.reset_index(drop=False)
-    df = df.set_index("**Name**")
-    df = df[["`suffix`", "**Description**"]]
-
-    # Print it as markdown
-    table_str = tabulate(df, headers="keys", tablefmt=tablefmt)
-    return table_str
-
-
-def make_metadata_table(schema, field_info, tablefmt="github"):
-    """Produce metadata table (markdown) based on requested fields.
-
-    Parameters
-    ----------
-    schema : dict
-        The BIDS schema.
-    field_info : dict of strings or tuples
-        A dictionary mapping metadata keys to requirement levels in the
-        rendered metadata table.
-        The dictionary values may be strings, in which case the string
-        is the requirement level information, or two-item tuples of strings,
-        in which case the first string is the requirement level information
-        and the second string is additional table-specific information
-        about the metadata field that will be appended to the field's base
-        definition from the schema.
-    tablefmt : string, optional
-        The target table format. The default is "github" (GitHub format).
-
-    Returns
-    -------
-    table_str : str
-        The tabulated table as a Markdown string.
-    """
-    fields = list(field_info.keys())
-    # The filter function doesn't work here.
-    metadata_schema = schema["objects"]["metadata"]
-
-    retained_fields = [f for f in fields if f in metadata_schema.keys()]
-    dropped_fields = [f for f in fields if f not in metadata_schema.keys()]
-    if dropped_fields:
-        print("Warning: Missing fields: {}".format(", ".join(dropped_fields)))
-
-    # Use the "name" field in the table, to allow for filenames to not match
-    # "names".
-    df = pd.DataFrame(
-        index=[metadata_schema[f]["name"] for f in retained_fields],
-        columns=["**Requirement Level**", "**Data type**", "**Description**"],
-    )
-    df.index.name = "**Key name**"
-    for field in retained_fields:
-        field_name = metadata_schema[field]["name"]
-        requirement_info = field_info[field]
-        description_addendum = ""
-        if isinstance(requirement_info, tuple):
-            requirement_info, description_addendum = requirement_info
-
-        requirement_info = requirement_info.replace(
-            "DEPRECATED",
-            "[DEPRECATED](/02-common-principles.html#definitions)",
-        )
-
-        type_string = utils.resolve_metadata_type(metadata_schema[field])
-
-        description = (
-            metadata_schema[field]["description"] + " " + description_addendum
-        )
-        # A backslash before a newline means continue a string
-        description = description.replace("\\\n", "")
-        # Two newlines should be respected
-        description = description.replace("\n\n", "<br>")
-        # Otherwise a newline corresponds to a space
-        description = description.replace("\n", " ")
-
-        df.loc[field_name] = [requirement_info, type_string, description]
-
-    # Print it as markdown
-    table_str = tabulate(df, headers="keys", tablefmt=tablefmt)
-    return table_str
diff --git a/tools/schemacode/schemacode/tests/conftest.py b/tools/schemacode/schemacode/tests/conftest.py
new file mode 100644
index 0000000000..7737987903
--- /dev/null
+++ b/tools/schemacode/schemacode/tests/conftest.py
@@ -0,0 +1,10 @@
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture(scope="session")
+def schema_dir():
+    """Path to the schema housed in the bids-specification repo."""
+    bids_schema = Path(__file__).parent.parent.parent.parent.parent / "src" / "schema"
+    return bids_schema
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
index 91d7de897b..f44e868729 100644
--- a/tools/schemacode/schemacode/tests/test_schema.py
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -1 +1,13 @@
-"""Tests for the schemacode package."""
\ No newline at end of file
+"""Tests for the schemacode package."""
+import pytest
+
+from schemacode import schema
+
+
+def test_load_schema(schema_dir):
+    bad_path = "/path/to/nowhere"
+    with pytest.raises(ValueError):
+        schema.load_schema(bad_path)
+
+    schema_obj = schema.load_schema(schema_dir)
+    assert isinstance(schema_obj, dict)

From 2a638c6d79c7d77bd27985e70fd9877cea48589e Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 11 Oct 2021 14:06:50 -0400
Subject: [PATCH 024/347] [ENH] introduce GeneratedBy to "core" BIDS

#487 (and originally #439) is a `WIP ENH` to introduce standardized provenance
capture/expression for BIDS datasets.  This PR just follows the idea of #371
(small atomic ENHs), and is based on current state of the specification where
we have GeneratedBy to describe how a BIDS derivative dataset came to its
existence.

## Rationale

As I had  previously stated in many (face-to-face when it was still
possible ;)) conversations, in my view, any BIDS dataset is a derivative
dataset.  Even if it contains "raw" data, it is never given by gods, but is a
result of some process (let's call it pipeline for consistency) which produced
it out of some other data. That is why there is 1) `sourcedata/` to provide
placement for such original (as "raw" in terms of processing, but "raw"er in
terms of its relation to actual data acquired by equipment), and 2) `code/` to
provide placement for scripts used to produce or "tune" the dataset.  Typically
"sourcedata" is either a collection of DICOMs or a collection of data in some
other formats (e.g. nifti) which is then either converted or just renamed into
BIDS layout. When encountering a new BIDS dataset ATM it requires forensics
and/or data archaeology to discover how this BIDS dataset came about, to e.g.
possibly figure out the source of the buggy (meta)data it contains.

At the level of individual files, some tools already add ad-hoc fields
during conversion into side car .json files they produce,

<details>
<summary>e.g. dcm2niix adds ConversionSoftware and ConversionSoftwareVersion</summary>

```shell
(git-annex)lena:~/datalad/dbic/QA[master]git
$> git grep ConversionSoftware | head -n 2
sub-amit/ses-20180508/anat/sub-amit_ses-20180508_acq-MPRAGE_T1w.json:  "ConversionSoftware": "dcm2niix",
sub-amit/ses-20180508/anat/sub-amit_ses-20180508_acq-MPRAGE_T1w.json:  "ConversionSoftwareVersion": "v1.0.20170923 (OpenJPEG build) GCC6.3.0",

```
</details>

ATM I need to add such metadata to datasets produced by heudiconv to make
sure that in case of incremental conversions there is no switch in versions of
the software.
---
 src/03-modality-agnostic-files.md | 58 ++++++++++++++++++++-----------
 src/schema/objects/metadata.yaml  |  2 +-
 2 files changed, 38 insertions(+), 22 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 7833f96b60..704a9038f1 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -28,9 +28,22 @@ Every dataset MUST include this file with the following fields:
       "EthicsApprovals": "OPTIONAL",
       "ReferencesAndLinks": "OPTIONAL",
       "DatasetDOI": "OPTIONAL",
+      "GeneratedBy": "RECOMMENDED",
+      "SourceDatasets": "RECOMMENDED",
    }
 ) }}
 
+Each object in the `GeneratedBy` list includes the following REQUIRED, RECOMMENDED
+and OPTIONAL keys:
+
+| **Key name** | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                        |
+|--------------|-----------------------|---------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Name         | REQUIRED              | [string][]    | Name of the pipeline or process that generated the outputs. Use `"Manual"` to indicate the derivatives were generated by hand, or adjusted manually after an initial run of an automated pipeline.     |
+| Version      | RECOMMENDED           | [string][]    | Version of the pipeline.                                                                                                                                                                               |
+| Description  | OPTIONAL              | [string][]    | Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if `Name` is `"Manual"`.                                                                                     |
+| CodeURL      | OPTIONAL              | [string][]    | URL where the code used to generate the dataset may be found.                                                                                                                                          |
+| Container    | OPTIONAL              | [object][]    | Used to specify the location and relevant attributes of software container image used to produce the dataset. Valid keys in this object include `Type`, `Tag` and [`URI`][uri] with [string][] values. |
+
 Example:
 
 ```JSON
@@ -57,7 +70,23 @@ Example:
     "Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
   ],
   "DatasetDOI": "doi:10.0.2.3/dfjj.10",
-  "HEDVersion": "7.1.1"
+  "HEDVersion": "7.1.1",
+  "GeneratedBy": [
+    {
+      "Name": "reproin",
+      "Version": "0.6.0",
+      "Container": {
+        "Type": "docker",
+        "Tag": "repronim/reproin:0.6.0"
+      }
+    }
+  ],
+  "SourceDatasets": [
+    {
+      "URL": "s3://dicoms/studies/correlates",
+      "Version": "April 11 2011"
+    }
+  ]
 }
 ```
 
@@ -67,27 +96,19 @@ As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
 
-In addition to the keys for raw BIDS datasets,
-derived BIDS datasets include the following REQUIRED and RECOMMENDED
-`dataset_description.json` keys:
+In contrast to raw BIDS datasets, derived BIDS datasets MUST include
+`GeneratedBy` key:
 
 {{ MACROS___make_metadata_table(
    {
-      "GeneratedBy": "REQUIRED",
-      "SourceDatasets": "RECOMMENDED",
+      "GeneratedBy": "REQUIRED"
    }
 ) }}
 
-Each object in the `GeneratedBy` list includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-| **Key name** | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                           |
-|--------------|-----------------------|---------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Name         | REQUIRED              | [string][]    | Name of the pipeline or process that generated the outputs. Use `"Manual"` to indicate the derivatives were generated by hand, or adjusted manually after an initial run of an automated pipeline.        |
-| Version      | RECOMMENDED           | [string][]    | Version of the pipeline.                                                                                                                                                                                  |
-| Description  | OPTIONAL              | [string][]    | Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if `Name` is `"Manual"`.                                                                                        |
-| CodeURL      | OPTIONAL              | [string][]    | URL where the code used to generate the derivatives may be found.                                                                                                                                         |
-| Container    | OPTIONAL              | [object][]    | Used to specify the location and relevant attributes of software container image used to produce the derivative. Valid keys in this object include `Type`, `Tag` and [`URI`][uri] with [string][] values. |
+If a derived dataset is stored as a subfolder of the raw dataset, then the `Name` field
+of the first `GeneratedBy` object MUST be a substring of the derived dataset folder name.
+That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
+`GeneratedBy` object should have a `Name` of `<pipeline>`.
 
 Example:
 
@@ -120,11 +141,6 @@ Example:
 }
 ```
 
-If a derived dataset is stored as a subfolder of the raw dataset, then the `Name` field
-of the first `GeneratedBy` object MUST be a substring of the derived dataset folder name.
-That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
-`GeneratedBy` object should have a `Name` of `<pipeline>`.
-
 ### `README`
 
 Every BIDS dataset SHOULD come with a free form text file (`README`) describing the dataset in more detail.
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index a8e572a878..1a7e44c271 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -866,7 +866,7 @@ Funding:
 GeneratedBy:
   name: GeneratedBy
   description: |
-    Used to specify provenance of the derived dataset.
+    Used to specify provenance of the dataset.
     See table below for contents of each object.
   type: array
   minItems: 1

From a63b5b79585a9340bce21d31a96ca1425ff764b1 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 15 Oct 2021 08:52:09 -0400
Subject: [PATCH 025/347] Update "Recommended participant data" after merge of
 PR #816

---
 src/04-modality-specific-files/10-microscopy.md | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a7eb189108..e750d1d76a 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -331,18 +331,9 @@ For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples
 Additional optional columns in `samples.tsv` MAY be used to describe other samples' attributes.
 
 ## Recommended participant data (`participants.tsv`)
-<!---
-This section may be removed or modified depending if it is included in the "general"
-participants.tsv file in PR #816.
-(https://github.com/bids-standard/bids-specification/pull/816#issuecomment-909343123)
--->
-In addition to the species column in the [Participants file](../03-modality-agnostic-files.md#participants-file),
-the following data SHOULD be included for species different from `homo sapiens`:
-
--   `strain`: string value indicating the strain of the species, for example: `C57BL/6J`.
 
--   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
-    of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
+For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and `strain_rrid`
+in the [Participants file](../03-modality-agnostic-files.md#participants-file) when applicable.
 
 For example:
 ```Text

From f9c21254dc0ae1d71ed9bf172128b003cac49a4f Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Sat, 16 Oct 2021 14:50:22 -0400
Subject: [PATCH 026/347] Resolve conflict with master for entities.yaml

---
 src/schema/objects/entities.yaml | 323 +++++++++++++++++++++++++++++++
 1 file changed, 323 insertions(+)
 create mode 100644 src/schema/objects/entities.yaml

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
new file mode 100644
index 0000000000..b5d4339d68
--- /dev/null
+++ b/src/schema/objects/entities.yaml
@@ -0,0 +1,323 @@
+---
+# This file describes entities present in BIDS filenames.
+# WARNING: The entities are presented here in alphabetical order!
+# The appropriate order of entities in filenames is defined in `rules/entities.yaml`,
+# rather than this file (`objects/entities.yaml`).
+acquisition:
+  name: Acquisition
+  entity: acq
+  description: |
+    The `acq-<label>` key/value pair corresponds to a custom label the
+    user MAY use to distinguish a different set of parameters used for
+    acquiring the same modality.
+    For example this should be used when a study includes two T1w images - one
+    full brain low resolution and and one restricted field of view but high
+    resolution.
+    In such case two files could have the following names:
+    `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
+    the user is free to choose any other label than highres and lowres as long
+    as they are consistent across subjects and sessions.
+    In case different sequences are used to record the same modality
+    (for example, RARE and FLASH for T1w)
+    this field can also be used to make that distinction.
+    At what level of detail to make the distinction (for example,
+    just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
+    remains at the discretion of the researcher.
+  type: string
+  format: label
+ceagent:
+  name: Contrast Enhancing Agent
+  entity: ce
+  description: |
+    The `ce-<label>` key/value can be used to distinguish
+    sequences using different contrast enhanced images.
+    The label is the name of the contrast agent.
+    The key `ContrastBolusIngredient` MAY also be added in the JSON file,
+    with the same label.
+  type: string
+  format: label
+density:
+  name: Density
+  entity: den
+  description: |
+    Density of non-parametric surfaces.
+    MUST have a corresponding `Density` metadata field to provide
+    interpretation.
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
+description:
+  name: Description
+  entity: desc
+  description: |
+    When necessary to distinguish two files that do not otherwise have a
+    distinguishing entity, the `_desc-<label>` keyword-value SHOULD be used.
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
+direction:
+  name: Phase-Encoding Direction
+  entity: dir
+  description: |
+    The `dir-<label>` key/value can be set to an arbitrary alphanumeric label
+    (for example, `dir-LR` or `dir-AP`) to distinguish different phase-encoding
+    directions.
+  type: string
+  format: label
+echo:
+  name: Echo
+  entity: echo
+  description: |
+    If files belonging to an entity-linked file collection are acquired at different
+    echo times, the `_echo-<index>` key/value pair MUST be used to distinguish
+    individual files.
+    This entity represents the `EchoTime` metadata field. Please note that the `<index>`
+    denotes the number/index (in the form of a nonnegative integer), not the
+    `EchoTime` value which needs to be stored in the field `EchoTime` of the separate
+    JSON file.
+  type: string
+  format: index
+flip:
+  name: Flip Angle
+  entity: flip
+  description: |
+    If files belonging to an entity-linked file collection are acquired at different
+    flip angles, the `_flip-<index>` key/value pair MUST be used to distinguish
+    individual files.
+    This entity represents the `FlipAngle` metadata field. Please note that the `<index>`
+    denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
+    value which needs to be stored in the field `FlipAngle` of the separate JSON file.
+  type: string
+  format: index
+inversion:
+  name: Inversion Time
+  entity: inv
+  description: |
+    If files belonging to an entity-linked file collection are acquired at different
+    inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
+    individual files.
+    This entity represents the `InversionTime` metadata field. Please note that the `<index>`
+    denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
+    value which needs to be stored in the field `InversionTime` of the separate JSON file.
+  type: string
+  format: index
+label:
+  name: Label
+  entity: label
+  description: |
+    Tissue-type label, following a prescribed vocabulary.
+    Applies to binary masks and probabilistic/partial volume segmentations
+    that describe a single tissue type.
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
+modality:
+  name: Corresponding Modality
+  entity: mod
+  description: |
+    The `mod-<label>` key/value pair corresponds to modality label for defacing
+    masks, for example, T1w, inplaneT1, referenced by a defacemask image.
+    For example, `sub-01_mod-T1w_defacemask.nii.gz`.
+  type: string
+  format: label
+mtransfer:
+  name: Magnetization Transfer
+  entity: mt
+  description: |
+    If files belonging to an entity-linked file collection are acquired at different
+    magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
+    distinguish individual files.
+    This entity represents the `MTState` metadata field. Allowed label values for this
+    entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
+    respectively.
+  type: string
+  enum:
+  - 'on'
+  - 'off'
+part:
+  name: Part
+  entity: part
+  description: |
+    This entity is used to indicate which component of the complex
+    representation of the MRI signal is represented in voxel data.
+    The `part-<label>` key/value pair is associated with the DICOM Tag
+    `0008, 9208`.
+    Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+    which are typically used in `part-mag`/`part-phase` or
+    `part-real`/`part-imag` pairs of files.
+
+    Phase images MAY be in radians or in arbitrary units.
+    The sidecar JSON file MUST include the units of the `phase` image.
+    The possible options are `rad` or `arbitrary`.
+
+    When there is only a magnitude image of a given type, the `part` key MAY be
+    omitted.
+  type: string
+  enum:
+  - mag
+  - phase
+  - real
+  - imag
+processing:
+  name: Processed (on device)
+  entity: proc
+  description: |
+    The proc label is analogous to rec for MR and denotes a variant of
+    a file that was a result of particular processing performed on the device.
+
+    This is useful for files produced in particular by Elekta's MaxFilter
+    (for example, sss, tsss, trans, quat or mc),
+    which some installations impose to be run on raw data because of active
+    shielding software corrections before the MEG data can actually be
+    exploited.
+  type: string
+  format: label
+reconstruction:
+  name: Reconstruction
+  entity: rec
+  description: |
+    The `rec-<label>` key/value can be used to distinguish
+    different reconstruction algorithms (for example ones using motion
+    correction).
+  type: string
+  format: label
+recording:
+  name: Recording
+  entity: recording
+  description: |
+    More than one continuous recording file can be included (with different
+    sampling frequencies).
+    In such case use different labels.
+    For example: `_recording-contrast`, `_recording-saturation`.
+  type: string
+  format: label
+resolution:
+  name: Resolution
+  entity: res
+  description: |
+    Resolution of regularly sampled N-dimensional data.
+    MUST have a corresponding `Resolution` metadata field to provide
+    interpretation.
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
+run:
+  name: Run
+  entity: run
+  description: |
+    If several scans with the same acquisition parameters are acquired in the same session,
+    they MUST be indexed with the [`run-<index>`](../99-appendices/09-entities.md#run) entity:
+    `_run-1`, `_run-2`, `_run-3`, and so on (only nonnegative integers are allowed as
+    run labels).
+
+    If different entities apply,
+    such as a different session indicated by [`ses-<label>`](../99-appendices/09-entities.md#ses),
+    or different acquisition parameters indicated by
+    [`acq-<label>`](../99-appendices/09-entities.md#acq),
+    then `run` is not needed to distinguish the scans and MAY be omitted.
+  type: string
+  format: index
+sample:
+  name: Sample
+  entity: sample
+  description: |
+    A sample pertaining to a subject such as tissue, primary cell
+    or cell-free sample.
+    The `sample-<label>` key/value pair is used to distinguish between different
+    samples from the same subject.
+    The label MUST be unique per subject and is RECOMMENDED to be unique
+    throughout the dataset.
+  type: string
+  format: label
+session:
+  name: Session
+  entity: ses
+  description: |
+    A logical grouping of neuroimaging and behavioral data consistent across
+    subjects.
+    Session can (but doesn't have to) be synonymous to a visit in a
+    longitudinal study.
+    In general, subjects will stay in the scanner during one session.
+    However, for example, if a subject has to leave the scanner room and then
+    be re-positioned on the scanner bed, the set of MRI acquisitions will still
+    be considered as a session and match sessions acquired in other subjects.
+    Similarly, in situations where different data types are obtained over
+    several visits (for example fMRI on one day followed by DWI the day after)
+    those can be grouped in one session.
+    Defining multiple sessions is appropriate when several identical or similar
+    data acquisitions are planned and performed on all -or most- subjects,
+    often in the case of some intervention between sessions
+    (for example, training).
+  type: string
+  format: label
+space:
+  name: Space
+  entity: space
+  description: |
+    The space entity can be used to indicate
+    the way in which electrode positions are interpreted
+    (for EEG/MEG/iEEG data) or
+    the spatial reference to which a file has been aligned (for MRI data).
+    The space `<label>` MUST be taken from one of the modality specific lists in
+    [Appendix VIII](../99-appendices/08-coordinate-systems.md).
+    For example for iEEG data, the restricted keywords listed under
+    [iEEG Specific Coordinate Systems](../99-appendices/08-coordinate-systems.md#ieeg-specific-coordinate-systems)
+    are acceptable for `<label>`.
+
+    For EEG/MEG/iEEG data, this entity can be applied to raw data, but
+    for other data types, it is restricted to derivative data.
+  type: string
+  format: label
+split:
+  name: Split
+  entity: split
+  description: |
+    In the case of long data recordings that exceed a file size of 2Gb, the
+    .fif files are conventionally split into multiple parts.
+    Each of these files has an internal pointer to the next file.
+    This is important when renaming these split recordings to the BIDS
+    convention.
+
+    Instead of a simple renaming, files should be read in and saved under their
+    new names with dedicated tools like [MNE-Python](https://mne.tools/),
+    which will ensure that not only the file names, but also the internal file
+    pointers will be updated.
+    It is RECOMMENDED that .fif files with multiple parts use the
+    `split-<index>` entity to indicate each part.
+    If there are multiple parts of a recording and the optional `scans.tsv` is provided,
+    remember to list all files separately in `scans.tsv` and that the entries for the
+    `acq_time` column in `scans.tsv` MUST all be identical, as described in
+    [Scans file](../03-modality-agnostic-files.md#scans-file).
+  type: string
+  format: index
+subject:
+  name: Subject
+  entity: sub
+  description: |
+    A person or animal participating in the study.
+  type: string
+  format: label
+task:
+  name: Task
+  entity: task
+  description: |
+    Each task has a unique label that MUST only consist of letters and/or
+    numbers (other characters, including spaces and underscores, are not
+    allowed).
+    Those labels MUST be consistent across subjects and sessions.
+  type: string
+  format: label
+tracer:
+  name: Tracer
+  entity: trc
+  description: |
+    The `trc-<label>` key/value can be used to distinguish
+    sequences using different tracers.
+    The key `TracerName` MUST also be included in the associated JSON file,
+    although the label may be different.
+  type: string
+  format: label

From b2e1f8ade9c6db15e5f3fb27eb83b08bf1cd97ee Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Sat, 16 Oct 2021 14:56:28 -0400
Subject: [PATCH 027/347] Update entities.yaml in objects and rules schema
 folders

---
 src/schema/objects/entities.yaml | 20 ++++++++++++++++++++
 src/schema/rules/entities.yaml   |  2 ++
 2 files changed, 22 insertions(+)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index b5d4339d68..6781e9d16f 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -36,6 +36,15 @@ ceagent:
     with the same label.
   type: string
   format: label
+chunk:
+  name: Chunk
+  entity: chunk
+  description: |
+    The `chunk-<index>` key/value pair is used to distinguish between different
+    regions, 2D images or 3D volumes files, of the same physical sample with
+    different fields of view acquired in the same imaging experiment.
+  type: string
+  format: index
 density:
   name: Density
   entity: den
@@ -294,6 +303,17 @@ split:
     [Scans file](../03-modality-agnostic-files.md#scans-file).
   type: string
   format: index
+stain:
+  name: Stain
+  entity: stain
+  description: |
+    The `stain-<label>` key/pair values can be used to distinguish image files
+    from the same sample using different stains or antibodies for contrast enhancement.
+    Stains or antibodies SHOULD be indicated as appropriate in the `SampleStaining`,
+    `SamplePrimaryAntibodies` and/or `SampleSecondaryAntobodies` keys in the JSON file,
+    although the label may be different.
+  type: string
+  format: label
 subject:
   name: Subject
   entity: sub
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index c36b591b72..be2784520b 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -8,6 +8,7 @@
 - acquisition
 - ceagent
 - tracer
+- stain
 - reconstruction
 - direction
 - run
@@ -21,6 +22,7 @@
 - processing
 - space
 - split
+- chunk
 - resolution
 - density
 - label

From 7a904be9d4f467f6244e19996cf85226f58d6bc9 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Sat, 16 Oct 2021 15:01:53 -0400
Subject: [PATCH 028/347] Update microscopy.yaml datatypes rules schema folder

---
 .../{ => rules}/datatypes/microscopy.yaml     | 53 ++++++++++---------
 1 file changed, 27 insertions(+), 26 deletions(-)
 rename src/schema/{ => rules}/datatypes/microscopy.yaml (54%)

diff --git a/src/schema/datatypes/microscopy.yaml b/src/schema/rules/datatypes/microscopy.yaml
similarity index 54%
rename from src/schema/datatypes/microscopy.yaml
rename to src/schema/rules/datatypes/microscopy.yaml
index f3f8bdf1df..cb821d68b7 100644
--- a/src/schema/datatypes/microscopy.yaml
+++ b/src/schema/rules/datatypes/microscopy.yaml
@@ -1,29 +1,29 @@
 ---
 # Microscopy
 - suffixes:
-    - TEM
-    - SEM
-    - uCT
-    - BF
-    - DF
-    - PC
-    - DIC
-    - FLUO
-    - CONF
-    - PLI
-    - CARS
-    - 2PE
-    - MPE
-    - SR
-    - NLO
-    - OCT
-    - SPIM
+  - TEM
+  - SEM
+  - uCT
+  - BF
+  - DF
+  - PC
+  - DIC
+  - FLUO
+  - CONF
+  - PLI
+  - CARS
+  - 2PE
+  - MPE
+  - SR
+  - NLO
+  - OCT
+  - SPIM
   extensions:
-    - .ome.tif
-    - .ome.btf
-    - .png
-    - .tiff
-    - .json
+  - .ome.tif
+  - .ome.btf
+  - .png
+  - .tiff
+  - .json
   entities:
     subject: required
     session: optional
@@ -32,12 +32,13 @@
     stain: optional
     run: optional
     chunk: optional
+
 - suffixes:
-    - photo
+  - photo
   extensions:
-    - .jpg
-    - .png
-    - .tif
+  - .jpg
+  - .png
+  - .tif
   entities:
     subject: required
     session: optional

From 32496fd6e21d54fda8cb521652c44e52df9e87c2 Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Wed, 27 Oct 2021 14:16:43 -0400
Subject: [PATCH 029/347] Apply suggestions from code review

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
---
 src/04-modality-specific-files/10-microscopy.md | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index e750d1d76a..33268a0263 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -190,9 +190,12 @@ spatial relation between them.
 Examples of different chunks configurations can be seen in Figure 1.
 ![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
 
-Figure 1: Examples of chunks configurations. a) ordered 2D chunks without overlap,
-b) ordered 2D chunks with overlap, c) unordered 2D chunks with and without overlap,
-d) and e) ordered 2D chunks on different 3D planes, f) ordered 3D chunks
+Figure 1: Examples of chunks configurations. 
+- a) ordered 2D chunks without overlap,
+- b) ordered 2D chunks with overlap, 
+- c) unordered 2D chunks with and without overlap,
+- d) and e) ordered 2D chunks on different 3D planes, 
+- f) ordered 3D chunks
 
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,
@@ -209,7 +212,7 @@ my_dataset/
             sub-01/
                 microscopy/
                     sub-01_sample-01_res-4x_TEM.png
-                    sub-01_sample-01_res-4x.json
+                    sub-01_sample-01_res-4x_TEM.json
     sub-01/
         microscopy/
             sub-01_sample-01_TEM.png

From 711fdace53101767cafd340534781bb42a18e9ff Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Wed, 27 Oct 2021 14:30:41 -0400
Subject: [PATCH 030/347] Fix md formatting

---
 src/04-modality-specific-files/10-microscopy.md | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 33268a0263..e678e99f6b 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -190,12 +190,13 @@ spatial relation between them.
 Examples of different chunks configurations can be seen in Figure 1.
 ![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
 
-Figure 1: Examples of chunks configurations. 
-- a) ordered 2D chunks without overlap,
-- b) ordered 2D chunks with overlap, 
-- c) unordered 2D chunks with and without overlap,
-- d) and e) ordered 2D chunks on different 3D planes, 
-- f) ordered 3D chunks
+Figure 1: Examples of chunks configurations.
+
+-   a) ordered 2D chunks without overlap,
+-   b) ordered 2D chunks with overlap,
+-   c) unordered 2D chunks with and without overlap,
+-   d) and e) ordered 2D chunks on different 3D planes,
+-   f) ordered 3D chunks.
 
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,

From d9060ae0f52dfd39ae5e0cf1bebbc78dfa3fd30b Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 28 Oct 2021 09:39:34 -0400
Subject: [PATCH 031/347] Apply suggestions from code review by @tsalo and
 @sappelhoff

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 src/03-modality-agnostic-files.md | 4 ++--
 src/schema/objects/metadata.yaml  | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 704a9038f1..60c236abd5 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -33,7 +33,7 @@ Every dataset MUST include this file with the following fields:
    }
 ) }}
 
-Each object in the `GeneratedBy` list includes the following REQUIRED, RECOMMENDED
+Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
 and OPTIONAL keys:
 
 | **Key name** | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                        |
@@ -96,7 +96,7 @@ As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline_name>/dataset_description.json`.
 
-In contrast to raw BIDS datasets, derived BIDS datasets MUST include
+In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
 `GeneratedBy` key:
 
 {{ MACROS___make_metadata_table(
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 1a7e44c271..6f57b698a1 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -867,7 +867,6 @@ GeneratedBy:
   name: GeneratedBy
   description: |
     Used to specify provenance of the dataset.
-    See table below for contents of each object.
   type: array
   minItems: 1
   items:

From c33c6f69696696e7a32bdac21c681509c2bcc06f Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 28 Oct 2021 12:00:38 -0400
Subject: [PATCH 032/347] Make protocols.io an example in
 SampleExtractionProtocol and ImageAcquisitionProtocol

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index e678e99f6b..cd70d5cac0 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -256,7 +256,7 @@ A "manual" table is provided to facilitate the review process.
 | Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
 | NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
 | Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
-| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][uri] | Description of the image acquisition protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                     |
+| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][uri] | Description of the image acquisition protocol or URI (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                       |
 | OtherAcquisitionParameters | OPTIONAL              | [string][]               | Description of other relevant image acquisition parameters.                                                                                                                                                                                                                                                                                                                                                                                                              |
 
 #### Sample
@@ -282,7 +282,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
 | SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | TissueDeformationScaling    | OPTIONAL              | [number][]                             | Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is `97`; and for an expansion of 100%, the value is `200`).                                                                                                                                                                                                                                                                                                                         |
-| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                                                                         |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
 #### Chunk transformations

From 8ccf4defe20097dd16c829c0a349168859f3e5d3 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 4 Nov 2021 16:16:53 -0400
Subject: [PATCH 033/347] Re-wording of chunk-index section and chunk
 transformation matrix is recommended for ordered chunks

---
 .../10-microscopy.md                          | 65 +++++++++++--------
 1 file changed, 37 insertions(+), 28 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index cd70d5cac0..bfe59541c9 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -114,8 +114,8 @@ sub-01/
         sub-01_sample-03_<modality_suffix>.<ext>
         sub-01_<modality_suffix>.json
 ```
-In this example, JSON metadata is common for all samples of `sub-01`.
-JSON metadata may be defined per subject or per sample as appropriate, per the
+In this example, the JSON metadata is common for all samples of `sub-01`.
+JSON metadata may be defined per subject or per sample as appropriate, as per the
 [inheritance principle](../02-common-principles.md#the-inheritance-principle).
 
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
@@ -131,7 +131,7 @@ image files from the same sample using different stains or antibodies for contra
 
 <!--- The following example will be generated automatically with macros after community review. -->
 For example:
-Brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three stains
+One brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three stains
 (`stain-01`, `stain-02`, `stain-03`) in three separate files.
 In this example, the entity stain is used to distinguish images with different
 stains in separate files from the same sample.
@@ -163,9 +163,26 @@ The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when
 regions (2D images or 3D volumes files) of the same physical sample are imaged with different
 fields of view, regardless if they overlap or not.
 
+In some cases, the chunks can be "ordered" and correspond to the displacement of the
+microscope stage, for example.
+In other cases, the chunks can be different images of the same sample with no explicit
+spatial relation between them.
+
+Examples of different chunks configurations can be seen in Figure 1.
+![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
+
+Figure 1: Examples of chunks configurations.
+
+-   a) ordered 2D chunks without overlap,
+-   b) ordered 2D chunks with overlap,
+-   c) unordered 2D chunks with and without overlap,
+-   d) and e) ordered 2D chunks on different 3D planes,
+-   f) ordered 3D chunks.
+
 <!--- The following example will be generated automatically with macros after community review. -->
-For example:
-Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`) of subject `sub-01`.
+For example, as illustrated in Figure 1b:
+Six chunks (`chunk-01` to `chunk-06`) from the same brain sample (`sample-01`) of subject `sub-01`,
+are named:
 ```Text
 sub-01/
     microscopy/
@@ -177,26 +194,18 @@ sub-01/
         sub-01_sample-01_chunk-03_<modality_suffix>.json
         sub-01_sample-01_chunk-04_<modality_suffix>.<ext>
         sub-01_sample-01_chunk-04_<modality_suffix>.json
+        sub-01_sample-01_chunk-05_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-05_<modality_suffix>.json
+        sub-01_sample-01_chunk-06_<modality_suffix>.<ext>
+        sub-01_sample-01_chunk-06_<modality_suffix>.json
 ```
-In this example, JSON metadata is different for each chunk of `sub-01_sample-01`.
-JSON metadata may be defined per sample or per chunk as appropriate, per the
-[inheritance principle](../02-common-principles.md#the-inheritance-principle).
-
-In some cases, the chunks can be "ordered" and correspond to the displacement of the
-microscope stage for example.
-In others cases, the chunks can be different images of the same sample with no explicit
-spatial relation between them.
+The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
+position relative to one another SHOULD be defined by an affine transformation matrix in the JSON
+sidecar file of each chunk, as described in [Chunk Tranformations](10-microscopy.md#chunk-transformations).
 
-Examples of different chunks configurations can be seen in Figure 1.
-![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
-
-Figure 1: Examples of chunks configurations.
-
--   a) ordered 2D chunks without overlap,
--   b) ordered 2D chunks with overlap,
--   c) unordered 2D chunks with and without overlap,
--   d) and e) ordered 2D chunks on different 3D planes,
--   f) ordered 3D chunks.
+In this example, the JSON metadata is different for each chunk of `sub-01_sample-01`.
+JSON metadata may be defined per sample or per chunk as appropriate, as per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
 
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,
@@ -285,7 +294,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                                                                         |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
-#### Chunk transformations
+#### Chunk Transformations
 
 Chunk transformations metadata describes the spatial relation between chunks
 of the same sample in an implicit coordinate system.
@@ -305,10 +314,10 @@ of the same sample in an implicit coordinate system.
 The following table will be generated automatically with macros after community review.
 A "manual" table is provided to facilitate the review process.
 -->
-| **Key name**                  | **Requirement level**                                            | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| ----------------------------- | ---------------------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ChunkTransformationMatrix     | OPTIONAL                                                         | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
-| ChunkTransformationMatrixAxis | OPTIONAL, but REQUIRED if `ChunkTransformationMatrix` is present | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`)                                                                                                                                                                                                                                                                                                                                                             |
+| **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| ----------------------------- | --------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
+| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`)                                                                                                                                                                                                                                                                                                                                                             |
 
 #### Example (`*_<suffix>.json`)
 ```JSON

From cab50db18fa202aba3ab259359d484aaaf352f4f Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 4 Nov 2021 16:53:39 -0400
Subject: [PATCH 034/347] Fix typos

---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index bfe59541c9..4c3ab5218c 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -200,8 +200,8 @@ sub-01/
         sub-01_sample-01_chunk-06_<modality_suffix>.json
 ```
 The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
-position relative to one another SHOULD be defined by an affine transformation matrix in the JSON
-sidecar file of each chunk, as described in [Chunk Tranformations](10-microscopy.md#chunk-transformations).
+positions relative to one another SHOULD be defined by an affine transformation matrix in the JSON
+sidecar file of each chunk, as described in [Chunk Transformations](10-microscopy.md#chunk-transformations).
 
 In this example, the JSON metadata is different for each chunk of `sub-01_sample-01`.
 JSON metadata may be defined per sample or per chunk as appropriate, as per the
@@ -317,7 +317,7 @@ A "manual" table is provided to facilitate the review process.
 | **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ----------------------------- | --------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
-| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `['X', 'Y']` or `['Z', 'Y', 'X']`)                                                                                                                                                                                                                                                                                                                                                             |
+| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                             |
 
 #### Example (`*_<suffix>.json`)
 ```JSON

From a4a5771ee45bc0b9149c7509b2a1e0a4d290cab5 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 9 Nov 2021 09:32:27 -0500
Subject: [PATCH 035/347] Fix wording

---
 src/04-modality-specific-files/10-microscopy.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 4c3ab5218c..6af2ba8c56 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -45,10 +45,10 @@ The OME-TIFF file allows for multi-page TIFF files to store multiple image plane
 multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
 file’s header.
 
-In Microscopy-BIDS, we accept different file formats to accommodate datasets stored in 2D image
-formats and whole-slide imaging formats, to accommodate lossless and lossy compression,
-and to avoid unnecessary conversions of the original data from a non-tiled to a tiled format,
-or vice-versa.
+The BIDS standard accepts microscopy data in different file formats to accommodate datasets
+stored in 2D image formats and whole-slide imaging formats, to accommodate lossless and lossy
+compression, and to avoid unnecessary conversions of the original data from a non-tiled to a
+tiled format, or vice-versa.
 
 For BIDS, Microscopy raw data MUST be stored in one of the following formats:
 
@@ -63,7 +63,7 @@ For BIDS, Microscopy raw data MUST be stored in one of the following formats:
 If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the native format MAY be
 stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
 
-Future versions of Microscopy-BIDS may extend this list of supported file formats.
+Future versions may extend this list of supported file formats.
 For example with the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) format currently
 developed by OME as a successor to OME-TIFF for better remote sharing of large datasets.
 

From c66687f023668d084530afc289371d431ee78b50 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 12 Nov 2021 10:57:15 -0500
Subject: [PATCH 036/347] Fix tif extension in
 src/schema/rules/datatypes/microscopy.yaml

---
 src/schema/rules/datatypes/microscopy.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/datatypes/microscopy.yaml b/src/schema/rules/datatypes/microscopy.yaml
index cb821d68b7..3af2fb86d3 100644
--- a/src/schema/rules/datatypes/microscopy.yaml
+++ b/src/schema/rules/datatypes/microscopy.yaml
@@ -22,7 +22,7 @@
   - .ome.tif
   - .ome.btf
   - .png
-  - .tiff
+  - .tif
   - .json
   entities:
     subject: required

From ed408c122a92bcb8ef42a9634ef8636a5dafab18 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 12 Nov 2021 12:02:19 -0500
Subject: [PATCH 037/347] Remove duplicated text in stain-label description

---
 src/04-modality-specific-files/10-microscopy.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 6af2ba8c56..d63fa81a5f 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -133,8 +133,6 @@ image files from the same sample using different stains or antibodies for contra
 For example:
 One brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three stains
 (`stain-01`, `stain-02`, `stain-03`) in three separate files.
-In this example, the entity stain is used to distinguish images with different
-stains in separate files from the same sample.
 ```Text
 sub-01/
     microscopy/

From b95163aa687f53c81e1f532b4a860d29217fcf8b Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 12 Nov 2021 12:41:34 -0500
Subject: [PATCH 038/347] Correction of the name of "Fluorescence" modality to
 "Fluorescence microscopy"

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index d63fa81a5f..8997298844 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -82,7 +82,7 @@ A "manual" table is provided to facilitate the review process.
 | Dark-field microscopy                         | DF       |
 | Phase-contrast microscopy                     | PC       |
 | Differential interference contrast microscopy | DIC      |
-| Fluorescence                                  | FLUO     |
+| Fluorescence microscopy                       | FLUO     |
 | Confocal microscopy                           | CONF     |
 | Polarized-light microscopy                    | PLI      |
 | Coherent anti-Stokes Raman spectroscopy       | CARS     |

From 6c595caaeb2dda8850fc0fcf98fbad06a9a04dab Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 12 Nov 2021 18:02:14 -0500
Subject: [PATCH 039/347] Add figure and example for chunk transformation

---
 .../10-microscopy.md                          |  38 +++++++++++++++++-
 ...copy_chunks.png => microscopy_chunks1.png} | Bin
 .../images/microscopy_chunks2.png             | Bin 0 -> 6837 bytes
 3 files changed, 36 insertions(+), 2 deletions(-)
 rename src/04-modality-specific-files/images/{microscopy_chunks.png => microscopy_chunks1.png} (100%)
 create mode 100644 src/04-modality-specific-files/images/microscopy_chunks2.png

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 8997298844..e8ee952319 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -167,7 +167,7 @@ In other cases, the chunks can be different images of the same sample with no ex
 spatial relation between them.
 
 Examples of different chunks configurations can be seen in Figure 1.
-![Figure 1](images/microscopy_chunks.png "Examples of Microscopy chunks")
+![Figure 1](images/microscopy_chunks1.png "Examples of Microscopy chunks")
 
 Figure 1: Examples of chunks configurations.
 
@@ -317,7 +317,41 @@ A "manual" table is provided to facilitate the review process.
 | ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
 | ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                             |
 
-#### Example (`*_<suffix>.json`)
+An example of chunk transformations JSON metadata for `chunk-01` and `chunk-05` of Figure 2
+is shown below:
+
+![Figure 2](images/microscopy_chunks2.png "Example figure for chunks transformations")
+
+Figure 2: Example figure for chunks transformations.
+
+In this example, there is no scaling and `chunk-01` is at the origin.
+`chunk-05` is translated of 5 um in `X` and 3 um in `Y`.
+
+**`*_chunk-01_<modality_suffix>.json`**:
+```JSON
+{
+        "PixelSize": [1, 1],
+        "PixelSizeUnits": "um",
+        "ChunkTransformationMatrix": [[1, 0, 0],
+                                      [0, 1, 0],
+                                      [0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y"]
+}
+```
+
+**`*_chunk-05_<modality_suffix>.json`**:
+```JSON
+{
+        "PixelSize": [1, 1],
+        "PixelSizeUnits": "um",
+        "ChunkTransformationMatrix": [[1, 0, 5],
+                                      [0, 1, 3],
+                                      [0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y"]
+}
+```
+
+#### Example of sidecar JSON file (`*_<suffix>.json`)
 ```JSON
 {
         "Manufacturer": "Hamamatsu",
diff --git a/src/04-modality-specific-files/images/microscopy_chunks.png b/src/04-modality-specific-files/images/microscopy_chunks1.png
similarity index 100%
rename from src/04-modality-specific-files/images/microscopy_chunks.png
rename to src/04-modality-specific-files/images/microscopy_chunks1.png
diff --git a/src/04-modality-specific-files/images/microscopy_chunks2.png b/src/04-modality-specific-files/images/microscopy_chunks2.png
new file mode 100644
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literal 0
HcmV?d00001


From f4c16fce9d0a65a0525252baba3754c7d74198f3 Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Sat, 13 Nov 2021 11:56:52 -0500
Subject: [PATCH 040/347] Update
 src/04-modality-specific-files/10-microscopy.md

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>
---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index e8ee952319..594f5da000 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -325,7 +325,7 @@ is shown below:
 Figure 2: Example figure for chunks transformations.
 
 In this example, there is no scaling and `chunk-01` is at the origin.
-`chunk-05` is translated of 5 um in `X` and 3 um in `Y`.
+`chunk-05` is translated by 5 um along `X+` and by 3 um along `Y+`.
 
 **`*_chunk-01_<modality_suffix>.json`**:
 ```JSON

From 545b19571991b0f8f8b2377fe8fd87053e916c20 Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Mon, 15 Nov 2021 17:34:05 -0500
Subject: [PATCH 041/347] Update README.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 69fe0beb5f..3ac31ba5ed 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - behavioral
 - physiological
 - PET
-- Microscopy
+- microscopy
 
 # Formatting your data with BIDS
 

From e0771869fc8ec9f583ade948f9dccb91dfa1f4fd Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 15 Nov 2021 18:00:52 -0500
Subject: [PATCH 042/347] Add full OME-NGFF name

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 594f5da000..d540482f11 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -63,8 +63,8 @@ For BIDS, Microscopy raw data MUST be stored in one of the following formats:
 If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the native format MAY be
 stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
 
-Future versions may extend this list of supported file formats.
-For example with the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) format currently
+Future versions may extend this list of supported file formats, for example with the
+Next-Generation File Formats ([OME-NGFF](https://ngff.openmicroscopy.org/latest/)) currently
 developed by OME as a successor to OME-TIFF for better remote sharing of large datasets.
 
 ### Modality suffixes

From e65b7f46b4f42c05bb2d97447935e286d8aaf8cf Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 15 Nov 2021 18:13:00 -0500
Subject: [PATCH 043/347] Correction

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index d540482f11..46ae4c1289 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -64,8 +64,8 @@ If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the na
 stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
 
 Future versions may extend this list of supported file formats, for example with the
-Next-Generation File Formats ([OME-NGFF](https://ngff.openmicroscopy.org/latest/)) currently
-developed by OME as a successor to OME-TIFF for better remote sharing of large datasets.
+Next-Generation File Formats currently developed by OME ([OME-NGFF](https://ngff.openmicroscopy.org/latest/))
+as a successor to OME-TIFF for better remote sharing of large datasets.
 
 ### Modality suffixes
 Microscopy data currently support the following imaging modalities:

From bfb027bd37fa09b1bcd8d7f294decb83dbab2364 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 15 Nov 2021 18:23:51 -0500
Subject: [PATCH 044/347] Fix formatting

---
 src/04-modality-specific-files/10-microscopy.md | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 46ae4c1289..a919a465b8 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -104,8 +104,7 @@ Microscopy data and is used to distinguish between different samples from the sa
 The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example:
-Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`.
+For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`.
 ```Text
 sub-01/
     microscopy/
@@ -130,9 +129,8 @@ The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity can be used
 image files from the same sample using different stains or antibodies for contrast enhancement.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example:
-One brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three stains
-(`stain-01`, `stain-02`, `stain-03`) in three separate files.
+For example: One brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three
+stains (`stain-01`, `stain-02`, `stain-03`) in three separate files.
 ```Text
 sub-01/
     microscopy/
@@ -178,9 +176,8 @@ Figure 1: Examples of chunks configurations.
 -   f) ordered 3D chunks.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example, as illustrated in Figure 1b:
-Six chunks (`chunk-01` to `chunk-06`) from the same brain sample (`sample-01`) of subject `sub-01`,
-are named:
+For example, as illustrated in Figure 1b: Six chunks (`chunk-01` to `chunk-06`) from the same
+brain sample (`sample-01`) of subject `sub-01`, are named:
 ```Text
 sub-01/
     microscopy/

From 60ecb3d1860648751abfa48eb2b31b72ba0dc645 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 15 Nov 2021 19:15:04 -0500
Subject: [PATCH 045/347] Make BodyPartDetails RECOMMENDED

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a919a465b8..8ca6ec2a3b 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -276,7 +276,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 | --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
-| BodyPartDetails             | OPTIONAL              | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
+| BodyPartDetails             | RECOMMENDED           | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
 | BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`).                                                                                                                                                                                                                                                                                                                                                                 |
 | SampleEnvironment           | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |

From d93aab94c7e5454317efa06e5899a5518fd91c73 Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Mon, 15 Nov 2021 19:31:46 -0500
Subject: [PATCH 046/347] Update
 src/04-modality-specific-files/10-microscopy.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 8ca6ec2a3b..5494bfb4ac 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -159,8 +159,8 @@ The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when
 regions (2D images or 3D volumes files) of the same physical sample are imaged with different
 fields of view, regardless if they overlap or not.
 
-In some cases, the chunks can be "ordered" and correspond to the displacement of the
-microscope stage, for example.
+In some cases, the chunks can be "ordered" and, for example, correspond to the displacement of the
+microscope stage.
 In other cases, the chunks can be different images of the same sample with no explicit
 spatial relation between them.
 

From c3dad748462a8b5d2b11fcbd107432277dfdf0a8 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 09:54:47 -0500
Subject: [PATCH 047/347] Clarify stain-label and SampleStaining text in
 Filename entities section

---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 5494bfb4ac..51b9d06196 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -146,9 +146,9 @@ stains in separate files from the same sample.
 In the case where a single file contains different staining in each channel, the
 `stain-<label>` is omitted.
 
-Stains or antibodies SHOULD be indicated as appropriate in the `"SampleStaining"`,
-`"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` keys in the sidecar JSON file,
-although the label may be different.
+Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
+although the label may be different. Description of antibodies SHOULD also be indicated in
+`"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` as appropriate.
 
 If more than one run of the same sample, acquisition and stain are acquired during the same
 session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:

From dca2763b104e17d6190438e981a67dc01985bc87 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 13:55:33 -0500
Subject: [PATCH 048/347] Update examples with real modality_suffix and file
 extensions

---
 .../10-microscopy.md                          | 67 +++++++++----------
 1 file changed, 33 insertions(+), 34 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 51b9d06196..19b932d6d6 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -104,14 +104,15 @@ Microscopy data and is used to distinguish between different samples from the sa
 The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`.
+For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`,
+imaged by scanning electron microscopy (SEM) in PNG format
 ```Text
 sub-01/
     microscopy/
-        sub-01_sample-01_<modality_suffix>.<ext>
-        sub-01_sample-02_<modality_suffix>.<ext>
-        sub-01_sample-03_<modality_suffix>.<ext>
-        sub-01_<modality_suffix>.json
+        sub-01_sample-01_SEM.png
+        sub-01_sample-02_SEM.png
+        sub-01_sample-03_SEM.png
+        sub-01_SEM.json
 ```
 In this example, the JSON metadata is common for all samples of `sub-01`.
 JSON metadata may be defined per subject or per sample as appropriate, as per the
@@ -119,27 +120,28 @@ JSON metadata may be defined per subject or per sample as appropriate, as per th
 
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
 MAY be used to distinguish a different set of parameters used for acquiring the same modality.
-For example, two images of the same sample acquired with different magnification of 40x and 60x.
-In such case two files could have the following names:
-`sub-01_sample-01_acq-40x_<modality_suffix>.<ext>` and
-`sub-01_sample-01_acq-60x_<modality_suffix>.<ext>`, however the user is free to choose any other
-label as long as they are consistent across subjects and sessions.
+For example, two images of the same sample acquired by bright-field microscopy (BF) in PNG format at
+different magnification of 40x and 60x.
+In such case two files could have the following names: `sub-01_sample-01_acq-40x_BF.png` and
+`sub-01_sample-01_acq-60x_BF.png`, however the user is free to choose any other label as long as
+they are consistent across subjects and sessions.
 
 The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity can be used to distinguish
 image files from the same sample using different stains or antibodies for contrast enhancement.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example: One brain slice (`sample-01`) extracted from subject `sub-01`, imaged with three
-stains (`stain-01`, `stain-02`, `stain-03`) in three separate files.
+For example: One brain slice (`sample-01`) extracted from subject `sub-01` with three
+stains (`stain-01`, `stain-02` and `stain-03`) in three separate files, imaged by selective plane
+illumination microscopy (SPIM) in OME-TIFF format
 ```Text
 sub-01/
     microscopy/
-        sub-01_sample-01_stain-01_<modality_suffix>.<ext>
-        sub-01_sample-01_stain-01_<modality_suffix>.json
-        sub-01_sample-01_stain-02_<modality_suffix>.<ext>
-        sub-01_sample-01_stain-02_<modality_suffix>.json
-        sub-01_sample-01_stain-03_<modality_suffix>.<ext>
-        sub-01_sample-01_stain-03_<modality_suffix>.json
+        sub-01_sample-01_stain-01_SPIM.ome.tif
+        sub-01_sample-01_stain-01_SPIM.json
+        sub-01_sample-01_stain-02_SPIM.ome.tif
+        sub-01_sample-01_stain-02_SPIM.json
+        sub-01_sample-01_stain-03_SPIM.ome.tif
+        sub-01_sample-01_stain-03_SPIM.json
 ```
 In this example, the entity stain is used to distinguish images with different
 stains in separate files from the same sample.
@@ -147,7 +149,8 @@ In the case where a single file contains different staining in each channel, the
 `stain-<label>` is omitted.
 
 Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
-although the label may be different. Description of antibodies SHOULD also be indicated in
+although the label may be different.
+Description of antibodies SHOULD also be indicated in
 `"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` as appropriate.
 
 If more than one run of the same sample, acquisition and stain are acquired during the same
@@ -176,23 +179,19 @@ Figure 1: Examples of chunks configurations.
 -   f) ordered 3D chunks.
 
 <!--- The following example will be generated automatically with macros after community review. -->
-For example, as illustrated in Figure 1b: Six chunks (`chunk-01` to `chunk-06`) from the same
-brain sample (`sample-01`) of subject `sub-01`, are named:
+For example: Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`)
+of subject `sub-01`, imaged by confocal microscopy (CONF) in OME-TIFF format
 ```Text
 sub-01/
     microscopy/
-        sub-01_sample-01_chunk-01_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-01_<modality_suffix>.json
-        sub-01_sample-01_chunk-02_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-02_<modality_suffix>.json
-        sub-01_sample-01_chunk-03_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-03_<modality_suffix>.json
-        sub-01_sample-01_chunk-04_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-04_<modality_suffix>.json
-        sub-01_sample-01_chunk-05_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-05_<modality_suffix>.json
-        sub-01_sample-01_chunk-06_<modality_suffix>.<ext>
-        sub-01_sample-01_chunk-06_<modality_suffix>.json
+        sub-01_sample-01_chunk-01_CONF.ome.tif
+        sub-01_sample-01_chunk-01_CONF.json
+        sub-01_sample-01_chunk-02_CONF.ome.tif
+        sub-01_sample-01_chunk-02_CONF.json
+        sub-01_sample-01_chunk-03_CONF.ome.tif
+        sub-01_sample-01_chunk-03_CONF.json
+        sub-01_sample-01_chunk-04_CONF.ome.tif
+        sub-01_sample-01_chunk-04_CONF.json
 ```
 The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
 positions relative to one another SHOULD be defined by an affine transformation matrix in the JSON
@@ -348,7 +347,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 }
 ```
 
-#### Example of sidecar JSON file (`*_<suffix>.json`)
+#### Example of sidecar JSON file (`*_<modality_suffix>.json`)
 ```JSON
 {
         "Manufacturer": "Hamamatsu",

From ac49f2d417ef31b43b5f5bf2370999fae566ffc5 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 14:04:57 -0500
Subject: [PATCH 049/347] Clarify text of chunk-index and chunk transformation

---
 src/04-modality-specific-files/10-microscopy.md | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 19b932d6d6..497be14173 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -194,8 +194,9 @@ sub-01/
         sub-01_sample-01_chunk-04_CONF.json
 ```
 The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
-positions relative to one another SHOULD be defined by an affine transformation matrix in the JSON
-sidecar file of each chunk, as described in [Chunk Transformations](10-microscopy.md#chunk-transformations).
+relative positions (in terms of scaling and translation) SHOULD be defined by an affine
+transformation matrix in the JSON sidecar file of each chunk, as described in
+[Chunk Transformations](10-microscopy.md#chunk-transformations).
 
 In this example, the JSON metadata is different for each chunk of `sub-01_sample-01`.
 JSON metadata may be defined per sample or per chunk as appropriate, as per the
@@ -299,8 +300,8 @@ of the same sample in an implicit coordinate system.
 
 -   The target frame of reference has the same units as the `PixelSizeUnits` metadata.
 
--   The chunk transform is described by 2 metadata fields: a transformation matrix and a
-    description of the axis of the matrix.
+-   The chunk transformation is described by 2 metadata fields: an affine transformation matrix
+    and a description of the axis of the matrix.
 
 -   Other transformations should be described in derivatives.
 
@@ -310,8 +311,8 @@ A "manual" table is provided to facilitate the review process.
 -->
 | **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ----------------------------- | --------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
-| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                             |
+| ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 affine transformation matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
+| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                                                   |
 
 An example of chunk transformations JSON metadata for `chunk-01` and `chunk-05` of Figure 2
 is shown below:

From ab149a524f6bd965e4f069ec95cee37e6fddfcb3 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 14:22:45 -0500
Subject: [PATCH 050/347] Update BodyPartDetailsOntology as URI

---
 src/04-modality-specific-files/10-microscopy.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 497be14173..eec0b8035a 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -260,7 +260,7 @@ A "manual" table is provided to facilitate the review process.
 | Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
 | NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
 | Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
-| ImageAcquisitionProtocol   | OPTIONAL              | [string][] or [URI][uri] | Description of the image acquisition protocol or URI (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                       |
+| ImageAcquisitionProtocol   | OPTIONAL              | [string][]               | Description of the image acquisition protocol or [URI][uri] (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                |
 | OtherAcquisitionParameters | OPTIONAL              | [string][]               | Description of other relevant image acquisition parameters.                                                                                                                                                                                                                                                                                                                                                                                                              |
 
 #### Sample
@@ -276,8 +276,8 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 | --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
-| BodyPartDetails             | RECOMMENDED           | [string][]                             | If needed, additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
-| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`).                                                                                                                                                                                                                                                                                                                                                                 |
+| BodyPartDetails             | RECOMMENDED           | [string][]                             | Additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
+| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | [URI][uri] of ontology used for BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).                                                                                                                                                                                                                                                                                                                                                                                             |
 | SampleEnvironment           | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 | SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
@@ -286,7 +286,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
 | SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | TissueDeformationScaling    | OPTIONAL              | [number][]                             | Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is `97`; and for an expansion of 100%, the value is `200`).                                                                                                                                                                                                                                                                                                                         |
-| SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                                                                         |
+| SampleExtractionProtocol    | OPTIONAL              | [string][]                             | Description of the sample extraction protocol or [URI][uri] (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                                                                  |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
 #### Chunk Transformations

From fd75df8791fe141dc45d18a9e8673795b0c50297 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 14:40:14 -0500
Subject: [PATCH 051/347] Correction to SampleEnvironment values

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index eec0b8035a..f0a7433aff 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -256,7 +256,7 @@ A "manual" table is provided to facilitate the review process.
 | **Key name**               | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
 | -------------------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | PixelSize                  | REQUIRED              | [array][] of [numbers][] | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
-| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be millimeter (`"mm"`), micrometer (`"um"`) or nanometer (`"nm"`).                                                                                                                                                                                                                                                                                                                                                          |
+| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be one of: `"mm"` (millimeter), `"um"` (micrometer) or `"nm"` (nanometer).                                                                                                                                                                                                                                                                                                                                                  |
 | Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
 | NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
 | Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
@@ -278,7 +278,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
 | BodyPartDetails             | RECOMMENDED           | [string][]                             | Additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
 | BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | [URI][uri] of ontology used for BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).                                                                                                                                                                                                                                                                                                                                                                                             |
-| SampleEnvironment           | RECOMMENDED           | [string][]                             | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| SampleEnvironment           | RECOMMENDED           | [string][]                             | Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"` or `"in vitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 | SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | SampleStaining              | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`).                                                                                                                                                                                                                                                                                                                                  |

From 3d50db2af46fc5d3b6dd521950e787e472252393 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 16 Nov 2021 14:53:21 -0500
Subject: [PATCH 052/347] Fix md formatting

---
 src/04-modality-specific-files/10-microscopy.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index f0a7433aff..b42f9568b6 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -276,8 +276,8 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 | --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
-| BodyPartDetails             | RECOMMENDED           | [string][]                             | Additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                              |
-| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | [URI][uri] of ontology used for BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).                                                                                                                                                                                                                                                                                                                                                                                             |
+| BodyPartDetails             | RECOMMENDED           | [string][]                             | Additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | [URI][uri] of ontology used for BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).                                                                                                                                                                                                                                                                                                                                                                                                            |
 | SampleEnvironment           | RECOMMENDED           | [string][]                             | Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"` or `"in vitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 | SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
@@ -309,8 +309,8 @@ of the same sample in an implicit coordinate system.
 The following table will be generated automatically with macros after community review.
 A "manual" table is provided to facilitate the review process.
 -->
-| **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| ----------------------------- | --------------------------------------------------- | -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+| ----------------------------- | --------------------------------------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 affine transformation matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
 | ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                                                   |
 

From ffa7088e310138d32738a98a285ee26f84eb513b Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 18 Nov 2021 14:26:58 -0500
Subject: [PATCH 053/347] Add mention that "session" is optional

---
 src/04-modality-specific-files/10-microscopy.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index b42f9568b6..02ca82fae1 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -98,6 +98,7 @@ A "manual" table is provided to facilitate the review process.
 In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))
 can refer to all the acquisitions between the start and the end of an imaging experiment
 for ex vivo imaging or a subject lab visit for biopsy procedure and/or in vivo imaging.
+Consistent with other data types in BIDS, the session entity is optional.
 
 The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRED for
 Microscopy data and is used to distinguish between different samples from the same subject.

From c735f313e6a6423a165341308270efe56a8f3197 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 18 Nov 2021 14:38:05 -0500
Subject: [PATCH 054/347] wording: replace some "can" with "MAY" or "MUST"

---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 02ca82fae1..7ef6fcd6da 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -127,7 +127,7 @@ In such case two files could have the following names: `sub-01_sample-01_acq-40x
 `sub-01_sample-01_acq-60x_BF.png`, however the user is free to choose any other label as long as
 they are consistent across subjects and sessions.
 
-The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity can be used to distinguish
+The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity MAY be used to distinguish
 image files from the same sample using different stains or antibodies for contrast enhancement.
 
 <!--- The following example will be generated automatically with macros after community review. -->
@@ -396,9 +396,9 @@ sub-<label>/
         microscopy/
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.<extension>
 ```
-The file `<extension>` for photos can be either `.jpg`, `.png` or `.tif`.
+The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to indicate
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity MAY be used to indicate
 acquisition of different photos of the same sample.
 <!--- The following example will be generated automatically with macros after community review. -->
 For example:

From 9a23a8bbbf36b34b1f056b861d421c496cbc3b4c Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 18 Nov 2021 14:57:58 -0500
Subject: [PATCH 055/347] Clarification on participants.tsv file

---
 src/04-modality-specific-files/10-microscopy.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 7ef6fcd6da..6f2bc7112a 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -375,8 +375,10 @@ Additional optional columns in `samples.tsv` MAY be used to describe other sampl
 
 ## Recommended participant data (`participants.tsv`)
 
-For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and `strain_rrid`
-in the [Participants file](../03-modality-agnostic-files.md#participants-file) when applicable.
+As for other data types in BIDS, the [Participants file](../03-modality-agnostic-files.md#participants-file)
+is RECOMMENDED and MUST contain the column `participant_id`.
+For Microscopy data, we RECOMMEND to also make use of the columns `species`, `strain` and
+`strain_rrid` when applicable.
 
 For example:
 ```Text
@@ -385,6 +387,8 @@ sub-01 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 ```
 
+Additional optional columns in `participants.tsv` MAY be used to describe other subjects' attributes.
+
 ## Photos of the samples (`*_photo.<extension>`)
 Photos of the tissue sample, overview microscopy scans or blockface images from cutting
 MAY be included for visualization of large samples or to indicate the location of chunks

From 0055ad6a3656ecbbcc7e29e61b39a755e68cf32b Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 19 Nov 2021 12:11:32 -0500
Subject: [PATCH 056/347] Correction to stain description in entities.yml

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 src/schema/objects/entities.yaml                | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 6f2bc7112a..6769d71c18 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -151,8 +151,8 @@ In the case where a single file contains different staining in each channel, the
 
 Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
 although the label may be different.
-Description of antibodies SHOULD also be indicated in
-`"SamplePrimaryAntibodies"` and/or `"SampleSecondaryAntobodies"` as appropriate.
+Description of antibodies SHOULD also be indicated in `"SamplePrimaryAntibodies"`
+and/or `"SampleSecondaryAntobodies"` as appropriate.
 
 If more than one run of the same sample, acquisition and stain are acquired during the same
 session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 6781e9d16f..9c5d5b1ffb 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -309,9 +309,10 @@ stain:
   description: |
     The `stain-<label>` key/pair values can be used to distinguish image files
     from the same sample using different stains or antibodies for contrast enhancement.
-    Stains or antibodies SHOULD be indicated as appropriate in the `SampleStaining`,
-    `SamplePrimaryAntibodies` and/or `SampleSecondaryAntobodies` keys in the JSON file,
+    Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
     although the label may be different.
+    Description of antibodies SHOULD also be indicated in `"SamplePrimaryAntibodies"`
+    and/or `"SampleSecondaryAntobodies"` as appropriate.
   type: string
   format: label
 subject:

From f067bc492932f702fbde8c463b294085fa2526ad Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Tue, 23 Nov 2021 09:06:05 -0500
Subject: [PATCH 057/347] Update src/02-common-principles.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 5ec5b9594b..da89aab67c 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -56,7 +56,7 @@ misunderstanding we clarify them here.
     1.  `ieeg` (intracranial electroencephalography)
     1.  `beh` (behavioral)
     1.  `pet` (positron emission tomography)
-    1.  `microscopy`
+    1.  `micr` (microscopy)
 
     Data files are contained in a directory named for the data type.
     In raw datasets, the data type directory is nested inside subject and

From 7edf319cc9637cfe5a1704d8c8fbd2290a8830d2 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 23 Nov 2021 09:14:25 -0500
Subject: [PATCH 058/347] 10-microscpy.md: Change "microscopy" data type for
 "micr"

---
 .../10-microscopy.md                           | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 6769d71c18..0b8b8528db 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -30,11 +30,11 @@ Template:
 ```Text
 sub-<label>/
     [ses-<label>/]
-        microscopy/
+        micr/
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.<extension>
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.json
 ```
-Microscopy data MUST be stored in the `microscopy` directory.
+Microscopy data MUST be stored in the `micr` directory.
 
 ### File formats
 The Microscopy community uses a variety of formats for storing raw data, and there is no single
@@ -109,7 +109,7 @@ For example: Three brain slices (`sample-01` to `sample-03`) extracted from subj
 imaged by scanning electron microscopy (SEM) in PNG format
 ```Text
 sub-01/
-    microscopy/
+    micr/
         sub-01_sample-01_SEM.png
         sub-01_sample-02_SEM.png
         sub-01_sample-03_SEM.png
@@ -136,7 +136,7 @@ stains (`stain-01`, `stain-02` and `stain-03`) in three separate files, imaged b
 illumination microscopy (SPIM) in OME-TIFF format
 ```Text
 sub-01/
-    microscopy/
+    micr/
         sub-01_sample-01_stain-01_SPIM.ome.tif
         sub-01_sample-01_stain-01_SPIM.json
         sub-01_sample-01_stain-02_SPIM.ome.tif
@@ -184,7 +184,7 @@ For example: Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (
 of subject `sub-01`, imaged by confocal microscopy (CONF) in OME-TIFF format
 ```Text
 sub-01/
-    microscopy/
+    micr/
         sub-01_sample-01_chunk-01_CONF.ome.tif
         sub-01_sample-01_chunk-01_CONF.json
         sub-01_sample-01_chunk-02_CONF.ome.tif
@@ -216,11 +216,11 @@ my_dataset/
     derivatives/
         downsampled/
             sub-01/
-                microscopy/
+                micr/
                     sub-01_sample-01_res-4x_TEM.png
                     sub-01_sample-01_res-4x_TEM.json
     sub-01/
-        microscopy/
+        micr/
             sub-01_sample-01_TEM.png
 ```
 See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes)
@@ -397,7 +397,7 @@ in a sample.
 ```Text
 sub-<label>/
     [ses-<label>/]
-        microscopy/
+        micr/
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.<extension>
 ```
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
@@ -408,7 +408,7 @@ acquisition of different photos of the same sample.
 For example:
 ```Text
 sub-01/
-    microscopy/
+    micr/
         sub-01_sample-01_acq-1_photo.jpg
         sub-01_sample-01_acq-2_photo.jpg
 ```

From 8414e89a64cc0ed313a0f9b50a9b2b6120fd99d5 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 23 Nov 2021 09:21:05 -0500
Subject: [PATCH 059/347] Update datatype micr.yaml in schema and fix macro in
 entity table

---
 src/99-appendices/04-entity-table.md                      | 2 +-
 src/schema/rules/datatypes/{microscopy.yaml => micr.yaml} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename src/schema/rules/datatypes/{microscopy.yaml => micr.yaml} (100%)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 92ae16c1e0..a85776f5a2 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -39,4 +39,4 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Microscopy
 
-{{ MACROS___make_entity_table(datatypes=["microscopy"], auxdatatypes=[]) }}
+{{ MACROS___make_entity_table(datatypes=["micr"], auxdatatypes=[]) }}
diff --git a/src/schema/rules/datatypes/microscopy.yaml b/src/schema/rules/datatypes/micr.yaml
similarity index 100%
rename from src/schema/rules/datatypes/microscopy.yaml
rename to src/schema/rules/datatypes/micr.yaml

From f280aba0225ad9ad1db09b94dc89bc0e9dfaa7f2 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 23 Nov 2021 11:34:40 -0500
Subject: [PATCH 060/347] Clarify usage of samples/participants tsv/json files

---
 .../10-microscopy.md                          | 30 +++++++++++++++----
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 0b8b8528db..9c5df885eb 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -369,25 +369,43 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 
 ## Required Samples file (`samples.tsv`)
 
-For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file) is REQUIRED.
+For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file) `samples.tsv`
+is REQUIRED and its associated metadata `samples.json` file is RECOMMENDED.
 
-Additional optional columns in `samples.tsv` MAY be used to describe other samples' attributes.
+Additional optional columns MAY be used to describe other samples' attributes.
 
-## Recommended participant data (`participants.tsv`)
+## Recommended Participants file (`participants.tsv`)
 
 As for other data types in BIDS, the [Participants file](../03-modality-agnostic-files.md#participants-file)
-is RECOMMENDED and MUST contain the column `participant_id`.
+`participants.tsv` is RECOMMENDED and MUST contain the column `participant_id`, and its associated
+`participants.json` file is RECOMMENDED as well.
+
 For Microscopy data, we RECOMMEND to also make use of the columns `species`, `strain` and
 `strain_rrid` when applicable.
 
-For example:
+Additional optional columns MAY be used to describe other subjects' attributes.
+
+`participants.tsv` example:
 ```Text
 participant_id species strain strain_rrid
 sub-01 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 ```
 
-Additional optional columns in `participants.tsv` MAY be used to describe other subjects' attributes.
+`participants.json` example:
+```JSON
+{
+    "species": {
+        "Description": "binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+    },
+    "strain": {
+        "Description": "name of the strain of the species"
+    },
+    "strain_rrid": {
+        "Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/Organisms/search)"
+    }
+}
+```
 
 ## Photos of the samples (`*_photo.<extension>`)
 Photos of the tissue sample, overview microscopy scans or blockface images from cutting

From 1ec7905f87ba58ce29089cd045077da92fd17df7 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 23 Nov 2021 11:35:26 -0500
Subject: [PATCH 061/347] Correction to "ex vivo" in JSON example

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 9c5df885eb..18a8653e67 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -359,7 +359,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
         "Magnification": 40,
         "BodyPart": "BRAIN",
         "BodyPartDetails": "corpus callosum",
-        "SampleEnvironment": "exvivo",
+        "SampleEnvironment": "ex vivo",
         "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
         "SampleStaining": "LFB",
         "SliceThickness": 5,

From 00abe1deeafd2c355b86b9abdd1e3e967734fa7e Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 23 Nov 2021 15:07:17 -0500
Subject: [PATCH 062/347] Correction samples/participants tsv/json file
 sections

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 18a8653e67..a2f367d03c 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -370,7 +370,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 ## Required Samples file (`samples.tsv`)
 
 For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file) `samples.tsv`
-is REQUIRED and its associated metadata `samples.json` file is RECOMMENDED.
+is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
 
 Additional optional columns MAY be used to describe other samples' attributes.
 
@@ -378,7 +378,7 @@ Additional optional columns MAY be used to describe other samples' attributes.
 
 As for other data types in BIDS, the [Participants file](../03-modality-agnostic-files.md#participants-file)
 `participants.tsv` is RECOMMENDED and MUST contain the column `participant_id`, and its associated
-`participants.json` file is RECOMMENDED as well.
+sidecar `participants.json` file is RECOMMENDED as well.
 
 For Microscopy data, we RECOMMEND to also make use of the columns `species`, `strain` and
 `strain_rrid` when applicable.

From 6dcc60f9124e7c5d66fbe1cfc316ea2625c8ccd4 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 29 Nov 2021 11:09:45 +0100
Subject: [PATCH 063/347] [FIX] issue with ieeg channels.tsv 'name' column

---
 .../04-intracranial-electroencephalography.md                | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index ef3f88172d..e130cea04e 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -224,8 +224,9 @@ MUST be present **in this specific order**:
 
 {{ MACROS___make_columns_table(
    {
-      "name__channels": ("REQUIRED", "The label must correspond to `_electrodes.tsv` name "
-                         "and all ieeg type channels are required to have a position."),
+      "name__channels": ("REQUIRED", "When a corresponding electrode is specified in `_electrodes.tsv`, "
+                         "the name of that electrode MAY be specified here and the reference electrode "
+                         "name MAY be provided in the `reference` column of the `_electrodes.tsv` file."),
       "type__channels": "REQUIRED",
       "units": "REQUIRED",
       "low_cutoff": "REQUIRED",

From b3d83655dfeac2f9070e10475016787d2a4ea8c8 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 29 Nov 2021 12:11:37 +0100
Subject: [PATCH 064/347] [FIX] dwi is specialized T2 weighting, not T2*

---
 src/schema/objects/suffixes.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 7449da2470..38911367ec 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -426,7 +426,7 @@ defacemask:
 dwi:
   name: Diffusion-weighted image
   description: |
-    Diffusion-weighted imaging contrast (specialized T2\* weighting).
+    Diffusion-weighted imaging contrast (specialized T2 weighting).
 eeg:
   name: Electroencephalography
   description: |

From 886fd149e837cf7df61de6ef2904e36dafdfa281 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 29 Nov 2021 17:43:50 -0500
Subject: [PATCH 065/347] Implement macros for examples

---
 .../10-microscopy.md                          | 138 +++++++++++-------
 1 file changed, 85 insertions(+), 53 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a2f367d03c..92a6334ec5 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -104,17 +104,22 @@ The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRE
 Microscopy data and is used to distinguish between different samples from the same subject.
 The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
 
-<!--- The following example will be generated automatically with macros after community review. -->
 For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`,
 imaged by scanning electron microscopy (SEM) in PNG format
-```Text
-sub-01/
-    micr/
-        sub-01_sample-01_SEM.png
-        sub-01_sample-02_SEM.png
-        sub-01_sample-03_SEM.png
-        sub-01_SEM.json
-```
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_SEM.png": "",
+         "sub-01_sample-02_SEM.png": "",
+         "sub-01_sample-03_SEM.png": "",
+         "sub-01_SEM.json": "",
+         },
+      }
+   }
+) }}
+
 In this example, the JSON metadata is common for all samples of `sub-01`.
 JSON metadata may be defined per subject or per sample as appropriate, as per the
 [inheritance principle](../02-common-principles.md#the-inheritance-principle).
@@ -130,20 +135,25 @@ they are consistent across subjects and sessions.
 The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity MAY be used to distinguish
 image files from the same sample using different stains or antibodies for contrast enhancement.
 
-<!--- The following example will be generated automatically with macros after community review. -->
 For example: One brain slice (`sample-01`) extracted from subject `sub-01` with three
 stains (`stain-01`, `stain-02` and `stain-03`) in three separate files, imaged by selective plane
 illumination microscopy (SPIM) in OME-TIFF format
-```Text
-sub-01/
-    micr/
-        sub-01_sample-01_stain-01_SPIM.ome.tif
-        sub-01_sample-01_stain-01_SPIM.json
-        sub-01_sample-01_stain-02_SPIM.ome.tif
-        sub-01_sample-01_stain-02_SPIM.json
-        sub-01_sample-01_stain-03_SPIM.ome.tif
-        sub-01_sample-01_stain-03_SPIM.json
-```
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_stain-01_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-01_SPIM.json": "",
+         "sub-01_sample-01_stain-02_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-02_SPIM.json": "",
+         "sub-01_sample-01_stain-03_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-03_SPIM.json": "",
+         },
+      }
+   }
+) }}
+
 In this example, the entity stain is used to distinguish images with different
 stains in separate files from the same sample.
 In the case where a single file contains different staining in each channel, the
@@ -179,21 +189,26 @@ Figure 1: Examples of chunks configurations.
 -   d) and e) ordered 2D chunks on different 3D planes,
 -   f) ordered 3D chunks.
 
-<!--- The following example will be generated automatically with macros after community review. -->
 For example: Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`)
 of subject `sub-01`, imaged by confocal microscopy (CONF) in OME-TIFF format
-```Text
-sub-01/
-    micr/
-        sub-01_sample-01_chunk-01_CONF.ome.tif
-        sub-01_sample-01_chunk-01_CONF.json
-        sub-01_sample-01_chunk-02_CONF.ome.tif
-        sub-01_sample-01_chunk-02_CONF.json
-        sub-01_sample-01_chunk-03_CONF.ome.tif
-        sub-01_sample-01_chunk-03_CONF.json
-        sub-01_sample-01_chunk-04_CONF.ome.tif
-        sub-01_sample-01_chunk-04_CONF.json
-```
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_chunk-01_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-01_CONF.json": "",
+         "sub-01_sample-01_chunk-02_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-02_CONF.json": "",
+         "sub-01_sample-01_chunk-03_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-03_CONF.json": "",
+         "sub-01_sample-01_chunk-04_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-04_CONF.json": "",
+         },
+      }
+   }
+) }}
+
 The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
 relative positions (in terms of scaling and translation) SHOULD be defined by an affine
 transformation matrix in the JSON sidecar file of each chunk, as described in
@@ -209,20 +224,31 @@ only the higher resolution file is present in the raw data.
 Lower resolutions files MUST be placed under the `derivatives` folder and use the
 [`res-<label>`](../99-appendices/09-entities.md#res) entity.
 
-<!--- The following example will be generated automatically with macros after community review. -->
 For example:
-```Text
-my_dataset/
-    derivatives/
-        downsampled/
-            sub-01/
-                micr/
-                    sub-01_sample-01_res-4x_TEM.png
-                    sub-01_sample-01_res-4x_TEM.json
-    sub-01/
-        micr/
-            sub-01_sample-01_TEM.png
-```
+
+{{ MACROS___make_filetree_example(
+   {
+   "my_dataset": {
+      "derivatives": {
+         "downsampled": {
+            "sub-01": {
+               "micr": {
+                  "sub-01_sample-01_res-4x_TEM.png": "",
+                  "sub-01_sample-01_res-4x_TEM.json": "",
+                  },
+               }
+            }
+         },
+      "sub-01": {
+         "micr": {
+            "sub-01_sample-01_TEM.png": "",
+            "sub-01_sample-01_TEM.json": "",
+            },
+         }
+      }
+   }
+) }}
+
 See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes)
 for details.
 
@@ -422,14 +448,20 @@ The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity MAY be used to indicate
 acquisition of different photos of the same sample.
-<!--- The following example will be generated automatically with macros after community review. -->
+
 For example:
-```Text
-sub-01/
-    micr/
-        sub-01_sample-01_acq-1_photo.jpg
-        sub-01_sample-01_acq-2_photo.jpg
-```
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_acq-1_photo.jpg": "",
+         "sub-01_sample-01_acq-2_photo.jpg": "",
+         },
+      }
+   }
+) }}
+
 Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2018.
 [doi:10.1038/s41598-018-22181-4](https://doi.org/10.1038/s41598-018-22181-4).
 ```Text

From 44e6992261021bf5f4e99d668a3706f34054197e Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 29 Nov 2021 17:47:49 -0500
Subject: [PATCH 066/347] Correction: replace <modality_suffix> by <suffix>

---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 92a6334ec5..a6d32d1587 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -351,7 +351,7 @@ Figure 2: Example figure for chunks transformations.
 In this example, there is no scaling and `chunk-01` is at the origin.
 `chunk-05` is translated by 5 um along `X+` and by 3 um along `Y+`.
 
-**`*_chunk-01_<modality_suffix>.json`**:
+**`*_chunk-01_<suffix>.json`**:
 ```JSON
 {
         "PixelSize": [1, 1],
@@ -363,7 +363,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 }
 ```
 
-**`*_chunk-05_<modality_suffix>.json`**:
+**`*_chunk-05_<suffix>.json`**:
 ```JSON
 {
         "PixelSize": [1, 1],
@@ -375,7 +375,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 }
 ```
 
-#### Example of sidecar JSON file (`*_<modality_suffix>.json`)
+#### Example of sidecar JSON file (`*_<suffix>.json`)
 ```JSON
 {
         "Manufacturer": "Hamamatsu",

From a7e34a37e78dda6937ed91266dc79a55cd2a1f25 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 30 Nov 2021 17:35:52 -0500
Subject: [PATCH 067/347] Add microscopy to schema/objects/datatypes.yaml

---
 src/schema/objects/datatypes.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml
index f17e8feb9f..58c40e39af 100644
--- a/src/schema/objects/datatypes.yaml
+++ b/src/schema/objects/datatypes.yaml
@@ -31,6 +31,9 @@ ieeg:
 meg:
   name: Magnetoencephalography
   description: Magnetoencephalography
+micr:
+  name: Microscopy
+  description: Microscopy
 perf:
   name: Perfusion imaging
   description: |

From c778029e9a2225358bd55fa3221581e39b0eb79d Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 30 Nov 2021 17:38:41 -0500
Subject: [PATCH 068/347] Add microscopy suffixes to
 schema/objects/suffixes.yaml

---
 src/schema/objects/suffixes.yaml | 71 +++++++++++++++++++++++++++++++-
 1 file changed, 69 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 7449da2470..1552d357d3 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -1,6 +1,14 @@
 ---
 # This file defines valid BIDS file suffixes.
 # For rules regarding how suffixes relate to datatypes, see files in `rules/datatypes/`.
+2PE:
+  name: 2-photon excitation microscopy
+  description: |
+    2-photon excitation microscopy imaging data
+BF:
+  name: Bright-field microscopy
+  description: |
+    Bright-field microscopy imaging data
 Chimap:
   name: Quantitative susceptibility map (QSM)
   description: |
@@ -11,6 +19,22 @@ Chimap:
     Chi maps are REQUIRED to use this suffix regardless of the method used to
     generate them.
   unit: ppm
+CARS:
+  name: Coherent anti-Stokes Raman spectroscopy
+  description: |
+    Coherent anti-Stokes Raman spectroscopy imaging data
+CONF:
+  name: Confocal microscopy
+  description: |
+    Confocal microscopy imaging data
+DIC:
+  name: Differential interference contrast microscopy
+  description: |
+    Differential interference contrast microscopy imaging data
+DF:
+  name: Dark-field microscopy
+  description: |
+    Dark-field microscopy imaging data
 FLAIR:
   name: Fluid attenuated inversion recovery image
   description: |
@@ -31,6 +55,10 @@ FLASH:
     When used in a file collection, it may result in conflicts across filenames of
     different applications.
     **Change:** Removed from suffixes.
+FLUO:
+  name: Fluorescence microscopy
+  description: |
+    Fluorescence microscopy imaging data
 IRT1:
   name: Inversion recovery T1 mapping
   description: |
@@ -66,6 +94,10 @@ MP2RAGE:
     different flip angles and inversion times to create a parametric T1map by
     combining the magnitude and phase images
     ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).
+MPE:
+  name: Multi-photon excitation microscopy
+  description: |
+    Multi-photon excitation microscopy imaging data
 MPM:
   name: Multi-parametric Mapping
   description: |
@@ -125,6 +157,18 @@ MWFmap:
   unit: arbitrary
   minValue: 0
   maxValue: 100
+NLO:
+  name: Nonlinear optical microscopy
+  description: |
+    Nonlinear optical microscopy imaging data
+OCT:
+  name: Optical coherence tomography
+  description: |
+    Optical coherence tomography imaging data
+PC:
+  name: Phase-contrast microscopy
+  description: |
+    Phase-contrast microscopy imaging data
 PD:
   name: Proton density image
   description: |
@@ -164,6 +208,10 @@ PDw:
     In a gradient-echo acquisition, PD weighting dominates the contrast at long
     repetition and short echo times, and at small flip angles.
   unit: arbitrary
+PLI:
+  name: Polarized-light microscopy
+  description: |
+    Polarized-light microscopy imaging data
 R1map:
   name: Longitudinal relaxation rate image
   description: |
@@ -213,6 +261,18 @@ S0map:
     [the tedana documentation](https://tedana.readthedocs.io/en/latest/\
     approach.html#monoexponential-decay-model-fit).
     S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset.
+SEM:
+  name: Scanning electron microscopy
+  description: |
+    Scanning electron microscopy imaging data
+SPIM:
+  name: Selective plane illumination microscopy
+  description: |
+    Selective plane illumination microscopy imaging data
+SR:
+  name: Super-resolution microscopy
+  description: |
+    Super-resolution microscopy imaging data
 T1map:
   name: Longitudinal relaxation time image
   description: |
@@ -347,6 +407,10 @@ TB1map:
     multiplicative factors such that FlipAngle<sub>effective</sub> =
     B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .
   unit: arbitrary
+TEM:
+  name: Transmission electron microscopy
+  description: |
+    Transmission electron microscopy imaging data
 UNIT1:
   name: Homogeneous (flat) T1-weighted MP2RAGE image
   description: |
@@ -544,8 +608,7 @@ phasediff:
 photo:
   name: Photo File
   description: |
-    Photos of the anatomical landmarks and/or head localization coils
-    (`*_photo.jpg`).
+    Photos of the anatomical landmarks, head localization coils or tissue sample.
 physio:
   name: Physiological recording
   description: |
@@ -558,3 +621,7 @@ stim:
   name: Continuous recording
   description: |
     Continuous measures, such as parameters of a film or audio stimulus.
+uCT:
+  name: Micro-CT
+  description: |
+    Micro-CT imaging data

From 5978a95a129e669007851990a5ae23bb6a6dca11 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 30 Nov 2021 17:40:31 -0500
Subject: [PATCH 069/347] Add microscopy to schema/rules/modalities.yaml

---
 src/schema/rules/modalities.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/rules/modalities.yaml b/src/schema/rules/modalities.yaml
index 9127db93e7..04b24489d7 100644
--- a/src/schema/rules/modalities.yaml
+++ b/src/schema/rules/modalities.yaml
@@ -22,3 +22,6 @@ beh:
 pet:
   datatypes:
   - pet
+micr:
+  datatypes:
+  - micr

From a6d6ece4ec386108badcda88529f4fa2975cb0d7 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 30 Nov 2021 18:03:29 -0500
Subject: [PATCH 070/347] Add make_filename_template MACROs

---
 .../10-microscopy.md                           | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a6d32d1587..0f9d1b2ac0 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -23,10 +23,7 @@ Further Microscopy datasets are available:
 
 ## Microscopy recording data
 <!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
--->
-Template:
+Intended template:
 ```Text
 sub-<label>/
     [ses-<label>/]
@@ -34,6 +31,12 @@ sub-<label>/
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.<extension>
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.json
 ```
+The current MACRO list ".ome.btf", ".png" and ".tif[.ome]", is it possible to have "<extension>" instead?
+If not, ".tif" and ".ome.tif" should be 2 separate lines but are concatenated as ".tif[.ome]"
+-->
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"]) }}
+
 Microscopy data MUST be stored in the `micr` directory.
 
 ### File formats
@@ -437,13 +440,18 @@ sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 Photos of the tissue sample, overview microscopy scans or blockface images from cutting
 MAY be included for visualization of large samples or to indicate the location of chunks
 in a sample.
-<!--- The following example will be generated automatically with macros after community review. -->
+<!---
+Intended template:
 ```Text
 sub-<label>/
     [ses-<label>/]
         micr/
             sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.<extension>
 ```
+The current MACRO list ".jpg", ".png" and ".tif", is it possible to have one line with "<extension>" instead?
+-->
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"]) }}
+
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity MAY be used to indicate

From de73132fa2345406d2e539d4927f73b2e9968990 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 30 Nov 2021 18:16:19 -0500
Subject: [PATCH 071/347] Add make_suffix_table MACRO

---
 .../10-microscopy.md                          | 30 +++++++++++++++++--
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 0f9d1b2ac0..3313a02116 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -73,9 +73,8 @@ as a successor to OME-TIFF for better remote sharing of large datasets.
 ### Modality suffixes
 Microscopy data currently support the following imaging modalities:
 <!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
--->
+Intended table:
+
 | **Name**                                      | `suffix` |
 | --------------------------------------------- | -------- |
 | Transmission electron microscopy              | TEM      |
@@ -96,6 +95,31 @@ A "manual" table is provided to facilitate the review process.
 | Optical coherence tomography                  | OCT      |
 | Selective plane illumination microscopy       | SPIM     |
 
+Can we remove the "Description" column of the table in the MACRO?
+-->
+{{ MACROS___make_suffix_table(
+      [
+         "TEM",
+         "SEM",
+         "uCT",
+         "BF",
+         "DF",
+         "PC",
+         "DIC",
+         "FLUO",
+         "CONF",
+         "PLI",
+         "CARS",
+         "2PE",
+         "MPE",
+         "SR",
+         "NLO",
+         "OCT",
+         "SPIM",
+      ]
+   )
+}}
+
 ### Filename entities
 
 In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))

From 68b91286d0daf6f932c20290c92196b5131c1137 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 15:31:54 -0500
Subject: [PATCH 072/347] Add microscopy json metadata to
 schema/objects/metadata.yaml

---
 src/schema/objects/metadata.yaml | 185 ++++++++++++++++++++++++++++++-
 1 file changed, 183 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 873f69a357..2f9e1fb43f 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -250,8 +250,19 @@ BodyPart:
   name: BodyPart
   description: |
     Body part of the organ / body region scanned.
-    Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
   type: string
+BodyPartDetails:
+  name: BodyPartDetails
+  description: |
+    Additional details about body part or location (for example: `"corpus callosum"`).
+  type: string
+BodyPartDetailsOntology:
+  name: BodyPartDetailsOntology
+  description: |
+    [URI](/02-common-principles.html#uniform-resource-indicator) of ontology used for
+    BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).
+  type: string
+  format: uri
 BolusCutOffDelayTime:
   name: BolusCutOffDelayTime
   description: |
@@ -323,6 +334,33 @@ CellType:
     Values SHOULD come from the
     [cell ontology](http://obofoundry.org/ontology/cl.html).
   type: string
+ChunkTransformationMatrix:
+  name: ChunkTransformationMatrix
+  description: |
+    3x3 or 4x4 affine transformation matrix describing spatial chunk transformation,
+    for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]`
+    in 2D for 2x and 3x scaling along the first and second axis respectively; or
+    `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x
+    scaling along the second and third axis respectively).
+    Note that non-spatial dimensions like time and channel are not included in the
+    transformation matrix.
+  type: array
+  minItems: 3
+  maxItems: 4
+  items:
+    type: array
+    minItems: 3
+    maxItems: 4
+    items:
+      type: number
+ChunkTransformationMatrixAxis:
+  name: ChunkTransformationMatrixAxis
+  description: |
+    Describe the axis of the ChunkTransformationMatrix
+    (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`).
+  type: array
+  items:
+    type: string
 Code:
   name: Code
   description: |
@@ -1081,6 +1119,13 @@ HowToAcknowledge:
     This field can also be used to define a publication that should be cited in
     publications that use the dataset.
   type: string
+ImageAcquisitionProtocol:
+  name: ImageAcquisitionProtocol
+  description: |
+    Description of the image acquisition protocol or
+    [URI](/02-common-principles.html#uniform-resource-indicator)
+    (for example from [protocols.io](https://www.protocols.io/)).
+  type: string
 ImageDecayCorrected:
   name: ImageDecayCorrected
   description: |
@@ -1093,6 +1138,12 @@ ImageDecayCorrectionTime:
     TimeZero in the default unit seconds.
   type: number
   unit: s
+Immersion:
+  name: Immersion
+  description: |
+    Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent
+    with the `Immersion` OME metadata field.
+  type: string
 InfusionRadioactivity:
   name: InfusionRadioactivity
   description: |
@@ -1524,6 +1575,12 @@ MagneticFieldStrength:
     Nominal field strength of MR magnet in Tesla.
     Corresponds to DICOM Tag 0018, 0087 `Magnetic Field Strength`.
   type: number
+Magnification:
+  name: Magnification
+  description: |
+    Lens magnification (for example: `40`). If the file format is OME-TIFF,
+    the value MUST be consistent with the `NominalMagnification` OME metadata field.
+  type: number
 Manual:
   name: Manual
   description: |
@@ -1708,12 +1765,23 @@ NumberShots:
   - type: array
     items:
       type: number
+NumericalAperture:
+  name: NumericalAperture
+  description: |
+    Lens numerical aperture (for example: `1.4`). If the file format is OME-TIFF,
+    the value MUST be consistent with the `LensNA` OME metadata field.
+  type: number
 OperatingSystem:
   name: OperatingSystem
   description: |
     Operating system used to run the stimuli presentation software
     (for formatting recommendations, see examples below this table).
   type: string
+OtherAcquisitionParameters:
+  name: OtherAcquisitionParameters
+  description: |
+    Description of other relevant image acquisition parameters.
+  type: string
 PASLType:
   name: PASLType
   description: |
@@ -1821,6 +1889,31 @@ PhaseEncodingDirection:
   - i-
   - j-
   - k-
+PixelSize:
+  name: PixelSize
+  description: |
+    A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]`
+    or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the
+    depth.
+    If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`,
+    `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in
+    `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and
+    `PhysicalSizeZunit` OME fields.
+  type: array
+  minItems: 2
+  maxItems: 3
+  items:
+    type: number
+PixelSizeUnits:
+  name: PixelSizeUnits
+  description: |
+    Unit format of the specified `PixelSize`. MUST be one of: `"mm"` (millimeter), `"um"`
+    (micrometer) or `"nm"` (nanometer).
+  type: string
+  enum:
+  - mm
+  - um
+  - nm
 PlasmaAvail:
   name: PlasmaAvail
   description: |
@@ -2096,6 +2189,40 @@ SEEGChannelCount:
     Number of SEEG channels.
   type: integer
   minimum: 0
+SampleEmbedding:
+  name: SampleEmbedding
+  description: |
+    Description of the tissue sample embedding (for example: `"Epoxy resin"`).
+  type: string
+SampleEnvironment:
+  name: SampleEnvironment
+  description: |
+    Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"`
+    or `"in vitro"`.
+  type: string
+  enum:
+  - in vivo
+  - ex vivo
+  - in vitro
+SampleExtractionInstitution:
+  name: SampleExtractionInstitution
+  description: |
+    The name of the institution in charge of the extraction of the sample,
+    if different from the institution in charge of the equipment that produced the image.
+  type: string
+SampleExtractionProtocol:
+  name: SampleExtractionProtocol
+  description: |
+    Description of the sample extraction protocol or
+    [URI](/02-common-principles.html#uniform-resource-indicator)
+    (for example from [protocols.io](https://www.protocols.io/)).
+  type: string
+SampleFixation:
+  name: SampleFixation
+  description: |
+    Description of the tissue sample fixation
+    (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).
+  type: string
 SampleOrigin:
   name: SampleOrigin
   description: |
@@ -2112,6 +2239,47 @@ SampleOrigin:
   - bile
   - amniotic fluid
   - other biospecimen
+SamplePrimaryAntibody:
+  name: SamplePrimaryAntibody
+  description: |
+    Description(s) of the primary antibody used for immunostaining.
+    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue
+    number of a commercial antibody.
+    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or
+    `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`).
+    MAY be an array of strings if different antibodies are used in each channel of the file.
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
+SampleSecondaryAntibody:
+  name: SampleSecondaryAntibody
+  description: |
+    Description(s) of the secondary antibody used for immunostaining.
+    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue
+    number of a commercial antibody.
+    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    host-animal and immunogen used (for examples: `"RRID:AB_228322"` or
+    `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`).
+    MAY be an array of strings if different antibodies are used in each channel of the file.
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
+SampleStaining:
+  name: SampleStaining
+  description: |
+    Description(s) of the tissue sample staining (for example: `"Osmium"`).
+    MAY be an array of strings if different stains are used in each channel of the file
+    (for example: `["LFB", "PLP"]`).
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
 SamplingFrequency:
   name: SamplingFrequency
   description: |
@@ -2220,6 +2388,12 @@ SliceEncodingDirection:
   - i-
   - j-
   - k-
+SliceThickness:
+  name: SliceThickness
+  description: |
+    Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).
+  type: number
+  unit: um
 SliceTiming:
   name: SliceTiming
   description: |
@@ -2423,7 +2597,6 @@ StationName:
   name: StationName
   description: |
     Institution defined name of the machine that produced the measurements.
-    Corresponds to DICOM Tag 0008, 1010 `Station Name`.
   type: string
 StimulusPresentation:
   name: StimulusPresentation
@@ -2482,6 +2655,14 @@ TimeZero:
     This should be equal to `InjectionStart` or `ScanStart`.
   type: string
   pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+TissueDeformationScaling:
+  name: TissueDeformationScaling
+  description: |
+    Estimated deformation of the tissue, given as a percentage of the original
+    tissue size (for examples: for a shrinkage of 3%, the value is `97`;
+    and for an expansion of 100%, the value is `200`).
+  type: number
+  exclusiveMinimum: 0
 TissueOrigin:
   name: TissueOrigin
   description: |

From a1bd2a05ae87fdf15b21c899b889d4f2edf7bd0f Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 15:38:27 -0500
Subject: [PATCH 073/347] Add metadata table macros to 10-microscopy.md

---
 .../10-microscopy.md                          | 108 ++++++++----------
 1 file changed, 48 insertions(+), 60 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 3313a02116..871cb71a68 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -97,6 +97,7 @@ Intended table:
 
 Can we remove the "Description" column of the table in the MACRO?
 -->
+
 {{ MACROS___make_suffix_table(
       [
          "TEM",
@@ -284,64 +285,53 @@ for details.
 Microscopy data MUST be described by metadata fields, stored in sidecar JSON files.
 
 #### Device Hardware
-<!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
 
-Note: For `StationName`, we removed "Corresponds to DICOM Tag 0008, 1010 `Station Name`." from the description.
-It will require changes to `src/schema/metatata/StationName.yaml` and `src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md`.
--->
-| **Key name**              | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                           |
-| ------------------------- | --------------------- | ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Manufacturer              | RECOMMENDED           | [string][]    | Manufacturer of the equipment that produced the measurements.                                                                                                                                             |
-| ManufacturersModelName    | RECOMMENDED           | [string][]    | Manufacturer’s model name of the equipment that produced the measurements.                                                                                                                                |
-| DeviceSerialNumber        | RECOMMENDED           | [string][]    | The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset. |
-| StationName               | RECOMMENDED           | [string][]    | Institution defined name of the machine that produced the measurements.                                                                                                                                   |
-| SoftwareVersions          | RECOMMENDED           | [string][]    | Manufacturer’s designation of software version of the equipment that produced the measurements.                                                                                                           |
-| InstitutionName           | RECOMMENDED           | [string][]    | The name of the institution in charge of the equipment that produced the measurements.                                                                                                                    |
-| InstitutionAddress        | RECOMMENDED           | [string][]    | The address of the institution in charge of the equipment that produced the measurements.                                                                                                                 |
-| InstitutionDepartmentName | RECOMMENDED           | [string][]    | The department in the institution in charge of the equipment that produced the measurements.                                                                                                              |
+{{ MACROS___make_metadata_table(
+   {
+      "Manufacturer": "RECOMMENDED",
+      "ManufacturersModelName": "RECOMMENDED",
+      "DeviceSerialNumber": "RECOMMENDED",
+      "StationName": "RECOMMENDED",
+      "SoftwareVersions": "RECOMMENDED",
+      "InstitutionName": "RECOMMENDED",
+      "InstitutionAddress": "RECOMMENDED",
+      "InstitutionalDepartmentName": "RECOMMENDED",
+   }
+) }}
 
 #### Image Acquisition
-<!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
--->
-| **Key name**               | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
-| -------------------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| PixelSize                  | REQUIRED              | [array][] of [numbers][] | A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]` or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`, `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and `PhysicalSizeZunit` OME fields. |
-| PixelSizeUnits             | REQUIRED              | [string][]               | Unit format of the specified PixelSize. MUST be one of: `"mm"` (millimeter), `"um"` (micrometer) or `"nm"` (nanometer).                                                                                                                                                                                                                                                                                                                                                  |
-| Immersion                  | OPTIONAL              | [string][]               | Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the `"Immersion"` OME metadata field.                                                                                                                                                                                                                                                                                                                                           |
-| NumericalAperture          | OPTIONAL              | [number][]               | Lens numerical aperture (for example, `1.4`). If the file format is OME-TIFF, the value MUST be consistent with the `"LensNA"` OME metadata field.                                                                                                                                                                                                                                                                                                                       |
-| Magnification              | OPTIONAL              | [number][]               | Lens magnification (for example, `40`) If the file format is OME-TIFF, the value MUST be consistent with the `"NominalMagnification"` OME metadata field.                                                                                                                                                                                                                                                                                                                |
-| ImageAcquisitionProtocol   | OPTIONAL              | [string][]               | Description of the image acquisition protocol or [URI][uri] (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                |
-| OtherAcquisitionParameters | OPTIONAL              | [string][]               | Description of other relevant image acquisition parameters.                                                                                                                                                                                                                                                                                                                                                                                                              |
+
+{{ MACROS___make_metadata_table(
+   {
+      "PixelSize": "REQUIRED",
+      "PixelSizeUnits": "REQUIRED",
+      "Immersion": "OPTIONAL",
+      "NumericalAperture": "OPTIONAL",
+      "Magnification": "OPTIONAL",
+      "ImageAcquisitionProtocol": "OPTIONAL",
+      "OtherAcquisitionParameters": "OPTIONAL",
+   }
+) }}
 
 #### Sample
-<!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
 
-Note: For `BodyPart`, we removed: "Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. For example: `"BRAIN"`."
-from the description, and replace with
-"from [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN".`)".
-It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modality-specific-files/09-positron-emission-tomography.md`.
--->
-| **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
-| --------------------------- | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| BodyPart                    | RECOMMENDED           | [string][]                             | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)".                                                                                                                                                                                                                                                                                                                         |
-| BodyPartDetails             | RECOMMENDED           | [string][]                             | Additional details about body part or location (for example: `"corpus callosum"`).                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-| BodyPartDetailsOntology     | OPTIONAL              | [string][]                             | [URI][uri] of ontology used for BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).                                                                                                                                                                                                                                                                                                                                                                                                            |
-| SampleEnvironment           | RECOMMENDED           | [string][]                             | Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"` or `"in vitro"`.                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| SampleEmbedding             | OPTIONAL              | [string][]                             | Description of the tissue sample embedding (for example: `"Epoxy resin"`).                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
-| SampleFixation              | OPTIONAL              | [string][]                             | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).                                                                                                                                                                                                                                                                                                                                                                                                                       |
-| SampleStaining              | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`).                                                                                                                                                                                                                                                                                                                                  |
-| SamplePrimaryAntibody       | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
-| SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
-| SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| TissueDeformationScaling    | OPTIONAL              | [number][]                             | Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is `97`; and for an expansion of 100%, the value is `200`).                                                                                                                                                                                                                                                                                                                         |
-| SampleExtractionProtocol    | OPTIONAL              | [string][]                             | Description of the sample extraction protocol or [URI][uri] (for example from [protocols.io](https://www.protocols.io/)).                                                                                                                                                                                                                                                                                                                                                                                                  |
-| SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
+{{ MACROS___make_metadata_table(
+   {
+      "BodyPart": ("RECOMMENDED", "From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example `\"BRAIN\"`)."),
+      "BodyPartDetails": "RECOMMENDED",
+      "BodyPartDetailsOntology": "OPTIONAL",
+      "SampleEnvironment": "RECOMMENDED",
+      "SampleEmbedding": "OPTIONAL",
+      "SampleFixation": "OPTIONAL",
+      "SampleStaining": "RECOMMENDED",
+      "SamplePrimaryAntibody": "RECOMMENDED",
+      "SampleSecondaryAntibody": "RECOMMENDED",
+      "SliceThickness": "OPTIONAL",
+      "TissueDeformationScaling": "OPTIONAL",
+      "SampleExtractionProtocol": "OPTIONAL",
+      "SampleExtractionInstitution": "OPTIONAL",
+   }
+) }}
 
 #### Chunk Transformations
 
@@ -359,14 +349,12 @@ of the same sample in an implicit coordinate system.
 
 -   Other transformations should be described in derivatives.
 
-<!---
-The following table will be generated automatically with macros after community review.
-A "manual" table is provided to facilitate the review process.
--->
-| **Key name**                  | **Requirement level**                               | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
-| ----------------------------- | --------------------------------------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ChunkTransformationMatrix     | RECOMMENDED if `<chunk-index>` is used in filenames | [array][] of [arrays][] of [numbers][] | 3x3 or 4x4 affine transformation matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]` in 2D for 2x and 3x scaling along the first and second axis respectively or `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix. |
-| ChunkTransformationMatrixAxis | REQUIRED if `ChunkTransformationMatrix` is present  | [arrays][] of [strings][]              | Describe the axis of the ChunkTransformationMatrix (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`)                                                                                                                                                                                                                                                                                                                                                                                   |
+{{ MACROS___make_metadata_table(
+   {
+      "ChunkTransformationMatrix": "RECOMMENDED if `<chunk-index>` is used in filenames",
+      "ChunkTransformationMatrixAxis": "REQUIRED if `ChunkTransformationMatrix` is present",
+   }
+) }}
 
 An example of chunk transformations JSON metadata for `chunk-01` and `chunk-05` of Figure 2
 is shown below:

From 202d507e5814d0d8fea4da21cd7a60d89f14b061 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 15:39:48 -0500
Subject: [PATCH 074/347] Adjust StationName definition in
 01-magnetic-resonance-imaging-data.md

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index aa5c2c7f12..3185b86191 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -17,7 +17,7 @@ by Ben Inglis.
       "Manufacturer": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0070 `Manufacturer`."),
       "ManufacturersModelName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`."),
       "DeviceSerialNumber": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`."),
-      "StationName": "RECOMMENDED",
+      "StationName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1010 `Station Name`."),
       "SoftwareVersions": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1020 `Software Versions`."),
       "HardcopyDeviceSoftwareVersion": "DEPRECATED",
       "MagneticFieldStrength": "RECOMMENDED, but REQUIRED for Arterial Spin Labeling",

From 9376c7284fa2a4bf6b674edb9bcfb4e64bbca8dc Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 15:40:44 -0500
Subject: [PATCH 075/347] Adjust BodyPart definition in
 09-positron-emission-tomography.md

---
 .../09-positron-emission-tomography.md                          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 134512b81d..70e6d77f18 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -143,7 +143,7 @@ which we divide into several categories:
       "InstitutionName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0080 `InstitutionName`."),
       "InstitutionAddress": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`."),
       "InstitutionalDepartmentName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`."),
-      "BodyPart": "RECOMMENDED",
+      "BodyPart": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`."),
    }
 ) }}
 

From f13ed591833f61e9f00d0f9c853b12594025c041 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 17:58:15 -0500
Subject: [PATCH 076/347] Change "recording data" for "imaging data"

---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 871cb71a68..dd21fb74de 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -21,7 +21,7 @@ Further Microscopy datasets are available:
 -   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
 -   In OME-TIFF format: [`Broca's Area Light-Sheet Microscopy`](https://doi.org/10.5281/zenodo.5517223)
 
-## Microscopy recording data
+## Microscopy imaging data
 <!---
 Intended template:
 ```Text

From 48d9ba9833104cafff61a3abe8b10570bb068de8 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 2 Dec 2021 18:03:54 -0500
Subject: [PATCH 077/347] Remove unused link definitions

---
 src/04-modality-specific-files/10-microscopy.md | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index dd21fb74de..821fb3e0a3 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -490,11 +490,3 @@ Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2
 ![SEM overview](images/microscopy_sem_overview.jpg "SEM overview")
 
 <!-- Link Definitions -->
-
-[strings]: https://www.w3schools.com/js/js_json_datatypes.asp
-[string]: https://www.w3schools.com/js/js_json_datatypes.asp
-[numbers]: https://www.w3schools.com/js/js_json_datatypes.asp
-[number]: https://www.w3schools.com/js/js_json_datatypes.asp
-[arrays]: https://www.w3schools.com/js/js_json_arrays.asp
-[array]: https://www.w3schools.com/js/js_json_arrays.asp
-[uri]: ../02-common-principles.md#uniform-resource-indicator

From 877e92016d32f570403f436bf9b1b6b27f9b43a2 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 3 Dec 2021 10:45:09 -0500
Subject: [PATCH 078/347] Clarify samples/participants sections

---
 src/04-modality-specific-files/10-microscopy.md | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 821fb3e0a3..42ff9b75d5 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -408,21 +408,18 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 }
 ```
 
-## Required Samples file (`samples.tsv`)
+## Required Samples file
 
-For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file) `samples.tsv`
-is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
+For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file)
+`samples.tsv` is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
 
 Additional optional columns MAY be used to describe other samples' attributes.
 
-## Recommended Participants file (`participants.tsv`)
+## Recommended Participants data
 
-As for other data types in BIDS, the [Participants file](../03-modality-agnostic-files.md#participants-file)
-`participants.tsv` is RECOMMENDED and MUST contain the column `participant_id`, and its associated
-sidecar `participants.json` file is RECOMMENDED as well.
-
-For Microscopy data, we RECOMMEND to also make use of the columns `species`, `strain` and
-`strain_rrid` when applicable.
+For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and
+`strain_rrid` in the [Participants file](../03-modality-agnostic-files.md#participants-file)
+when applicable.
 
 Additional optional columns MAY be used to describe other subjects' attributes.
 

From 79091c9a40baf915d4e11fe009bfc66b02b66234 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 3 Dec 2021 15:18:12 -0500
Subject: [PATCH 079/347] schema/objects/metadata.yaml: Apply review
 suggestions and add restrictions

---
 src/schema/objects/metadata.yaml | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 2f9e1fb43f..a2a6d9d955 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -344,15 +344,25 @@ ChunkTransformationMatrix:
     scaling along the second and third axis respectively).
     Note that non-spatial dimensions like time and channel are not included in the
     transformation matrix.
-  type: array
-  minItems: 3
-  maxItems: 4
-  items:
-    type: array
+  anyOf:
+  - type: array
     minItems: 3
+    maxItems: 3
+    items:
+      type: array
+      minItems: 3
+      maxItems: 3
+      tems:
+       type: number
+  - type: array
+    minItems: 4
     maxItems: 4
     items:
-      type: number
+      type: array
+      minItems: 4
+      maxItems: 4
+      items:
+        type: number
 ChunkTransformationMatrixAxis:
   name: ChunkTransformationMatrixAxis
   description: |
@@ -361,6 +371,8 @@ ChunkTransformationMatrixAxis:
   type: array
   items:
     type: string
+    minItems: 2
+    maxItems: 3
 Code:
   name: Code
   description: |
@@ -1581,6 +1593,7 @@ Magnification:
     Lens magnification (for example: `40`). If the file format is OME-TIFF,
     the value MUST be consistent with the `NominalMagnification` OME metadata field.
   type: number
+  exclusiveMinimum: 0
 Manual:
   name: Manual
   description: |
@@ -1771,6 +1784,7 @@ NumericalAperture:
     Lens numerical aperture (for example: `1.4`). If the file format is OME-TIFF,
     the value MUST be consistent with the `LensNA` OME metadata field.
   type: number
+  exclusiveMinimum: 0
 OperatingSystem:
   name: OperatingSystem
   description: |
@@ -1892,7 +1906,7 @@ PhaseEncodingDirection:
 PixelSize:
   name: PixelSize
   description: |
-    A 2- or 3-number array of the physical size of a pixel, either`[PixelSizeX, PixelSizeY]`
+    A 2- or 3-number array of the physical size of a pixel, either `[PixelSizeX, PixelSizeY]`
     or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the
     depth.
     If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`,
@@ -1904,6 +1918,7 @@ PixelSize:
   maxItems: 3
   items:
     type: number
+    minimum: 0
 PixelSizeUnits:
   name: PixelSizeUnits
   description: |
@@ -2394,6 +2409,7 @@ SliceThickness:
     Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).
   type: number
   unit: um
+  exclusiveMinimum: 0
 SliceTiming:
   name: SliceTiming
   description: |

From 7b63f8eaaf1da2ab5f30e2a5a4236938b502ba15 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 3 Dec 2021 15:23:08 -0500
Subject: [PATCH 080/347] Address BEP031 macro requests (#945)

* Allow table-specific numbers of duplicate suffixes/exts to combine.

* Only combine compressed versions of extensions.
---
 .../10-microscopy.md                          |  4 +-
 tools/schemacode/schema.py                    | 12 +++---
 tools/schemacode/utils.py                     | 38 +++++++++++--------
 3 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 42ff9b75d5..ceb1190f09 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -35,7 +35,7 @@ The current MACRO list ".ome.btf", ".png" and ".tif[.ome]", is it possible to ha
 If not, ".tif" and ".ome.tif" should be 2 separate lines but are concatenated as ".tif[.ome]"
 -->
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
-"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"]) }}
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=3) }}
 
 Microscopy data MUST be stored in the `micr` directory.
 
@@ -459,7 +459,7 @@ sub-<label>/
 ```
 The current MACRO list ".jpg", ".png" and ".tif", is it possible to have one line with "<extension>" instead?
 -->
-{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"]) }}
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 
diff --git a/tools/schemacode/schema.py b/tools/schemacode/schema.py
index f4ec722d69..9547c8ddd8 100644
--- a/tools/schemacode/schema.py
+++ b/tools/schemacode/schema.py
@@ -226,15 +226,17 @@ def _add_entity(filename_template, entity_pattern, requirement_level):
     return filename_template
 
 
-def make_filename_template(schema, **kwargs):
-    """Create codeblocks containing example filename patterns for a given
-    datatype.
+def make_filename_template(schema, n_dupes_to_combine=6, **kwargs):
+    """Create codeblocks containing example filename patterns for a given datatype.
 
     Parameters
     ----------
     schema : dict
         The schema object, which is a dictionary with nested dictionaries and
         lists stored within it.
+    n_dupes_to_combine : int
+        The minimum number of suffixes/extensions to combine in the template as
+        <suffix>/<extension>.
     kwargs : dict
         Keyword arguments used to filter the schema.
         Example kwargs that may be used include: "suffixes", "datatypes",
@@ -298,7 +300,7 @@ def make_filename_template(schema, **kwargs):
 
             # In cases of large numbers of suffixes,
             # we use the "suffix" variable and expect a table later in the spec
-            if len(group["suffixes"]) > 5:
+            if len(group["suffixes"]) >= n_dupes_to_combine:
                 suffix = "_<suffix>"
                 string += suffix
                 strings = [string]
@@ -314,7 +316,7 @@ def make_filename_template(schema, **kwargs):
                 ext if ext != "*" else ".<extension>" for ext in extensions
             ]
             extensions = utils.combine_extensions(extensions)
-            if len(extensions) > 5:
+            if len(extensions) >= n_dupes_to_combine:
                 # Combine exts when there are many, but keep JSON separate
                 if ".json" in extensions:
                     extensions = [".<extension>", ".json"]
diff --git a/tools/schemacode/utils.py b/tools/schemacode/utils.py
index d6d95b6fc3..aa0676b1fe 100644
--- a/tools/schemacode/utils.py
+++ b/tools/schemacode/utils.py
@@ -23,29 +23,35 @@ def get_schema_path():
 def combine_extensions(lst):
     """Combine extensions with their compressed versions in a list.
 
-    This is a basic solution to combining extensions with their
-    compressed versions in a list. Something more robust could
-    be written in the future.
+    Valid combinations are hardcoded in the function,
+    since some extensions look like compressed versions of one another, but are not.
 
     Parameters
     ----------
     lst : list of str
+        Raw list of extensions.
+
+    Returns
+    -------
+    new_lst : list of str
+        List of extensions, with compressed and uncompressed versions of the same extension
+        combined.
     """
+    COMPRESSION_EXTENSIONS = [".gz"]
+
     new_lst = []
-    # First, sort by length
-    lst = sorted(lst, key=len)
+    items_to_remove = []
     for item in lst:
-        temp_lst = new_lst[:]
-
-        item_found = False
-        for j, new_item in enumerate(temp_lst):
-            if new_item in item:
-                temp_item = new_item + "[" + item.replace(new_item, "", 1) + "]"
-                new_lst[j] = temp_item
-                item_found = True
-
-        if not item_found:
-            new_lst.append(item)
+        for ext in COMPRESSION_EXTENSIONS:
+            if item.endswith(ext) and item.replace(ext, "") in lst:
+                temp_item = item.replace(ext, "") + "[" + ext + "]"
+                new_lst.append(temp_item)
+                items_to_remove.append(item)
+                items_to_remove.append(item.replace(ext, ""))
+                continue
+
+    items_to_add = [item for item in lst if item not in items_to_remove]
+    new_lst += items_to_add
 
     return new_lst
 

From c303ce4d14aab3e9703ffce9e5150ff9765624a0 Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Fri, 3 Dec 2021 15:26:31 -0500
Subject: [PATCH 081/347] Update src/schema/objects/metadata.yaml

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 src/schema/objects/metadata.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index a2a6d9d955..14c13ce6f3 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -352,8 +352,8 @@ ChunkTransformationMatrix:
       type: array
       minItems: 3
       maxItems: 3
-      tems:
-       type: number
+      items:
+        type: number
   - type: array
     minItems: 4
     maxItems: 4

From c23030159b1071ce3b580b4238628eef063bbbaf Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 6 Dec 2021 10:38:48 +1100
Subject: [PATCH 082/347] [FIX] Rewrite inheritance principle

---
 src/02-common-principles.md | 145 +++++++++++++++++++++---------------
 1 file changed, 83 insertions(+), 62 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index e29d0b96ed..90ed991ea9 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -400,108 +400,129 @@ datasets and non-compliant derivatives.
 
 ## The Inheritance Principle
 
-Any metadata file (such as `.json`, `.bvec` or `.tsv`) may be defined at any
-directory level, but no more than one applicable file may be defined at a given
-level (Example 1). The values from the top level are inherited by all lower
-levels unless they are overridden by a file at the lower level. For example,
-`sub-*_task-rest_bold.json` may be specified at the participant level, setting
-TR to a specific value. If one of the runs has a different TR than the one
-specified in that file, another `sub-*_task-rest_bold.json` file can be placed
-within that specific series directory specifying the TR for that specific run.
-There is no notion of "unsetting" a key/value pair.
-Once a key/value pair is set in a given level in the dataset, lower down in
-the hierarchy that key/value pair will always have some assigned value.
-Files for a particular participant can exist only at participant level directory,
-that is, `/dataset/sub-*[/ses-*]/sub-*_T1w.json`. Similarly, any file that is not
-specific to a participant is to be declared only at top level of dataset for example:
-`task-sist_bold.json` must be placed under `/dataset/task-sist_bold.json`
-
-Example 1: Two JSON files that are erroneously at the same level
+Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any
+directory level. For any given data file, any metadata file at that directory
+level or higher that does not include any entities absent from the name of the
+data file and possesses the same suffix are applicable to that data file. Such
+files are loaded from the top of the directory hierarchy downwards, such that
+values from the top level are inherited by all data files at lower levels to
+which it is applicable unless overridden by a value for the same key present
+in another metadata file at a lower level (though it is RECOMMENDED to minimise
+the extent of such overrides). There is no notion of "unsetting" a
+key/value pair.
+
+Example 1: Demonstration of inheritance principle
+
+{{ MACROS___make_filetree_example(
+    {
+    "sub-01": {
+        "func": {
+            "sub-01_task-rest_acq-default_bold.nii.gz": "",
+            "sub-01_task-rest_acq-longtr_bold.nii.gz": "",
+            "sub-01_task-rest_acq-longtr_bold.json": "",
+            }
+        }
+    }
+    "task-rest_bold.json": "",
+) }}
+
+Contents of file "task-rest_bold.json":
+
+{{ MACROS___make_metadata_table(
+   {
+        "EchoTime": 40.0,
+        "RepetitionTime", 1000.0
+   }
+) }}
+
+Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
+
+{{ MACROS___make_metadata_table(
+   {
+        "RepetitionTime", 3000.0
+   }
+) }}
+
+When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
+metadata file `task-rest_bold.json` is read; file 
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
+entity "`acq-longtr`" that is absent from the image path. When reading image
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
+`task-rest_bold.json` at the top level is read first, followed by file
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level; the value
+for field "`RepetitionTime`" is therefore overridden to the value 3000.0. The value
+for field "`EchoTime`" remains applicable to that image, and is not unset by its
+absence in the metadata file at the lower level.
+
+Metadata files applicable only to a specific participant / session MUST be defined
+in or below the directory corresponding to that participant / session. Similarly,
+a metadata file that is applicable to multiple participants / sessions MUST NOT be
+placed within a directory corresponding to only one such participant / session.
+
+There MUST NOT be multiple metadata files applicable to a data file at one level
+of the directory hierarchy.
+
+Example 2: Impermissible use of multiple metadata files at one directory level
 
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
         "ses-test":{
-            "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
-            "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
             "anat": {
                 "sub-01_ses-test_T1w.nii.gz": "",
                 },
             "func": {
                 "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
                 "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
                 }
             }
         }
     }
 ) }}
 
-In the above example, two JSON files are listed under `sub-01/ses-test/`, which
-are each applicable to
-`sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz`, violating the
-constraint that no more than one file may be defined at a given level of the
-directory structure. Instead `sub-01_ses-test_task-overtverbgeneration_run-2_bold.json`
-should have been under `sub-01/ses-test/func/`.
-
-Example 2: Multiple `run`s and `rec`s with same acquisition (`acq`) parameters
+Example 3: Modification of filesystem structure from Example 2 to satisfy inheritance
+principle requirements
 
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
-        "anat": {},
-        "func": {
-            "sub-01_task-xyz_acq-test1_run-1_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_run-2_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_bold.json": "",
+        "ses-test":{
+            "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
+            "anat": {
+                "sub-01_ses-test_T1w.nii.gz": "",
+                },
+            "func": {
+                "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
+                }
             }
         }
     }
 ) }}
 
-For the above example, all NIfTI files are acquired with same scanning
-parameters (`acq-test1`). Hence a JSON file describing the acq parameters will
-apply to different runs and rec files. Also if the JSON file
-(`task-xyz_acq-test1_bold.json`) is defined at dataset top level directory, it
-will be applicable to all task runs with `test1` acquisition parameter.
+It is permissible for a single metadata file to be applicable to multiple data
+files at that level of the hierarchy. Where such metadata content is consistent
+across multiple data files, it is RECOMMENDED to store metadata in this
+way, rather than duplicating that metadata content across multiple metadata files.
 
-Example 3: Multiple JSON files at different levels for same task and acquisition parameters
+Example 4: Single metadata file applying to multiple data files
 
 {{ MACROS___make_filetree_example(
     {
-    "task-xyz_acq-test1_bold.json": "",
     "sub-01": {
         "anat": {},
         "func": {
             "sub-01_task-xyz_acq-test1_run-1_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz": "",
+            "sub-01_task-xyz_acq-test1_run-2_bold.nii.gz": "",
             "sub-01_task-xyz_acq-test1_bold.json": "",
             }
         }
     }
 ) }}
 
-In the above example, the fields from the `task-xyz_acq-test1_bold.json` file
-at the top directory will apply to all bold runs. However, if there is a key
-with different value in the
-`sub-01/func/sub-01_task-xyz_acq-test1_bold.json` file defined at a
-deeper level, that value will be applicable for that particular run/task NIfTI
-file/s. In other words, the `.json` file at the deeper level overrides values
-that are potentially also defined in the `.json` at a more shallow level. If the
-`.json` file at the more shallow level contains key-value-pairs that are not
-present in the `.json` file at the deeper level, these key-value-pairs are
-inherited by the `.json` file at the deeper level (but NOT vice versa!).
-
-### Good practice recommendations
-
-**Try to avoid excessive amount of overrides.**  Do not specify a field
-value in the upper levels if lower levels have more or less even
-distribution of multiple possible values. For example, if a field `X` has one
-value for all `ses-01/` and another for all `ses-02/` it better not to be
-defined at all in the `.json` at the upper level.
-
 ## File Formation specification
 
 ### Imaging files

From 2202697e71c0aac6ad64ee7761c993709d224f33 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 6 Dec 2021 11:18:32 +1100
Subject: [PATCH 083/347] [FIX] Fix trailing space src/02_common_principles.md
 #946

---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 90ed991ea9..bb446a7b91 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -444,7 +444,7 @@ Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
 ) }}
 
 When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
-metadata file `task-rest_bold.json` is read; file 
+metadata file `task-rest_bold.json` is read; file
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
 entity "`acq-longtr`" that is absent from the image path. When reading image
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file

From e1927c5fb3c24ba919c1547d9cc7feadf2c944a1 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 6 Dec 2021 12:59:53 +0100
Subject: [PATCH 084/347] fix: reference column is in channels.tsv, not elecs
 file

---
 .../04-intracranial-electroencephalography.md                   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index e130cea04e..2c2983e8ba 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -226,7 +226,7 @@ MUST be present **in this specific order**:
    {
       "name__channels": ("REQUIRED", "When a corresponding electrode is specified in `_electrodes.tsv`, "
                          "the name of that electrode MAY be specified here and the reference electrode "
-                         "name MAY be provided in the `reference` column of the `_electrodes.tsv` file."),
+                         "name MAY be provided in the `reference` column."),
       "type__channels": "REQUIRED",
       "units": "REQUIRED",
       "low_cutoff": "REQUIRED",

From 86eeb620679b34d6211dc4026ce1fa18ba1d0e59 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Mon, 6 Dec 2021 17:53:03 +0000
Subject: [PATCH 085/347] [DOC] Auto-generate changelog entry for PR #939

---
 src/CHANGES.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index aca5a89c5f..f5b686ae9a 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,8 +2,15 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
+-   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))
+-   \[INFRA] expand submenus on landing page automatically [#937](https://github.com/bids-standard/bids-specification/pull/937) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Add links from derivatives section to entity list [#936](https://github.com/bids-standard/bids-specification/pull/936) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Remove repeated words [#934](https://github.com/bids-standard/bids-specification/pull/934) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[INFRA/FIX] Use string concatenation in table macro [#933](https://github.com/bids-standard/bids-specification/pull/933) ([effigies](https://github.com/effigies))
 -   \[INFRA] Run linkchecker in stock docker image [#932](https://github.com/bids-standard/bids-specification/pull/932) ([effigies](https://github.com/effigies))
+-   \[INFRA] add (optional) pre-commit config file [#929](https://github.com/bids-standard/bids-specification/pull/929) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Clarify that EDF/BDF files MUST have lower case extensions in BIDS [#927](https://github.com/bids-standard/bids-specification/pull/927) ([adam2392](https://github.com/adam2392))
 -   \[ENH] add `hemi` entity to schema [#917](https://github.com/bids-standard/bids-specification/pull/917) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] PDF version of spec: fix handling of internal links [#915](https://github.com/bids-standard/bids-specification/pull/915) ([sappelhoff](https://github.com/sappelhoff))

From 8691bfaf6cfa95f4e09a14f3ddb4d2247886555b Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 6 Dec 2021 15:02:12 -0500
Subject: [PATCH 086/347] Update names of bids-examples datasets

---
 src/04-modality-specific-files/10-microscopy.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index ceb1190f09..92c251286d 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -13,8 +13,8 @@ update to 'https://github.com/bids-standard/bids-examples' when examples are mer
 -->
 Microscopy datasets formatted using this specification are available on the
 [BIDS examples repository](https://github.com/neuropoly/bids-examples/tree/bep031)
-(`microscopy_SEM001` and `microscopy_SPIM001`) and can be used for practical
-guidance when curating a new dataset.
+(`micr_SEM` and `micr_SPIM`) and can be used for practical guidance when curating
+a new dataset.
 
 Further Microscopy datasets are available:
 

From c264f7489a38865d022bfc1dada6578640839ae5 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 6 Dec 2021 15:18:13 -0500
Subject: [PATCH 087/347] Remove comments about filename templates

---
 .../10-microscopy.md                          | 26 +++----------------
 1 file changed, 3 insertions(+), 23 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 92c251286d..0f6b1a06ba 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -22,20 +22,9 @@ Further Microscopy datasets are available:
 -   In OME-TIFF format: [`Broca's Area Light-Sheet Microscopy`](https://doi.org/10.5281/zenodo.5517223)
 
 ## Microscopy imaging data
-<!---
-Intended template:
-```Text
-sub-<label>/
-    [ses-<label>/]
-        micr/
-            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.<extension>
-            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.json
-```
-The current MACRO list ".ome.btf", ".png" and ".tif[.ome]", is it possible to have "<extension>" instead?
-If not, ".tif" and ".ome.tif" should be 2 separate lines but are concatenated as ".tif[.ome]"
--->
+
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
-"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=3) }}
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }}
 
 Microscopy data MUST be stored in the `micr` directory.
 
@@ -449,16 +438,7 @@ sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
 Photos of the tissue sample, overview microscopy scans or blockface images from cutting
 MAY be included for visualization of large samples or to indicate the location of chunks
 in a sample.
-<!---
-Intended template:
-```Text
-sub-<label>/
-    [ses-<label>/]
-        micr/
-            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.<extension>
-```
-The current MACRO list ".jpg", ".png" and ".tif", is it possible to have one line with "<extension>" instead?
--->
+
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.

From fbea1317cd583aef0c58576e0ddc17f461fddb44 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 6 Dec 2021 15:20:55 -0500
Subject: [PATCH 088/347] Remove comments for modality suffix table

---
 .../10-microscopy.md                          | 25 -------------------
 1 file changed, 25 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 0f6b1a06ba..a3ecf69d63 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -61,31 +61,6 @@ as a successor to OME-TIFF for better remote sharing of large datasets.
 
 ### Modality suffixes
 Microscopy data currently support the following imaging modalities:
-<!---
-Intended table:
-
-| **Name**                                      | `suffix` |
-| --------------------------------------------- | -------- |
-| Transmission electron microscopy              | TEM      |
-| Scanning electron microscopy                  | SEM      |
-| Micro-CT                                      | uCT      |
-| Bright-field microscopy                       | BF       |
-| Dark-field microscopy                         | DF       |
-| Phase-contrast microscopy                     | PC       |
-| Differential interference contrast microscopy | DIC      |
-| Fluorescence microscopy                       | FLUO     |
-| Confocal microscopy                           | CONF     |
-| Polarized-light microscopy                    | PLI      |
-| Coherent anti-Stokes Raman spectroscopy       | CARS     |
-| 2-photon excitation microscopy                | 2PE      |
-| Multi-photon excitation microscopy            | MPE      |
-| Super-resolution microscopy                   | SR       |
-| Nonlinear optical microscopy                  | NLO      |
-| Optical coherence tomography                  | OCT      |
-| Selective plane illumination microscopy       | SPIM     |
-
-Can we remove the "Description" column of the table in the MACRO?
--->
 
 {{ MACROS___make_suffix_table(
       [

From f7d713960f506755347c1ce887d860720efcd73a Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Tue, 7 Dec 2021 17:13:17 +0000
Subject: [PATCH 089/347] [DOC] Auto-generate changelog entry for PR #938

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index f5b686ae9a..75cbee5268 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -5,6 +5,7 @@
 -   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] relax unrealistically strict requirements with ieeg channels.tsv 'name' column [#938](https://github.com/bids-standard/bids-specification/pull/938) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] expand submenus on landing page automatically [#937](https://github.com/bids-standard/bids-specification/pull/937) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Add links from derivatives section to entity list [#936](https://github.com/bids-standard/bids-specification/pull/936) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Remove repeated words [#934](https://github.com/bids-standard/bids-specification/pull/934) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))

From ef4154163772e986681015d0d34e10c4cc6abb44 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Wed, 8 Dec 2021 12:28:58 +1100
Subject: [PATCH 090/347] [FIX] Broken hyperlinks in entity-related appendices

---
 src/99-appendices/04-entity-table.md | 2 +-
 src/99-appendices/09-entities.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 0151c08738..6234431aaa 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -14,7 +14,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 <!--
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
-  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-bids-schema
 -->
 
 ## Magnetic Resonance Imaging
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 196ae27ac2..c7cebb27db 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -11,6 +11,6 @@ each is given in the [Entity Table](04-entity-table.md).
 
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
-  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-bids-schema
 -->
 {{ MACROS___make_entity_definitions() }}

From 093754ff54c33a0a5de69f0fdba0c14a8f35d630 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Wed, 8 Dec 2021 16:18:55 +1100
Subject: [PATCH 091/347] Fix spelling errors in appendices

---
 src/99-appendices/03-hed.md  | 2 +-
 src/99-appendices/11-qmri.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/03-hed.md b/src/99-appendices/03-hed.md
index d6e5c39117..1526c1b036 100644
--- a/src/99-appendices/03-hed.md
+++ b/src/99-appendices/03-hed.md
@@ -40,7 +40,7 @@ automatically generated.
 Usually annotations that appear in the `HED` column are specific to each individual event.
 Information that is common to groups of events can be annotated by category.
 Numerical values associated with each event can be annotated by value type.
-Annotating by category and by valuegreatly reduces the effort required to HED tag
+Annotating by category and by value greatly reduces the effort required to HED tag
 data and improves the clarity for data users.
 
 ## Annotating events by categories
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 2a29ca1461..6c4a349907 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -349,7 +349,7 @@ required metadata field (second column).
 
 A derived qMRI application becomes available if all the optional metadata fields
 listed for the respective file collection suffix are provided for the data. In addition,
-conditional rules based on the value of a given required metada field can be set
+conditional rules based on the value of a given required metadata field can be set
 for the description of a derived qMRI application. Note that the value of this
 required metadata is fixed across constituent images of a file collection and defined
 in [Method-specific priority levels for qMRI file collections](#method-specific-priority-levels-for-qmri-file-collections).

From d0ad1376eedcfb3c7149f69e5a52898804bcec19 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 8 Dec 2021 09:06:30 +0000
Subject: [PATCH 092/347] [DOC] Auto-generate changelog entry for PR #951

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 75cbee5268..9cda29a5ed 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
 -   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))

From a49701822969db77d4af9c9ca2ddff07ff5cd737 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 8 Dec 2021 09:12:49 +0000
Subject: [PATCH 093/347] [DOC] Auto-generate changelog entry for PR #949

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 9cda29a5ed..956548b242 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -3,6 +3,7 @@
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
 -   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
+-   \[FIX] Broken hyperlink in entity list file [#949](https://github.com/bids-standard/bids-specification/pull/949) ([Lestropie](https://github.com/Lestropie))
 -   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))

From 206b3a0e23988f1671b003a11da33c1834f6997a Mon Sep 17 00:00:00 2001
From: Eric Earl <eric.earl@nih.gov>
Date: Wed, 8 Dec 2021 07:09:26 -0800
Subject: [PATCH 094/347] Update DECISION-MAKING.md

Add Eric Earl to the Maintainers Group table.
---
 DECISION-MAKING.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index a2bc9d8de6..3250390561 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -32,6 +32,7 @@ BIDS governance.
 | Taylor Salo ([@tsalo](https://github.com/tsalo))                               | 3h/week         | MRI                        |
 | Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau))                            | 3h/week         | Community development, MRI |
 | Anthony Galassi  ([@bendhouseart](https://github.com/bendhouseart))            | 3h/week         | PET, Community development |
+| Eric Earl ([@ericearl](https://github.com/ericearl))                           | 2h/week         |                            |
 
 In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
 classification of a maintainer, maintainers may declare a limited scope of responsibility.

From edac0366c1d6ddf560e449f43bb5d0c117cfd664 Mon Sep 17 00:00:00 2001
From: Eric Earl <eric.earl@nih.gov>
Date: Wed, 8 Dec 2021 07:24:07 -0800
Subject: [PATCH 095/347] Update 01-contributors.md

Add more Eric Earl contributions.
---
 src/99-appendices/01-contributors.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index 0e9be164c0..61c144a1fc 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -68,7 +68,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 -   Erin W. Dickie 📖🤔👀📢💬
 -   Eugene P. Duff 📖
 -   Elizabeth DuPre 📖💡🔍🤔💬
--   Eric A. Earl 🤔
+-   Eric Earl 📖💬🐛🚧🔧🤔
 -   Anders Eklund 📖📢💻
 -   Oscar Esteban 📖🔧🤔💬💻
 -   Franklin W. Feingold 📋📝✅💬🤔🎨📢👀🚇🖋📆

From 05f7ce1ae9cc72b087b57c39183e36afcf37cb00 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 8 Dec 2021 15:40:06 +0000
Subject: [PATCH 096/347] [DOC] Auto-generate changelog entry for PR #953

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 956548b242..a774a6f262 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MISC] Add Eric Earl as a Maintainer [#953](https://github.com/bids-standard/bids-specification/pull/953) ([ericearl](https://github.com/ericearl))
 -   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
 -   \[FIX] Broken hyperlink in entity list file [#949](https://github.com/bids-standard/bids-specification/pull/949) ([Lestropie](https://github.com/Lestropie))
 -   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))

From 898e4f7c564b4a61cf00b77b7ee089db04ba9d91 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 10:03:22 +1100
Subject: [PATCH 097/347] Entity table: Clarify meaning of empty cells

---
 src/99-appendices/04-entity-table.md | 3 ++-
 src/99-appendices/09-entities.md     | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 0151c08738..68ba9ff11e 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -4,7 +4,8 @@ This section compiles the entities (key-value pairs) described throughout this
 specification, and establishes a common order within a filename.
 For example, if a file has an acquisition and reconstruction label, the
 acquisition entity must precede the reconstruction entity.
-REQUIRED and OPTIONAL entities for a given file type are denoted.
+REQUIRED and OPTIONAL entities for a given file type are denoted;
+empty cells imply that entities MUST NOT be specified.
 Entity formats indicate whether the value is alphanumeric
 (`<label>`) or numeric (`<index>`).
 
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 196ae27ac2..f8f2250ef9 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -6,8 +6,8 @@ specification, and describes each.
 A general introduction to entities is given in the section on
 [file name structure](../02-common-principles.md#file-name-structure).
 
-The ordering of entities and whether it is allowed, OPTIONAL, or REQUIRED for
-each is given in the [Entity Table](04-entity-table.md).
+The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT
+be specified for a given file type, is specified in the [Entity Table](04-entity-table.md).
 
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.

From 0abc9300a9a92b48e53d75dc8a1479b70fbe85cf Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 10:11:15 +1100
Subject: [PATCH 098/347] Inheritance principle: Use bullet points

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
---
 src/02-common-principles.md | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index bb446a7b91..22cdfdb263 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -400,16 +400,17 @@ datasets and non-compliant derivatives.
 
 ## The Inheritance Principle
 
-Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any
-directory level. For any given data file, any metadata file at that directory
-level or higher that does not include any entities absent from the name of the
-data file and possesses the same suffix are applicable to that data file. Such
-files are loaded from the top of the directory hierarchy downwards, such that
-values from the top level are inherited by all data files at lower levels to
-which it is applicable unless overridden by a value for the same key present
-in another metadata file at a lower level (though it is RECOMMENDED to minimise
-the extent of such overrides). There is no notion of "unsetting" a
-key/value pair.
+- Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level. 
+- For a given data file, any metadata file at that directory level or higher 
+is applicable to that data file if:
+  - the metadata and the data filenames possess the same suffix,
+  - the metadata filename does not include any entity absent from the data filename. 
+- Such files are loaded from the top of the directory hierarchy downwards, 
+such that values from the top level are inherited by all data files 
+at lower levels to which it is applicable unless overridden 
+by a value for the same key present in another metadata file at a lower level 
+(though it is RECOMMENDED to minimise the extent of such overrides). 
+- There is no notion of "unsetting" a key/value pair.
 
 Example 1: Demonstration of inheritance principle
 

From 1bcf1b52a750d8bfa3f6121e893a2af6ffd861e1 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 10:51:42 +1100
Subject: [PATCH 099/347] Inheritance principle: Multiple changes

- Change primary rules from dot points to enumerations, and reference rules by number where applicable.
- Move from subsequent text into this list rules relating to improper placement of metadata files within the directory structure, and not permitting multiple applicable files at one level of the hierarchy.
- Add "corollaries" section incorporating text relating to interpretation and consequences of the rules, separating them from subsequent examples.
---
 src/02-common-principles.md | 71 +++++++++++++++++++++----------------
 1 file changed, 40 insertions(+), 31 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 22cdfdb263..3ef4406c49 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -400,17 +400,39 @@ datasets and non-compliant derivatives.
 
 ## The Inheritance Principle
 
-- Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level. 
-- For a given data file, any metadata file at that directory level or higher 
-is applicable to that data file if:
-  - the metadata and the data filenames possess the same suffix,
-  - the metadata filename does not include any entity absent from the data filename. 
-- Such files are loaded from the top of the directory hierarchy downwards, 
-such that values from the top level are inherited by all data files 
-at lower levels to which it is applicable unless overridden 
-by a value for the same key present in another metadata file at a lower level 
-(though it is RECOMMENDED to minimise the extent of such overrides). 
-- There is no notion of "unsetting" a key/value pair.
+1.  Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level.
+1.  For a given data file, any metadata file is applicable to that data file if:
+    1.  It is stored at the same directory level or higher;
+    1.  The metadata and the data filenames possess the same suffix;
+    1.  The metadata filename does not include any entity absent from the data filename.
+1.  A metadata file MUST NOT have a file name that would be otherwise applicable
+    to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
+    location in the directory structure as per rule 2.1.
+1.  There MUST NOT be multiple metadata files applicable to a data file at one level
+    of the directory hierarchy.
+1.  If multiple metadata files are applicable to a given data file:
+    1.  For [tabular files](#tabular-files) and other simple metadata files
+        (e.g. [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
+        only the file lowest in the filesystem hierarchy SHALL be treated as being
+        associated with that data file.
+    1.  For [JSON files](#key-value-files-dictionaries):
+        1.  Files are loaded from the top of the directory hierarchy downwards,
+            such that values from the top level are inherited by all data files
+            at lower levels to which it is applicable unless overridden
+            by a value for the same key present in another metadata file at a lower level
+            (though it is RECOMMENDED to minimise the extent of such overrides).
+        1.  There is no notion of "unsetting" a key/value pair.
+
+Corollaries:
+
+1.  As per rule 3, metadata files applicable only to a specific participant / session
+    MUST be defined in or below the directory corresponding to that participant / session;
+    similarly, a metadata file that is applicable to multiple participants / sessions
+    MUST NOT be placed within a directory corresponding to only one such participant / session.
+1.  It is permissible for a single metadata file to be applicable to multiple data
+    files at that level of the hierarchy. Where such metadata content is consistent
+    across multiple data files, it is RECOMMENDED to store metadata in this
+    way, rather than duplicating that metadata content across multiple metadata files.
 
 Example 1: Demonstration of inheritance principle
 
@@ -447,23 +469,15 @@ Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
 When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
 metadata file `task-rest_bold.json` is read; file
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
-entity "`acq-longtr`" that is absent from the image path. When reading image
+entity "`acq-longtr`" that is absent from the image path (rule 2.3). When reading image
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
 `task-rest_bold.json` at the top level is read first, followed by file
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level; the value
-for field "`RepetitionTime`" is therefore overridden to the value 3000.0. The value
-for field "`EchoTime`" remains applicable to that image, and is not unset by its
-absence in the metadata file at the lower level.
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2.1);
+the value for field "`RepetitionTime`" is therefore overridden to the value 3000.0.
+The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
+absence in the metadata file at the lower level (rule 5.2.2).
 
-Metadata files applicable only to a specific participant / session MUST be defined
-in or below the directory corresponding to that participant / session. Similarly,
-a metadata file that is applicable to multiple participants / sessions MUST NOT be
-placed within a directory corresponding to only one such participant / session.
-
-There MUST NOT be multiple metadata files applicable to a data file at one level
-of the directory hierarchy.
-
-Example 2: Impermissible use of multiple metadata files at one directory level
+Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
 
 {{ MACROS___make_filetree_example(
     {
@@ -504,12 +518,7 @@ principle requirements
     }
 ) }}
 
-It is permissible for a single metadata file to be applicable to multiple data
-files at that level of the hierarchy. Where such metadata content is consistent
-across multiple data files, it is RECOMMENDED to store metadata in this
-way, rather than duplicating that metadata content across multiple metadata files.
-
-Example 4: Single metadata file applying to multiple data files
+Example 4: Single metadata file applying to multiple data files (corollary 2)
 
 {{ MACROS___make_filetree_example(
     {

From 7f52984578ddc94eb263ba100f834cf25ca961a3 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 10:53:40 +1100
Subject: [PATCH 100/347] Inheritance principle: Move to follow "file formation
 specification"

As the inheritance principle makes reference to tabular files and JSON key-value dictionaries, but there are no such references in the opposite direction, these files should be defined prior to introduction of the Inheritance Principle.
---
 src/02-common-principles.md | 270 ++++++++++++++++++------------------
 1 file changed, 135 insertions(+), 135 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 3ef4406c49..7c35a2a29d 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -398,141 +398,6 @@ In particular, if a BIDS dataset contains a `derivatives/` sub-directory,
 the contents of that directory may be a heterogeneous mix of BIDS Derivatives
 datasets and non-compliant derivatives.
 
-## The Inheritance Principle
-
-1.  Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level.
-1.  For a given data file, any metadata file is applicable to that data file if:
-    1.  It is stored at the same directory level or higher;
-    1.  The metadata and the data filenames possess the same suffix;
-    1.  The metadata filename does not include any entity absent from the data filename.
-1.  A metadata file MUST NOT have a file name that would be otherwise applicable
-    to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
-    location in the directory structure as per rule 2.1.
-1.  There MUST NOT be multiple metadata files applicable to a data file at one level
-    of the directory hierarchy.
-1.  If multiple metadata files are applicable to a given data file:
-    1.  For [tabular files](#tabular-files) and other simple metadata files
-        (e.g. [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
-        only the file lowest in the filesystem hierarchy SHALL be treated as being
-        associated with that data file.
-    1.  For [JSON files](#key-value-files-dictionaries):
-        1.  Files are loaded from the top of the directory hierarchy downwards,
-            such that values from the top level are inherited by all data files
-            at lower levels to which it is applicable unless overridden
-            by a value for the same key present in another metadata file at a lower level
-            (though it is RECOMMENDED to minimise the extent of such overrides).
-        1.  There is no notion of "unsetting" a key/value pair.
-
-Corollaries:
-
-1.  As per rule 3, metadata files applicable only to a specific participant / session
-    MUST be defined in or below the directory corresponding to that participant / session;
-    similarly, a metadata file that is applicable to multiple participants / sessions
-    MUST NOT be placed within a directory corresponding to only one such participant / session.
-1.  It is permissible for a single metadata file to be applicable to multiple data
-    files at that level of the hierarchy. Where such metadata content is consistent
-    across multiple data files, it is RECOMMENDED to store metadata in this
-    way, rather than duplicating that metadata content across multiple metadata files.
-
-Example 1: Demonstration of inheritance principle
-
-{{ MACROS___make_filetree_example(
-    {
-    "sub-01": {
-        "func": {
-            "sub-01_task-rest_acq-default_bold.nii.gz": "",
-            "sub-01_task-rest_acq-longtr_bold.nii.gz": "",
-            "sub-01_task-rest_acq-longtr_bold.json": "",
-            }
-        }
-    }
-    "task-rest_bold.json": "",
-) }}
-
-Contents of file "task-rest_bold.json":
-
-{{ MACROS___make_metadata_table(
-   {
-        "EchoTime": 40.0,
-        "RepetitionTime", 1000.0
-   }
-) }}
-
-Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
-
-{{ MACROS___make_metadata_table(
-   {
-        "RepetitionTime", 3000.0
-   }
-) }}
-
-When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
-metadata file `task-rest_bold.json` is read; file
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
-entity "`acq-longtr`" that is absent from the image path (rule 2.3). When reading image
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
-`task-rest_bold.json` at the top level is read first, followed by file
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2.1);
-the value for field "`RepetitionTime`" is therefore overridden to the value 3000.0.
-The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
-absence in the metadata file at the lower level (rule 5.2.2).
-
-Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
-
-{{ MACROS___make_filetree_example(
-    {
-    "sub-01": {
-        "ses-test":{
-            "anat": {
-                "sub-01_ses-test_T1w.nii.gz": "",
-                },
-            "func": {
-                "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
-                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
-                "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
-                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
-                }
-            }
-        }
-    }
-) }}
-
-Example 3: Modification of filesystem structure from Example 2 to satisfy inheritance
-principle requirements
-
-{{ MACROS___make_filetree_example(
-    {
-    "sub-01": {
-        "ses-test":{
-            "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
-            "anat": {
-                "sub-01_ses-test_T1w.nii.gz": "",
-                },
-            "func": {
-                "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
-                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
-                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
-                }
-            }
-        }
-    }
-) }}
-
-Example 4: Single metadata file applying to multiple data files (corollary 2)
-
-{{ MACROS___make_filetree_example(
-    {
-    "sub-01": {
-        "anat": {},
-        "func": {
-            "sub-01_task-xyz_acq-test1_run-1_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_run-2_bold.nii.gz": "",
-            "sub-01_task-xyz_acq-test1_bold.json": "",
-            }
-        }
-    }
-) }}
-
 ## File Formation specification
 
 ### Imaging files
@@ -675,6 +540,141 @@ for more information.
 }
 ```
 
+## The Inheritance Principle
+
+1.  Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level.
+1.  For a given data file, any metadata file is applicable to that data file if:
+    1.  It is stored at the same directory level or higher;
+    1.  The metadata and the data filenames possess the same suffix;
+    1.  The metadata filename does not include any entity absent from the data filename.
+1.  A metadata file MUST NOT have a file name that would be otherwise applicable
+    to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
+    location in the directory structure as per rule 2.1.
+1.  There MUST NOT be multiple metadata files applicable to a data file at one level
+    of the directory hierarchy.
+1.  If multiple metadata files are applicable to a given data file:
+    1.  For [tabular files](#tabular-files) and other simple metadata files
+        (e.g. [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
+        only the file lowest in the filesystem hierarchy SHALL be treated as being
+        associated with that data file.
+    1.  For [JSON files](#key-value-files-dictionaries):
+        1.  Files are loaded from the top of the directory hierarchy downwards,
+            such that values from the top level are inherited by all data files
+            at lower levels to which it is applicable unless overridden
+            by a value for the same key present in another metadata file at a lower level
+            (though it is RECOMMENDED to minimise the extent of such overrides).
+        1.  There is no notion of "unsetting" a key/value pair.
+
+Corollaries:
+
+1.  As per rule 3, metadata files applicable only to a specific participant / session
+    MUST be defined in or below the directory corresponding to that participant / session;
+    similarly, a metadata file that is applicable to multiple participants / sessions
+    MUST NOT be placed within a directory corresponding to only one such participant / session.
+1.  It is permissible for a single metadata file to be applicable to multiple data
+    files at that level of the hierarchy. Where such metadata content is consistent
+    across multiple data files, it is RECOMMENDED to store metadata in this
+    way, rather than duplicating that metadata content across multiple metadata files.
+
+Example 1: Demonstration of inheritance principle
+
+{{ MACROS___make_filetree_example(
+    {
+    "sub-01": {
+        "func": {
+            "sub-01_task-rest_acq-default_bold.nii.gz": "",
+            "sub-01_task-rest_acq-longtr_bold.nii.gz": "",
+            "sub-01_task-rest_acq-longtr_bold.json": "",
+            }
+        }
+    }
+    "task-rest_bold.json": "",
+) }}
+
+Contents of file "task-rest_bold.json":
+
+{{ MACROS___make_metadata_table(
+   {
+        "EchoTime": 40.0,
+        "RepetitionTime", 1000.0
+   }
+) }}
+
+Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
+
+{{ MACROS___make_metadata_table(
+   {
+        "RepetitionTime", 3000.0
+   }
+) }}
+
+When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
+metadata file `task-rest_bold.json` is read; file
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
+entity "`acq-longtr`" that is absent from the image path (rule 2.3). When reading image
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
+`task-rest_bold.json` at the top level is read first, followed by file
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2.1);
+the value for field "`RepetitionTime`" is therefore overridden to the value 3000.0.
+The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
+absence in the metadata file at the lower level (rule 5.2.2).
+
+Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
+
+{{ MACROS___make_filetree_example(
+    {
+    "sub-01": {
+        "ses-test":{
+            "anat": {
+                "sub-01_ses-test_T1w.nii.gz": "",
+                },
+            "func": {
+                "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
+                }
+            }
+        }
+    }
+) }}
+
+Example 3: Modification of filesystem structure from Example 2 to satisfy inheritance
+principle requirements
+
+{{ MACROS___make_filetree_example(
+    {
+    "sub-01": {
+        "ses-test":{
+            "sub-01_ses-test_task-overtverbgeneration_bold.json": "",
+            "anat": {
+                "sub-01_ses-test_T1w.nii.gz": "",
+                },
+            "func": {
+                "sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz": "",
+                "sub-01_ses-test_task-overtverbgeneration_run-2_bold.json": "",
+                }
+            }
+        }
+    }
+) }}
+
+Example 4: Single metadata file applying to multiple data files (corollary 2)
+
+{{ MACROS___make_filetree_example(
+    {
+    "sub-01": {
+        "anat": {},
+        "func": {
+            "sub-01_task-xyz_acq-test1_run-1_bold.nii.gz": "",
+            "sub-01_task-xyz_acq-test1_run-2_bold.nii.gz": "",
+            "sub-01_task-xyz_acq-test1_bold.json": "",
+            }
+        }
+    }
+) }}
+
 ## Participant names and other labels
 
 BIDS allows for custom user-defined `<label>`s and `<index>`es for example,

From 399a9072d6daa78801619d05e84aa8f37733f1af Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 11:04:54 +1100
Subject: [PATCH 101/347] Inheritance principle: Formatting fixes

---
 src/02-common-principles.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 7c35a2a29d..ea5f46136d 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -543,20 +543,26 @@ for more information.
 ## The Inheritance Principle
 
 1.  Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level.
+
 1.  For a given data file, any metadata file is applicable to that data file if:
     1.  It is stored at the same directory level or higher;
     1.  The metadata and the data filenames possess the same suffix;
     1.  The metadata filename does not include any entity absent from the data filename.
+
 1.  A metadata file MUST NOT have a file name that would be otherwise applicable
     to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
     location in the directory structure as per rule 2.1.
+
 1.  There MUST NOT be multiple metadata files applicable to a data file at one level
     of the directory hierarchy.
+
 1.  If multiple metadata files are applicable to a given data file:
+
     1.  For [tabular files](#tabular-files) and other simple metadata files
         (e.g. [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
         only the file lowest in the filesystem hierarchy SHALL be treated as being
         associated with that data file.
+
     1.  For [JSON files](#key-value-files-dictionaries):
         1.  Files are loaded from the top of the directory hierarchy downwards,
             such that values from the top level are inherited by all data files

From 8091e3c81f37073e79d09bc8e63f0436d09ff6d7 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 13 Dec 2021 11:06:16 +1100
Subject: [PATCH 102/347] Inheritance principle: Tweak to corollary

Having a metadata file applicable to multiple data files can occur not only at one level of the directory hierarchy, but additionally to many data files at lower levels of the hierarchy.
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index ea5f46136d..859fb3547a 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -578,7 +578,7 @@ Corollaries:
     similarly, a metadata file that is applicable to multiple participants / sessions
     MUST NOT be placed within a directory corresponding to only one such participant / session.
 1.  It is permissible for a single metadata file to be applicable to multiple data
-    files at that level of the hierarchy. Where such metadata content is consistent
+    files at that level of the hierarchy or below. Where such metadata content is consistent
     across multiple data files, it is RECOMMENDED to store metadata in this
     way, rather than duplicating that metadata content across multiple metadata files.
 

From 1a7e713e6ba67555dcd051080bef67208d1bfc6d Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 15 Dec 2021 10:53:39 -0500
Subject: [PATCH 103/347] RF: Use setup.cfg over info.py

---
 tools/schemacode/schemacode/info.py | 84 -----------------------------
 tools/schemacode/setup.cfg          | 47 +++++++++++++++-
 tools/schemacode/setup.py           | 71 ++++++------------------
 3 files changed, 62 insertions(+), 140 deletions(-)
 delete mode 100644 tools/schemacode/schemacode/info.py

diff --git a/tools/schemacode/schemacode/info.py b/tools/schemacode/schemacode/info.py
deleted file mode 100644
index 6ed687c144..0000000000
--- a/tools/schemacode/schemacode/info.py
+++ /dev/null
@@ -1,84 +0,0 @@
-"""Base module variables."""
-import importlib.util
-import os.path as op
-from pathlib import Path
-
-# Get version
-spec = importlib.util.spec_from_file_location(
-    "_version", op.join(op.dirname(__file__), "schemacode/_version.py")
-)
-_version = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(_version)
-
-VERSION = _version.get_versions()["version"]
-del _version
-
-# Get package description from README
-# Since this file is executed from ../setup.py, the path to the README is determined by the
-# location of setup.py.
-readme_path = Path(__file__).parent.joinpath("README.md")
-longdesc = readme_path.open().read()
-
-# Fields
-AUTHOR = "bids-standard developers"
-COPYRIGHT = "Copyright 2021, bids-standard developers"
-CREDITS = "bids-standard developers"
-LICENSE = "MIT"
-MAINTAINER = ""
-EMAIL = ""
-STATUS = "Prototype"
-URL = "https://github.com/bids-standard/schemacode"
-PACKAGENAME = "schemacode"
-DESCRIPTION = "Python tools for working with the BIDS schema."
-LONGDESC = longdesc
-
-DOWNLOAD_URL = "https://github.com/bids-standard/{name}/archive/{ver}.tar.gz".format(
-    name=PACKAGENAME, ver=VERSION
-)
-
-REQUIRES = [
-    "numpy",
-    "pandas",
-    "tabulate",
-    "pyyaml",
-]
-
-TESTS_REQUIRES = [
-    "codecov",
-    "coverage<5.0",
-    "flake8>=3.7",
-    "flake8-black",
-    "flake8-isort",
-    "pytest",
-    "pytest-cov",
-]
-
-EXTRA_REQUIRES = {
-    "dev": ["versioneer"],
-    "doc": [
-        "sphinx>=1.5.3",
-        "sphinx_rtd_theme",
-    ],
-    "tests": TESTS_REQUIRES,
-}
-
-ENTRY_POINTS = {}
-
-# Enable a handle to install all extra dependencies at once
-EXTRA_REQUIRES["all"] = list(set([v for deps in EXTRA_REQUIRES.values() for v in deps]))
-
-# Supported Python versions using PEP 440 version specifiers
-# Should match the same set of Python versions as classifiers
-PYTHON_REQUIRES = ">=3.6"
-
-# Package classifiers
-CLASSIFIERS = [
-    "Development Status :: 2 - Pre-Alpha",
-    "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering :: Information Analysis",
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python :: 3.6",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-]
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
index ae6de3aed3..821d22c1ef 100644
--- a/tools/schemacode/setup.cfg
+++ b/tools/schemacode/setup.cfg
@@ -1,9 +1,54 @@
+[metadata]
+name = schemacode
+url = https://github.com/bids-standard/schemacode
+author = bids-standard developers
+author_email = bids.maintenance@gmail.com
+description = Python tools for working with the BIDS schema.
+long_description = file:README.md
+long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
+license = MIT
+classifiers =
+    Development Status :: 2 - Pre-Alpha
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering :: Information Analysis
+    License :: OSI Approved :: MIT License
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+
+[options]
+python_requires = >=3.6
+install_requires =
+    numpy
+    pandas
+    tabulate
+    pyyaml
+packages = find:
+include_package_data = False
+
+[options.extras_require]
+doc =
+    sphinx>=1.5.3
+    sphinx_rtd_theme
+tests =
+    codecov
+    coverage<5.0
+    flake8>=3.7
+    flake8-black
+    flake8-isort
+    pytest
+    pytest-cov
+all =
+    %(doc)s
+    %(tests)s
+
 [versioneer]
 VCS = git
 style = pep440
 versionfile_source = schemacode/_version.py
 versionfile_build = schemacode/_version.py
-tag_prefix =
+tag_prefix = v
 parentdir_prefix =
 
 [flake8]
diff --git a/tools/schemacode/setup.py b/tools/schemacode/setup.py
index 413a51cf28..b50d479bf2 100644
--- a/tools/schemacode/setup.py
+++ b/tools/schemacode/setup.py
@@ -1,57 +1,18 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
-""" schemacode setup script """
+import sys
+from setuptools import setup
+import versioneer
+
+# Give setuptools a hint to complain if it's too old a version
+# 30.3.0 allows us to put most metadata in setup.cfg
+# Should match pyproject.toml
+SETUP_REQUIRES = ['setuptools >= 30.3.0']
+# This enables setuptools to install wheel on-the-fly
+SETUP_REQUIRES += ['wheel'] if 'bdist_wheel' in sys.argv else []
+
+if __name__ == '__main__':
+    setup(name="pybids",
+          version=versioneer.get_version(),
+          cmdclass=versioneer.get_cmdclass(),
+          setup_requires=SETUP_REQUIRES)
 
-
-def main():
-    """ Install entry-point """
-    import os.path as op
-    from inspect import currentframe, getfile
-    from io import open
-
-    from setuptools import find_packages, setup
-
-    import versioneer
-
-    ver_file = op.join("schemacode", "info.py")
-    with open(ver_file) as f:
-        exec(f.read())
-    vars = locals()
-
-    root_dir = op.dirname(op.abspath(getfile(currentframe())))
-    cmdclass = versioneer.get_cmdclass()
-
-    pkg_data = {
-        "schemacode": [
-            "tests/data/*",
-        ]
-    }
-
-    setup(
-        name=vars["PACKAGENAME"],
-        version=vars["VERSION"],
-        description=vars["DESCRIPTION"],
-        long_description=vars["LONGDESC"],
-        long_description_content_type="text/markdown",
-        author=vars["AUTHOR"],
-        author_email=vars["EMAIL"],
-        maintainer=vars["MAINTAINER"],
-        maintainer_email=vars["EMAIL"],
-        url=vars["URL"],
-        license=vars["LICENSE"],
-        classifiers=vars["CLASSIFIERS"],
-        download_url=vars["DOWNLOAD_URL"],
-        # Dependencies handling
-        python_requires=vars["PYTHON_REQUIRES"],
-        install_requires=vars["REQUIRES"],
-        tests_require=vars["TESTS_REQUIRES"],
-        extras_require=vars["EXTRA_REQUIRES"],
-        entry_points=vars["ENTRY_POINTS"],
-        packages=find_packages(exclude=("tests",)),
-        zip_safe=False,
-        cmdclass=cmdclass,
-    )
-
-
-if __name__ == "__main__":
-    main()

From 7489ff5195588d24c3150e813933bca4086f1b80 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 15 Dec 2021 11:05:21 -0500
Subject: [PATCH 104/347] [ENH] Generate glossary page from schema (#923)

* Use two underscores for multi-sense metadata entries.

* Fill in missing object descriptions.

* Draft glossary page.

* Use better key.

* Place marker.
---
 mkdocs.yml                                    |  1 +
 .../01-magnetic-resonance-imaging-data.md     |  4 +-
 src/99-appendices/14-glossary.md              |  9 +++
 src/schema/objects/associated_data.yaml       |  3 +-
 src/schema/objects/datatypes.yaml             |  3 +-
 src/schema/objects/metadata.yaml              |  6 +-
 tools/mkdocs_macros_bids/macros.py            | 15 ++++
 tools/mkdocs_macros_bids/main.py              |  1 +
 tools/schemacode/schema.py                    | 78 +++++++++++++++++++
 9 files changed, 114 insertions(+), 6 deletions(-)
 create mode 100644 src/99-appendices/14-glossary.md

diff --git a/mkdocs.yml b/mkdocs.yml
index 8cfc8853d9..96b856c6db 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -59,6 +59,7 @@ nav:
         - Quantitative MRI: 99-appendices/11-qmri.md
         - Arterial Spin Labeling: 99-appendices/12-arterial-spin-labeling.md
         - Cross modality correspondence: 99-appendices/13-cross-modality-correspondence.md
+        - Glossary: 99-appendices/14-glossary.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index aa5c2c7f12..a6c911a2c4 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -150,7 +150,7 @@ Useful for multimodal co-registration with MEG, (S)EEG, TMS, and so on.
 
 {{ MACROS___make_metadata_table(
    {
-      "AnatomicalLandmarkCoordinates_mri": "RECOMMENDED",
+      "AnatomicalLandmarkCoordinates__mri": "RECOMMENDED",
    }
 ) }}
 
@@ -1072,7 +1072,7 @@ Required fields:
 
 {{ MACROS___make_metadata_table(
    {
-      "EchoTime_fmap": "REQUIRED",
+      "EchoTime__fmap": "REQUIRED",
    }
 ) }}
 
diff --git a/src/99-appendices/14-glossary.md b/src/99-appendices/14-glossary.md
new file mode 100644
index 0000000000..8f9affb6f1
--- /dev/null
+++ b/src/99-appendices/14-glossary.md
@@ -0,0 +1,9 @@
+# Appendix XIV: Glossary of schema objects
+
+This section compiles the object definitions in the schema.
+
+<!--
+  This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+-->
+{{ MACROS___make_glossary() }}
diff --git a/src/schema/objects/associated_data.yaml b/src/schema/objects/associated_data.yaml
index 50fa80247c..901e17bdac 100644
--- a/src/schema/objects/associated_data.yaml
+++ b/src/schema/objects/associated_data.yaml
@@ -10,7 +10,8 @@ code:
     source data.
 derivatives:
   name: Derivative data
-  description:
+  description: |
+    Derivative data
 sourcedata:
   name: Source data
   description: |
diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml
index f17e8feb9f..1366f66da9 100644
--- a/src/schema/objects/datatypes.yaml
+++ b/src/schema/objects/datatypes.yaml
@@ -37,4 +37,5 @@ perf:
     Blood perfusion imaging data, including arterial spin labeling (ASL)
 pet:
   name: Positron Emission Tomography
-  description:
+  description: |
+    Positron emission tomography data
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 873f69a357..f8118c6351 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -104,7 +104,8 @@ AnatomicalLandmarkCoordinates:
       type: number
     minItems: 3
     maxItems: 3
-AnatomicalLandmarkCoordinates_mri:
+# Redefinition of AnatomicalLandmarkCoordinates for MRI data
+AnatomicalLandmarkCoordinates__mri:
   name: AnatomicalLandmarkCoordinates
   description: |
     Key:value pairs of any number of additional anatomical landmarks and their
@@ -682,7 +683,8 @@ EchoTime2:
   type: number
   unit: s
   exclusiveMinimum: 0
-EchoTime_fmap:
+# Redefinition of EchoTime for fieldmap data
+EchoTime__fmap:
   name: EchoTime
   description: |
     The time (in seconds) when the echo corresponding to this map was acquired.
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index 2cfa5e4b78..0531203e24 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -70,6 +70,21 @@ def make_entity_definitions():
     return text
 
 
+def make_glossary():
+    """Generate glossary.
+
+    Returns
+    -------
+    text : str
+        A multiline string containing descriptions and some formatting
+        information about the entities in the schema.
+    """
+    schemapath = utils.get_schema_path()
+    schema_obj = schema.load_schema(schemapath)
+    text = schema.make_glossary(schema_obj)
+    return text
+
+
 def make_suffix_table(suffixes):
     """Generate a markdown table of suffix information.
 
diff --git a/tools/mkdocs_macros_bids/main.py b/tools/mkdocs_macros_bids/main.py
index 8db94a0411..56c1d725ed 100644
--- a/tools/mkdocs_macros_bids/main.py
+++ b/tools/mkdocs_macros_bids/main.py
@@ -35,6 +35,7 @@ def define_env(env):
         macros.make_entity_definitions,
         "MACROS___make_entity_definitions",
     )
+    env.macro(macros.make_glossary, "MACROS___make_glossary")
     env.macro(macros.make_suffix_table, "MACROS___make_suffix_table")
     env.macro(macros.make_metadata_table, "MACROS___make_metadata_table")
     env.macro(macros.make_columns_table, "MACROS___make_columns_table")
diff --git a/tools/schemacode/schema.py b/tools/schemacode/schema.py
index f4ec722d69..77529e45d5 100644
--- a/tools/schemacode/schema.py
+++ b/tools/schemacode/schema.py
@@ -13,6 +13,9 @@
 
 from . import utils
 
+# import utils
+
+
 lgr = utils.get_logger()
 # Basic settings for output, for now just basic
 utils.set_logger_level(
@@ -208,6 +211,81 @@ def make_entity_definitions(schema):
     return text
 
 
+def make_glossary(schema):
+    """Generate glossary.
+
+    Parameters
+    ----------
+    schema : dict
+        The schema object, which is a dictionary with nested dictionaries and
+        lists stored within it.
+
+    Returns
+    -------
+    text : str
+        A string containing descriptions and some formatting
+        information about the entities in the schema.
+    """
+    all_objects = {}
+
+    for group, group_objects in schema["objects"].items():
+        group_obj_keys = list(group_objects.keys())
+        # Remove private objects
+        group_obj_keys = [k for k in group_obj_keys if not k.startswith("_")]
+
+        multi_sense_objects = []
+        # Identify multi-sense objects (multiple entries, some with __ in them)
+        for key in group_obj_keys:
+            if "__" in key:
+                temp_key = key.split("__")[0]
+                multi_sense_objects.append(temp_key)
+
+        multi_sense_objects = sorted(list(set(multi_sense_objects)))
+        sense_keys = {mso: [] for mso in multi_sense_objects}
+
+        for key in group_obj_keys:
+            for sense_key in sense_keys.keys():
+                if (key == sense_key) or (key.startswith(sense_key + "__")):
+                    sense_keys[sense_key].append(key)
+
+        sense_names = {}
+        for sense_key, key_list in sense_keys.items():
+            for i_key, key in enumerate(key_list):
+                new_key_name = f"{sense_key} _sense {i_key + 1}_"
+                sense_names[key] = new_key_name
+
+        for key in group_obj_keys:
+            new_name = sense_names.get(key, key)
+            new_name = f"{new_name} ({group})"
+            all_objects[new_name] = {}
+            all_objects[new_name]["key"] = f"objects.{group}.{key}"
+            all_objects[new_name]["definition"] = group_objects[key]
+
+    text = ""
+    for obj_key in sorted(all_objects.keys()):
+        obj = all_objects[obj_key]
+        obj_marker = obj["key"]
+        obj_def = obj["definition"]
+        obj_name = obj_def["name"]
+        obj_desc = obj_def["description"]
+        # A backslash before a newline means continue a string
+        obj_desc = obj_desc.replace("\\\n", "")
+        # Two newlines should be respected
+        obj_desc = obj_desc.replace("\n\n", "<br>")
+        # Otherwise a newline corresponds to a space
+        obj_desc = obj_desc.replace("\n", " ")
+
+        text += f'\n<a name="{obj_marker}"></a>'
+        text += f"\n## {obj_key}\n\n"
+        text += f"name: {obj_name}\n\n"
+        text += f"description:\n>{obj_desc}\n\n"
+
+        temp_obj_def = {k: v for k, v in obj_def.items() if k not in ("description", "name")}
+        text += f"schema information:\n```yaml\n{temp_obj_def}\n```"
+
+    return text
+
+
 def _add_entity(filename_template, entity_pattern, requirement_level):
     """Add entity pattern to filename template based on requirement level."""
     if requirement_level == "required":

From 97db196afa203baccfc67e8a091efd2488764c5a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 15 Dec 2021 11:07:22 -0500
Subject: [PATCH 105/347] [MAINT] Update links to starter kit website (#957)

* [MAINT] Upate link to starter kit website

* MAINT: Update ToC for starter kit
---
 mkdocs.yml   | 4 ++--
 src/index.md | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index 96b856c6db..08f809aa0e 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -62,6 +62,6 @@ nav:
         - Glossary: 99-appendices/14-glossary.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
+      - Website: https://bids-standard.github.io/bids-starter-kit
+      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
-      - Tutorials: https://github.com/bids-standard/bids-starter-kit/wiki/Tutorials
-      - Wiki: https://github.com/bids-standard/bids-starter-kit/wiki
diff --git a/src/index.md b/src/index.md
index 3cb10529d8..cfe83401e7 100644
--- a/src/index.md
+++ b/src/index.md
@@ -4,6 +4,6 @@ This resource defines the Brain Imaging Data Structure (BIDS) specification, inc
 
 To get started, [check out the introduction](01-introduction.md). If you'd like
 more information on how to adapt your own datasets to match the BIDS
-specification, we recommend exploring the [bids-specification starter kit](https://github.com/bids-standard/bids-starter-kit).
+specification, we recommend exploring the [BIDS Starter Kit](https://bids-standard.github.io/bids-starter-kit/)
 
 For an overview of the BIDS ecosystem, visit the [BIDS homepage](https://bids.neuroimaging.io).  The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.3686061).

From 74b5e3197b7650b06824c7c10c239761135e439d Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 15 Dec 2021 11:12:09 -0500
Subject: [PATCH 106/347] ENH: Link schema code into package

---
 tools/schemacode/schemacode/data/schema |  1 +
 tools/schemacode/setup.cfg              | 10 +++++-----
 2 files changed, 6 insertions(+), 5 deletions(-)
 create mode 120000 tools/schemacode/schemacode/data/schema

diff --git a/tools/schemacode/schemacode/data/schema b/tools/schemacode/schemacode/data/schema
new file mode 120000
index 0000000000..a06955547a
--- /dev/null
+++ b/tools/schemacode/schemacode/data/schema
@@ -0,0 +1 @@
+../../../../src/schema
\ No newline at end of file
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
index 821d22c1ef..3d9e3419fa 100644
--- a/tools/schemacode/setup.cfg
+++ b/tools/schemacode/setup.cfg
@@ -43,6 +43,11 @@ all =
     %(doc)s
     %(tests)s
 
+[options.package_data]
+schemacode =
+    data/schema/*/*.yaml
+    data/schema/*/*/*.yaml
+
 [versioneer]
 VCS = git
 style = pep440
@@ -60,8 +65,3 @@ per-file-ignores =
 
 [tool:pytest]
 log_cli = true
-
-[options.package_data]
-* =
-    resources/*
-    tests/data/*

From 89115cd9ef0d4676ae78cfa1e9e78fa1048869a2 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 15 Dec 2021 16:17:00 +0000
Subject: [PATCH 107/347] [DOC] Auto-generate changelog entry for PR #955

---
 src/CHANGES.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index a774a6f262..41ad4f92aa 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,8 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MAINT] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies))
+-   \[FIX] Entity table: Clarify meaning of empty cells [#955](https://github.com/bids-standard/bids-specification/pull/955) ([Lestropie](https://github.com/Lestropie))
 -   \[MISC] Add Eric Earl as a Maintainer [#953](https://github.com/bids-standard/bids-specification/pull/953) ([ericearl](https://github.com/ericearl))
 -   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
 -   \[FIX] Broken hyperlink in entity list file [#949](https://github.com/bids-standard/bids-specification/pull/949) ([Lestropie](https://github.com/Lestropie))
@@ -16,6 +18,7 @@
 -   \[INFRA] Run linkchecker in stock docker image [#932](https://github.com/bids-standard/bids-specification/pull/932) ([effigies](https://github.com/effigies))
 -   \[INFRA] add (optional) pre-commit config file [#929](https://github.com/bids-standard/bids-specification/pull/929) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Clarify that EDF/BDF files MUST have lower case extensions in BIDS [#927](https://github.com/bids-standard/bids-specification/pull/927) ([adam2392](https://github.com/adam2392))
+-   \[ENH] Generate glossary page from schema [#923](https://github.com/bids-standard/bids-specification/pull/923) ([tsalo](https://github.com/tsalo))
 -   \[ENH] add `hemi` entity to schema [#917](https://github.com/bids-standard/bids-specification/pull/917) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] PDF version of spec: fix handling of internal links [#915](https://github.com/bids-standard/bids-specification/pull/915) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] update and reformat table for template in coordinate system page [#903](https://github.com/bids-standard/bids-specification/pull/903) ([Remi-Gau](https://github.com/Remi-Gau))

From af516d8b342513ec965e6e1522250f1db20eac39 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 15 Dec 2021 11:19:34 -0500
Subject: [PATCH 108/347] RF: Use packaged schema

---
 tools/schemacode/schemacode/utils.py | 5 +----
 tools/schemacode/setup.cfg           | 3 ++-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index a2a033bf3b..3380016796 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -14,10 +14,7 @@ def get_schema_path():
     str
         Absolute path to the folder containing schema-related files.
     """
-    schema_dir = op.abspath(
-        op.join(op.dirname(op.dirname(op.dirname(op.dirname(__file__)))), "src", "schema") + op.sep
-    )
-    return schema_dir
+    return op.abspath(op.join(op.dirname(__file__), "data", "schema"))
 
 
 def combine_extensions(lst):
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
index 3d9e3419fa..59d4889d92 100644
--- a/tools/schemacode/setup.cfg
+++ b/tools/schemacode/setup.cfg
@@ -25,7 +25,8 @@ install_requires =
     tabulate
     pyyaml
 packages = find:
-include_package_data = False
+include_package_data = false
+zip_safe = false
 
 [options.extras_require]
 doc =

From fadc12c0e605c9345653f8fe05249d145fb58bac Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 15 Dec 2021 11:27:47 -0500
Subject: [PATCH 109/347] MNT: Require schemacode package to build docs

---
 requirements.txt | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 806c28a3c1..92fa48536f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,4 @@ mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3
 mkdocs-macros-plugin
-numpy
-pandas
-PYYaml
-tabulate
+tools/schemacode/

From 61b13feac33762625f9df765449f8153ae6fd5f0 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 15 Dec 2021 11:58:52 -0500
Subject: [PATCH 110/347] Fix locations of functions.

---
 tools/mkdocs_macros_bids/macros.py | 5 ++---
 tools/schemacode/pyproject.toml    | 2 --
 tools/schemacode/setup.py          | 5 +++--
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index d36e488d0d..6f4363fbff 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -8,7 +8,6 @@
 sys.path.append(code_path)
 
 from examplecode import example
-from schemacode import schema, utils
 
 
 def make_filename_template(**kwargs):
@@ -83,7 +82,7 @@ def make_glossary():
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    text = schema.make_glossary(schema_obj)
+    text = render.make_glossary(schema_obj)
     return text
 
 
@@ -153,7 +152,7 @@ def make_columns_table(column_info):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_columns_table(schema_obj, column_info)
+    table = render.make_columns_table(schema_obj, column_info)
     return table
 
 
diff --git a/tools/schemacode/pyproject.toml b/tools/schemacode/pyproject.toml
index d362784a8c..2568b7167e 100644
--- a/tools/schemacode/pyproject.toml
+++ b/tools/schemacode/pyproject.toml
@@ -17,9 +17,7 @@ exclude = '''
     | build
     | dist
   )/
-  | get_version.py
   | versioneer.py
-  | schemacode/info.py
   | schemacode/_version.py
 )
 '''
diff --git a/tools/schemacode/setup.py b/tools/schemacode/setup.py
index b50d479bf2..a3d81a9ce2 100644
--- a/tools/schemacode/setup.py
+++ b/tools/schemacode/setup.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 import sys
+
 from setuptools import setup
+
 import versioneer
 
 # Give setuptools a hint to complain if it's too old a version
@@ -11,8 +13,7 @@
 SETUP_REQUIRES += ['wheel'] if 'bdist_wheel' in sys.argv else []
 
 if __name__ == '__main__':
-    setup(name="pybids",
+    setup(name="schemacode",
           version=versioneer.get_version(),
           cmdclass=versioneer.get_cmdclass(),
           setup_requires=SETUP_REQUIRES)
-

From 43c7a370f45220e71d3bd6ddc003f0057262b061 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 15 Dec 2021 13:12:00 -0500
Subject: [PATCH 111/347] Add a couple of tests.

---
 tools/schemacode/schemacode/render.py            |  3 ---
 tools/schemacode/schemacode/tests/conftest.py    | 12 +++++++++---
 tools/schemacode/schemacode/tests/test_schema.py | 16 ++++++++++++++++
 3 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index 0f78c2ef73..b4954d3321 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -8,9 +8,6 @@
 from . import utils
 from .schema import filter_schema
 
-# import utils
-
-
 lgr = utils.get_logger()
 # Basic settings for output, for now just basic
 utils.set_logger_level(
diff --git a/tools/schemacode/schemacode/tests/conftest.py b/tools/schemacode/schemacode/tests/conftest.py
index 7737987903..5bc4f2dc9e 100644
--- a/tools/schemacode/schemacode/tests/conftest.py
+++ b/tools/schemacode/schemacode/tests/conftest.py
@@ -1,10 +1,16 @@
-from pathlib import Path
-
 import pytest
 
+from schemacode import schema, utils
+
 
 @pytest.fixture(scope="session")
 def schema_dir():
     """Path to the schema housed in the bids-specification repo."""
-    bids_schema = Path(__file__).parent.parent.parent.parent.parent / "src" / "schema"
+    bids_schema = utils.get_schema_path()
     return bids_schema
+
+
+@pytest.fixture(scope="session")
+def schema_obj(schema_dir):
+    """Schema object."""
+    return schema.load_schema(schema_dir)
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
index f44e868729..5d1400a778 100644
--- a/tools/schemacode/schemacode/tests/test_schema.py
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -5,9 +5,25 @@
 
 
 def test_load_schema(schema_dir):
+    """Smoke test for schemacode.schema.load_schema."""
+    # Pointing to a nonexistent folder should raise a ValueError
     bad_path = "/path/to/nowhere"
     with pytest.raises(ValueError):
         schema.load_schema(bad_path)
 
+    # Otherwise the function should return a dictionary
     schema_obj = schema.load_schema(schema_dir)
     assert isinstance(schema_obj, dict)
+
+
+def test_object_definitions(schema_obj):
+    """Ensure that object definitions in the schema contain required fields."""
+    for obj_type, obj_type_def in schema_obj["objects"].items():
+        for obj_key, obj_def in obj_type_def.items():
+            # Private/inheritable definitions (ones starting with "_") do not need to conform to
+            # the same rules as user-facing terms, so we skip them
+            if obj_key.startswith("_"):
+                continue
+
+            assert "name" in obj_def.keys(), obj_key
+            assert "description" in obj_def.keys(), obj_key

From 3b54a6123da0d1f5032e149adf0b3c48dde3aca6 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 15 Dec 2021 13:26:35 -0500
Subject: [PATCH 112/347] Draft a couple more tests.

---
 .../schemacode/schemacode/tests/test_utils.py | 30 +++++++++++++++++++
 tools/schemacode/schemacode/utils.py          | 13 +++++++-
 2 files changed, 42 insertions(+), 1 deletion(-)
 create mode 100644 tools/schemacode/schemacode/tests/test_utils.py

diff --git a/tools/schemacode/schemacode/tests/test_utils.py b/tools/schemacode/schemacode/tests/test_utils.py
new file mode 100644
index 0000000000..dc2773e8c6
--- /dev/null
+++ b/tools/schemacode/schemacode/tests/test_utils.py
@@ -0,0 +1,30 @@
+from schemacode import utils
+
+
+def test_combine_extensions():
+    """A unit test for utils.combine_extensions."""
+    test_extensions = ["nii.gz", "nii", "json"]
+    target_combined = ["nii[.gz]", "json"]
+    test_combined = utils.combine_extensions(test_extensions)
+    assert test_combined == target_combined
+
+
+def test_resolve_metadata_type():
+    """A unit test for utils.resolve_metadata_type."""
+    base_definition = {
+        "name": "Term",
+        "description": "A description",
+    }
+
+    # Basic string
+    term_definition1 = base_definition.copy()
+    term_definition1["type"] = "string"
+    target_description = "[string](https://www.w3schools.com/js/js_json_datatypes.asp)"
+    type_description = utils.resolve_metadata_type(term_definition1)
+    assert target_description == type_description
+
+    # When n/a is the only allowed value, the type should say "n/a"
+    term_definition1["enum"] = ["n/a"]
+    target_description = '`"n/a"`'
+    type_description = utils.resolve_metadata_type(term_definition1)
+    assert target_description == type_description
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 3380016796..d593b9ff3c 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -151,7 +151,18 @@ def get_link(string):
 
 
 def resolve_metadata_type(definition):
-    """Generate string of metadata type from dictionary."""
+    """Generate string of metadata type from dictionary.
+
+    Parameters
+    ----------
+    definition : :obj:`dict`
+        A schema object definition for a metadata term.
+
+    Returns
+    -------
+    string : :obj:`str`
+        A string describing the valid value types for the metadata term.
+    """
     if "type" in definition.keys():
         string = get_link(definition["type"])
 

From 376fbcb382349370b004b3e4ca68af9e23be5698 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 10:43:50 -0500
Subject: [PATCH 113/347] Draft Action for schemacode CI.

I based this one off of a similar Action in nilearn. It'll probably require some debugging...
---
 .github/workflows/schemacode_ci.yml | 64 +++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 .github/workflows/schemacode_ci.yml

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
new file mode 100644
index 0000000000..563ef094dd
--- /dev/null
+++ b/.github/workflows/schemacode_ci.yml
@@ -0,0 +1,64 @@
+name: "schemacode_ci"
+
+on:
+  push:
+    branches:
+      - "master"
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  check_skip:
+    runs-on: ubuntu-latest
+    outputs:
+      skip: ${{ steps.result_step.outputs.ci-skip }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - id: result_step
+        uses: mstachniuk/ci-skip@master
+        with:
+          commit-filter: "[skip ci];[ci skip];[skip github]"
+          commit-filter-separator: ";"
+
+  latest:
+    needs: check_skip
+    if: ${{ needs.check_skip.outputs.skip == 'false' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+            python-version: ["3.8"]
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v2
+        with:
+            python-version: ${{ matrix.python-version }}
+
+      - name: "Display Python version"
+        shell: bash {0}
+        run: python -c "import sys; print(sys.version)"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel flake8
+          python -m pip install ./tools/schemacode/
+
+      - name: "Run tests"
+        shell: bash {0}
+        run: |
+          python -m pytest --pyargs schemacode --cov=schemacode ./tools/schemacode/
+
+      - name: "Upload coverage to CodeCov"
+        uses: codecov/codecov-action@v1
+        if: success()

From 1332c9e0304d391f8822be93cae234b81ea3f312 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 10:46:33 -0500
Subject: [PATCH 114/347] Fix installation.

---
 .github/workflows/schemacode_ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 563ef094dd..667e22f066 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -51,8 +51,8 @@ jobs:
       - name: "Install the schemacode package"
         shell: bash {0}
         run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel flake8
-          python -m pip install ./tools/schemacode/
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install ./tools/schemacode[tests]
 
       - name: "Run tests"
         shell: bash {0}

From 78581065d4394c0fe0d71461ac3ab14f47df11c3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 10:50:38 -0500
Subject: [PATCH 115/347] Update schemacode_ci.yml

---
 .github/workflows/schemacode_ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 667e22f066..e654a2218e 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -52,7 +52,7 @@ jobs:
         shell: bash {0}
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
-          python -m pip install ./tools/schemacode[tests]
+          python -m pip install -e ./tools/schemacode[tests]
 
       - name: "Run tests"
         shell: bash {0}

From 2e48e7d8793cc94790fa029abd5bc0c354596691 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 10:54:54 -0500
Subject: [PATCH 116/347] Add badge.

---
 tools/schemacode/README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/schemacode/README.md b/tools/schemacode/README.md
index e2b682a800..0781fd5e8d 100644
--- a/tools/schemacode/README.md
+++ b/tools/schemacode/README.md
@@ -1,3 +1,5 @@
 # schemacode
 
 A Python library for working with the BIDS schema.
+
+[![codecov](https://codecov.io/gh/bids-standard/bids-specification/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-specification)

From 963ad6171a05436e8f64bb00a7179de305d449da Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 11:16:37 -0500
Subject: [PATCH 117/347] Add schema-related files to the CODEOWNERS file.

---
 CODEOWNERS | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CODEOWNERS b/CODEOWNERS
index 5dbad3bf60..24cc697363 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -18,3 +18,7 @@
 /src/05-derivatives/05-functional-derivatives.md @effigies
 /src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 /src/99-appendices/06-meg-file-formats.md @monkeyman192
+
+# The schema
+/src/schema/ @tsalo
+/tools/schemacode/ @tsalo

From 31bcd196b601481b73c5c6f1101d9f60cdb37fc9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 14:21:39 -0500
Subject: [PATCH 118/347] Run versioneer 0.21 instead of 0.18 and run black.

---
 .gitattributes                          |   1 +
 tools/schemacode/MANIFEST.in            |   1 +
 tools/schemacode/schemacode/__init__.py |   4 +
 tools/schemacode/schemacode/_version.py | 368 ++++++----
 tools/schemacode/schemacode/render.py   |  26 +-
 tools/schemacode/schemacode/schema.py   |   8 +-
 tools/schemacode/schemacode/utils.py    |   7 +-
 tools/schemacode/setup.py               |  16 +-
 tools/schemacode/versioneer.py          | 935 +++++++++++++++---------
 9 files changed, 833 insertions(+), 533 deletions(-)

diff --git a/.gitattributes b/.gitattributes
index 2bd791b40d..d2563f43d1 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -2,3 +2,4 @@
 *.png -text
 *.jpg -text
 *.webm -text
+tools/schemacode/schemacode/_version.py export-subst
diff --git a/tools/schemacode/MANIFEST.in b/tools/schemacode/MANIFEST.in
index a24694ff41..c67a6ea54b 100644
--- a/tools/schemacode/MANIFEST.in
+++ b/tools/schemacode/MANIFEST.in
@@ -1 +1,2 @@
 include versioneer.py
+include schemacode/_version.py
diff --git a/tools/schemacode/schemacode/__init__.py b/tools/schemacode/schemacode/__init__.py
index d01d8a33d3..a00379421a 100644
--- a/tools/schemacode/schemacode/__init__.py
+++ b/tools/schemacode/schemacode/__init__.py
@@ -6,3 +6,7 @@
     "schema",
     "utils",
 ]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]
diff --git a/tools/schemacode/schemacode/_version.py b/tools/schemacode/schemacode/_version.py
index 8c0102e67f..537930fbb8 100644
--- a/tools/schemacode/schemacode/_version.py
+++ b/tools/schemacode/schemacode/_version.py
@@ -1,3 +1,4 @@
+
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -5,7 +6,7 @@
 # that just contains the computed version number.
 
 # This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# versioneer-0.21 (https://github.com/python-versioneer/python-versioneer)
 
 """Git implementation of _version.py."""
 
@@ -14,6 +15,7 @@
 import re
 import subprocess
 import sys
+from typing import Callable, Dict
 
 
 def get_keywords():
@@ -40,7 +42,7 @@ def get_config():
     cfg = VersioneerConfig()
     cfg.VCS = "git"
     cfg.style = "pep440"
-    cfg.tag_prefix = ""
+    cfg.tag_prefix = "v"
     cfg.parentdir_prefix = ""
     cfg.versionfile_source = "schemacode/_version.py"
     cfg.verbose = False
@@ -51,40 +53,36 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-
+    """Create decorator to mark a method as the handler of a VCS."""
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
-
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-            )
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None))
             break
-        except EnvironmentError:
+        except OSError:
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -96,15 +94,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
         if verbose:
             print("unable to find command, tried %s" % (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
             print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
 def versions_from_parentdir(parentdir_prefix, root, verbose):
@@ -116,25 +112,18 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {
-                "version": dirname[len(parentdir_prefix) :],
-                "full-revisionid": None,
-                "dirty": False,
-                "error": None,
-                "date": None,
-            }
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
-        )
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -147,22 +136,21 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
@@ -170,10 +158,14 @@ def git_get_keywords(versionfile_abs):
 @register_vcs_handler("git", "keywords")
 def git_versions_from_keywords(keywords, tag_prefix, verbose):
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -186,11 +178,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -199,7 +191,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r"\d", r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -207,30 +199,28 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
-            return {
-                "version": r,
-                "full-revisionid": keywords["full"].strip(),
-                "dirty": False,
-                "error": None,
-                "date": date,
-            }
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {
-        "version": "0+unknown",
-        "full-revisionid": keywords["full"].strip(),
-        "dirty": False,
-        "error": "no suitable tags",
-        "date": None,
-    }
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -238,10 +228,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
+    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
+        TAG_PREFIX_REGEX = r"\*"
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -249,24 +242,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(
-        GITS,
-        [
-            "describe",
-            "--tags",
-            "--dirty",
-            "--always",
-            "--long",
-            "--match",
-            "%s*" % tag_prefix,
-        ],
-        cwd=root,
-    )
+    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
+                                     "--always", "--long",
+                                     "--match",
+                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
+                              cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
@@ -276,6 +261,39 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -284,16 +302,17 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[: git_describe.rindex("-dirty")]
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
             return pieces
 
         # tag
@@ -302,12 +321,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
-                full_tag,
-                tag_prefix,
-            )
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -318,11 +335,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
+        count_out, rc = runner(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
@@ -353,25 +373,74 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces):
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver):
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces):
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version+1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0.post0.dev%d" % pieces["distance"]
     return rendered
 
 
@@ -402,12 +471,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
+def render_pep440_post_branch(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
 def render_pep440_old(pieces):
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -467,23 +565,25 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {
-            "version": "unknown",
-            "full-revisionid": pieces.get("long"),
-            "dirty": None,
-            "error": pieces["error"],
-            "date": None,
-        }
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
 
     if not style or style == "default":
         style = "pep440"  # the default
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -493,13 +593,9 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
 
 
 def get_versions():
@@ -513,7 +609,8 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
     except NotThisMethod:
         pass
 
@@ -522,16 +619,13 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split("/"):
+        for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
-        return {
-            "version": "0+unknown",
-            "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to find root of source tree",
-            "date": None,
-        }
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -545,10 +639,6 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index b4954d3321..47f44a2113 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -10,9 +10,7 @@
 
 lgr = utils.get_logger()
 # Basic settings for output, for now just basic
-utils.set_logger_level(
-    lgr, os.environ.get("BIDS_SCHEMA_LOG_LEVEL", logging.INFO)
-)
+utils.set_logger_level(lgr, os.environ.get("BIDS_SCHEMA_LOG_LEVEL", logging.INFO))
 logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
 
 
@@ -227,16 +225,12 @@ def make_filename_template(schema, **kwargs):
                 string += suffix
                 strings = [string]
             else:
-                strings = [
-                    string + "_" + suffix for suffix in group["suffixes"]
-                ]
+                strings = [string + "_" + suffix for suffix in group["suffixes"]]
 
             # Add extensions
             full_strings = []
             extensions = group["extensions"]
-            extensions = [
-                ext if ext != "*" else ".<extension>" for ext in extensions
-            ]
+            extensions = [ext if ext != "*" else ".<extension>" for ext in extensions]
             extensions = utils.combine_extensions(extensions)
             if len(extensions) > 5:
                 # Combine exts when there are many, but keep JSON separate
@@ -426,11 +420,7 @@ def make_suffix_table(schema, suffixes, tablefmt="github"):
     suffixes_found = [f for f in suffixes if f in suffix_schema.keys()]
     suffixes_not_found = [f for f in suffixes if f not in suffix_schema.keys()]
     if suffixes_not_found:
-        raise Exception(
-            "Warning: Missing suffixes: {}".format(
-                ", ".join(suffixes_not_found)
-            )
-        )
+        raise Exception("Warning: Missing suffixes: {}".format(", ".join(suffixes_not_found)))
 
     df = pd.DataFrame(
         index=suffixes_found,
@@ -513,9 +503,7 @@ def make_metadata_table(schema, field_info, tablefmt="github"):
 
         type_string = utils.resolve_metadata_type(metadata_schema[field])
 
-        description = (
-            metadata_schema[field]["description"] + " " + description_addendum
-        )
+        description = metadata_schema[field]["description"] + " " + description_addendum
         # A backslash before a newline means continue a string
         description = description.replace("\\\n", "")
         # Two newlines should be respected
@@ -584,9 +572,7 @@ def make_columns_table(schema, column_info, tablefmt="github"):
 
         type_string = utils.resolve_metadata_type(column_schema[field])
 
-        description = (
-            column_schema[field]["description"] + " " + description_addendum
-        )
+        description = column_schema[field]["description"] + " " + description_addendum
         # A backslash before a newline means continue a string
         description = description.replace("\\\n", "")
         # Two newlines should be respected
diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index efb976e491..805a4f5177 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -12,9 +12,7 @@
 
 lgr = utils.get_logger()
 # Basic settings for output, for now just basic
-utils.set_logger_level(
-    lgr, os.environ.get("BIDS_SCHEMA_LOG_LEVEL", logging.INFO)
-)
+utils.set_logger_level(lgr, os.environ.get("BIDS_SCHEMA_LOG_LEVEL", logging.INFO))
 logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
 
 
@@ -151,9 +149,7 @@ def filter_schema(schema, **kwargs):
             if k in new_schema.keys():
                 filtered_item = deepcopy(new_schema[k])
                 if isinstance(filtered_item, dict):
-                    filtered_item = {
-                        k1: v1 for k1, v1 in filtered_item.items() if k1 in v
-                    }
+                    filtered_item = {k1: v1 for k1, v1 in filtered_item.items() if k1 in v}
                 else:
                     filtered_item = [i for i in filtered_item if i in v]
                 new_schema[k] = filtered_item
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index d593b9ff3c..3b25b2cd61 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -176,14 +176,11 @@ def resolve_metadata_type(definition):
 
         elif "type" in definition.get("additionalProperties", {}):
             # Values within objects
-            string += " of " + get_link(
-                definition["additionalProperties"]["type"] + "s"
-            )
+            string += " of " + get_link(definition["additionalProperties"]["type"] + "s")
 
     elif "anyOf" in definition:
         # Use dictionary to get unique substrings while preserving insertion order
-        substrings = {resolve_metadata_type(subdict): None
-                      for subdict in definition["anyOf"]}
+        substrings = {resolve_metadata_type(subdict): None for subdict in definition["anyOf"]}
 
         string = " or ".join(substrings)
 
diff --git a/tools/schemacode/setup.py b/tools/schemacode/setup.py
index a3d81a9ce2..26ade778c2 100644
--- a/tools/schemacode/setup.py
+++ b/tools/schemacode/setup.py
@@ -8,12 +8,14 @@
 # Give setuptools a hint to complain if it's too old a version
 # 30.3.0 allows us to put most metadata in setup.cfg
 # Should match pyproject.toml
-SETUP_REQUIRES = ['setuptools >= 30.3.0']
+SETUP_REQUIRES = ["setuptools >= 30.3.0"]
 # This enables setuptools to install wheel on-the-fly
-SETUP_REQUIRES += ['wheel'] if 'bdist_wheel' in sys.argv else []
+SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
 
-if __name__ == '__main__':
-    setup(name="schemacode",
-          version=versioneer.get_version(),
-          cmdclass=versioneer.get_cmdclass(),
-          setup_requires=SETUP_REQUIRES)
+if __name__ == "__main__":
+    setup(
+        name="schemacode",
+        version=versioneer.get_version(),
+        cmdclass=versioneer.get_cmdclass(),
+        setup_requires=SETUP_REQUIRES,
+    )
diff --git a/tools/schemacode/versioneer.py b/tools/schemacode/versioneer.py
index 323046a244..b4cd1d6c7c 100644
--- a/tools/schemacode/versioneer.py
+++ b/tools/schemacode/versioneer.py
@@ -1,4 +1,5 @@
-# Version: 0.18
+
+# Version: 0.21
 
 """The Versioneer - like a rocketeer, but for versions.
 
@@ -6,16 +7,12 @@
 ==============
 
 * like a rocketeer, but for versions!
-* https://github.com/warner/python-versioneer
+* https://github.com/python-versioneer/python-versioneer
 * Brian Warner
 * License: Public Domain
-* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
-* [![Latest Version]
-(https://pypip.in/version/versioneer/badge.svg?style=flat)
-](https://pypi.python.org/pypi/versioneer/)
-* [![Build Status]
-(https://travis-ci.org/warner/python-versioneer.png?branch=master)
-](https://travis-ci.org/warner/python-versioneer)
+* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
+* [![Latest Version][pypi-image]][pypi-url]
+* [![Build Status][travis-image]][travis-url]
 
 This is a tool for managing a recorded version number in distutils-based
 python projects. The goal is to remove the tedious and error-prone "update
@@ -26,9 +23,10 @@
 
 ## Quick Install
 
-* `pip install versioneer` to somewhere to your $PATH
-* add a `[versioneer]` section to your setup.cfg (see below)
+* `pip install versioneer` to somewhere in your $PATH
+* add a `[versioneer]` section to your setup.cfg (see [Install](INSTALL.md))
 * run `versioneer install` in your source tree, commit the results
+* Verify version information with `python setup.py version`
 
 ## Version Identifiers
 
@@ -60,7 +58,7 @@
 for example `git describe --tags --dirty --always` reports things like
 "0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
 0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
-uncommitted changes.
+uncommitted changes).
 
 The version identifier is used for multiple purposes:
 
@@ -165,7 +163,7 @@
 
 Some situations are known to cause problems for Versioneer. This details the
 most significant ones. More can be found on Github
-[issues page](https://github.com/warner/python-versioneer/issues).
+[issues page](https://github.com/python-versioneer/python-versioneer/issues).
 
 ### Subprojects
 
@@ -193,9 +191,9 @@
 Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
 some later version.
 
-[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
+[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking
 this issue. The discussion in
-[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
+[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the
 issue from the Versioneer side in more detail.
 [pip PR#3176](https://github.com/pypa/pip/pull/3176) and
 [pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
@@ -223,22 +221,10 @@
 cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
 a different virtualenv), so this can be surprising.
 
-[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
+[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes
 this one, but upgrading to a newer version of setuptools should probably
 resolve it.
 
-### Unicode version strings
-
-While Versioneer works (and is continually tested) with both Python 2 and
-Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
-Newer releases probably generate unicode version strings on py2. It's not
-clear that this is wrong, but it may be surprising for applications when then
-write these strings to a network connection or include them in bytes-oriented
-APIs like cryptographic checksums.
-
-[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
-this question.
-
 
 ## Updating Versioneer
 
@@ -264,6 +250,14 @@
 direction and include code from all supported VCS systems, reducing the
 number of intermediate scripts.
 
+## Similar projects
+
+* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time
+  dependency
+* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of
+  versioneer
+* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools
+  plugin
 
 ## License
 
@@ -273,21 +267,27 @@
 Dedication" license (CC0-1.0), as described in
 https://creativecommons.org/publicdomain/zero/1.0/ .
 
-"""
-
-from __future__ import print_function
+[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg
+[pypi-url]: https://pypi.python.org/pypi/versioneer/
+[travis-image]:
+https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg
+[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer
 
-try:
-    import configparser
-except ImportError:
-    import ConfigParser as configparser
+"""
+# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring
+# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements
+# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error
+# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with
+# pylint:disable=attribute-defined-outside-init,too-many-arguments
 
+import configparser
 import errno
 import json
 import os
 import re
 import subprocess
 import sys
+from typing import Callable, Dict
 
 
 class VersioneerConfig:
@@ -309,13 +309,11 @@ def get_root():
         setup_py = os.path.join(root, "setup.py")
         versioneer_py = os.path.join(root, "versioneer.py")
     if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = (
-            "Versioneer was unable to run the project root directory. "
-            "Versioneer requires setup.py to be executed from "
-            "its immediate directory (like 'python setup.py COMMAND'), "
-            "or in a way that lets it use sys.argv[0] to find the root "
-            "(like 'python path/to/setup.py COMMAND')."
-        )
+        err = ("Versioneer was unable to run the project root directory. "
+               "Versioneer requires setup.py to be executed from "
+               "its immediate directory (like 'python setup.py COMMAND'), "
+               "or in a way that lets it use sys.argv[0] to find the root "
+               "(like 'python path/to/setup.py COMMAND').")
         raise VersioneerBadRootError(err)
     try:
         # Certain runtime workflows (setup.py install/develop in a setuptools
@@ -324,14 +322,12 @@ def get_root():
         # module-import table will cache the first one. So we can't use
         # os.path.dirname(__file__), as that will find whichever
         # versioneer.py was first imported, even in later projects.
-        me = os.path.realpath(os.path.abspath(__file__))
-        me_dir = os.path.normcase(os.path.splitext(me)[0])
+        my_path = os.path.realpath(os.path.abspath(__file__))
+        me_dir = os.path.normcase(os.path.splitext(my_path)[0])
         vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
         if me_dir != vsr_dir:
-            print(
-                "Warning: build in %s is using versioneer.py from %s"
-                % (os.path.dirname(me), versioneer_py)
-            )
+            print("Warning: build in %s is using versioneer.py from %s"
+                  % (os.path.dirname(my_path), versioneer_py))
     except NameError:
         pass
     return root
@@ -339,31 +335,29 @@ def get_root():
 
 def get_config_from_root(root):
     """Read the project setup.cfg file to determine Versioneer config."""
-    # This might raise EnvironmentError (if setup.cfg is missing), or
+    # This might raise OSError (if setup.cfg is missing), or
     # configparser.NoSectionError (if it lacks a [versioneer] section), or
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
-    with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+    parser = configparser.ConfigParser()
+    with open(setup_cfg, "r") as cfg_file:
+        parser.read_file(cfg_file)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
-    def get(parser, name):
-        if parser.has_option("versioneer", name):
-            return parser.get("versioneer", name)
-        return None
+    # Dict-like interface for non-mandatory entries
+    section = parser["versioneer"]
 
     cfg = VersioneerConfig()
     cfg.VCS = VCS
-    cfg.style = get(parser, "style") or ""
-    cfg.versionfile_source = get(parser, "versionfile_source")
-    cfg.versionfile_build = get(parser, "versionfile_build")
-    cfg.tag_prefix = get(parser, "tag_prefix")
+    cfg.style = section.get("style", "")
+    cfg.versionfile_source = section.get("versionfile_source")
+    cfg.versionfile_build = section.get("versionfile_build")
+    cfg.tag_prefix = section.get("tag_prefix")
     if cfg.tag_prefix in ("''", '""'):
         cfg.tag_prefix = ""
-    cfg.parentdir_prefix = get(parser, "parentdir_prefix")
-    cfg.verbose = get(parser, "verbose")
+    cfg.parentdir_prefix = section.get("parentdir_prefix")
+    cfg.verbose = section.get("verbose")
     return cfg
 
 
@@ -372,40 +366,34 @@ class NotThisMethod(Exception):
 
 
 # these dictionaries contain VCS-specific tools
-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-
+    """Create decorator to mark a method as the handler of a VCS."""
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
-        if vcs not in HANDLERS:
-            HANDLERS[vcs] = {}
-        HANDLERS[vcs][method] = f
+        HANDLERS.setdefault(vcs, {})[method] = f
         return f
-
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-            )
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None))
             break
-        except EnvironmentError:
+        except OSError:
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -417,20 +405,16 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
         if verbose:
             print("unable to find command, tried %s" % (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
             print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
-LONG_VERSION_PY[
-    "git"
-] = '''
+LONG_VERSION_PY['git'] = r'''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -438,7 +422,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
 # that just contains the computed version number.
 
 # This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# versioneer-0.21 (https://github.com/python-versioneer/python-versioneer)
 
 """Git implementation of _version.py."""
 
@@ -447,6 +431,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
 import re
 import subprocess
 import sys
+from typing import Callable, Dict
 
 
 def get_keywords():
@@ -484,12 +469,12 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
+    """Create decorator to mark a method as the handler of a VCS."""
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
@@ -503,17 +488,17 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
                 env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None))
             break
-        except EnvironmentError:
+        except OSError:
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -525,15 +510,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         if verbose:
             print("unable to find command, tried %%s" %% (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %%s (error)" %% dispcmd)
             print("stdout was %%s" %% stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
 def versions_from_parentdir(parentdir_prefix, root, verbose):
@@ -545,15 +528,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
             return {"version": dirname[len(parentdir_prefix):],
                     "full-revisionid": None,
                     "dirty": False, "error": None, "date": None}
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
         print("Tried directories %%s but none started with prefix %%s" %%
@@ -570,22 +552,21 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
@@ -593,10 +574,14 @@ def git_get_keywords(versionfile_abs):
 @register_vcs_handler("git", "keywords")
 def git_versions_from_keywords(keywords, tag_prefix, verbose):
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -609,11 +594,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %%d
@@ -622,7 +607,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%%s', no digits" %% ",".join(refs - tags))
     if verbose:
@@ -631,6 +616,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %%s" %% r)
             return {"version": r,
@@ -646,7 +636,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -654,11 +644,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
+    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
+        TAG_PREFIX_REGEX = r"\*"
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %%s not under git control" %% root)
@@ -666,15 +658,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%%s*" %% tag_prefix],
-                                   cwd=root)
+    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
+                                     "--always", "--long",
+                                     "--match",
+                                     "%%s%%s" %% (tag_prefix, TAG_PREFIX_REGEX)],
+                              cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
@@ -684,6 +677,39 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -725,13 +751,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
+        count_out, rc = runner(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
-                       cwd=root)[0].strip()
+    date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
@@ -769,19 +796,67 @@ def render_pep440(pieces):
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces):
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%%d.g%%s" %% (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver):
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces):
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%%d" %% pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%%d.dev%%d" %% (post_version+1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%%d" %% (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%%d" %% pieces["distance"]
+        rendered = "0.post0.dev%%d" %% pieces["distance"]
     return rendered
 
 
@@ -812,12 +887,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
+def render_pep440_post_branch(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%%s" %% pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%%s" %% pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
 def render_pep440_old(pieces):
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -888,10 +992,14 @@ def render(pieces, style):
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -927,7 +1035,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
+        for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
         return {"version": "0+unknown", "full-revisionid": None,
@@ -962,22 +1070,21 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
@@ -985,10 +1092,14 @@ def git_get_keywords(versionfile_abs):
 @register_vcs_handler("git", "keywords")
 def git_versions_from_keywords(keywords, tag_prefix, verbose):
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -1001,11 +1112,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -1014,7 +1125,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r"\d", r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -1022,30 +1133,28 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
-            return {
-                "version": r,
-                "full-revisionid": keywords["full"].strip(),
-                "dirty": False,
-                "error": None,
-                "date": date,
-            }
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {
-        "version": "0+unknown",
-        "full-revisionid": keywords["full"].strip(),
-        "dirty": False,
-        "error": "no suitable tags",
-        "date": None,
-    }
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -1053,10 +1162,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     version string, meaning we're inside a checked out source tree.
     """
     GITS = ["git"]
+    TAG_PREFIX_REGEX = "*"
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
+        TAG_PREFIX_REGEX = r"\*"
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -1064,24 +1176,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(
-        GITS,
-        [
-            "describe",
-            "--tags",
-            "--dirty",
-            "--always",
-            "--long",
-            "--match",
-            "%s*" % tag_prefix,
-        ],
-        cwd=root,
-    )
+    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
+                                     "--always", "--long",
+                                     "--match",
+                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
+                              cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
@@ -1091,6 +1195,39 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -1099,16 +1236,17 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[: git_describe.rindex("-dirty")]
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
             return pieces
 
         # tag
@@ -1117,12 +1255,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
-                full_tag,
-                tag_prefix,
-            )
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -1133,13 +1269,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
+        count_out, rc = runner(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
-        0
-    ].strip()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
@@ -1158,27 +1295,26 @@ def do_vcs_install(manifest_in, versionfile_source, ipy):
     if ipy:
         files.append(ipy)
     try:
-        me = __file__
-        if me.endswith(".pyc") or me.endswith(".pyo"):
-            me = os.path.splitext(me)[0] + ".py"
-        versioneer_file = os.path.relpath(me)
+        my_path = __file__
+        if my_path.endswith(".pyc") or my_path.endswith(".pyo"):
+            my_path = os.path.splitext(my_path)[0] + ".py"
+        versioneer_file = os.path.relpath(my_path)
     except NameError:
         versioneer_file = "versioneer.py"
     files.append(versioneer_file)
     present = False
     try:
-        f = open(".gitattributes", "r")
-        for line in f.readlines():
-            if line.strip().startswith(versionfile_source):
-                if "export-subst" in line.strip().split()[1:]:
-                    present = True
-        f.close()
-    except EnvironmentError:
+        with open(".gitattributes", "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith(versionfile_source):
+                    if "export-subst" in line.strip().split()[1:]:
+                        present = True
+                        break
+    except OSError:
         pass
     if not present:
-        f = open(".gitattributes", "a+")
-        f.write("%s export-subst\n" % versionfile_source)
-        f.close()
+        with open(".gitattributes", "a+") as fobj:
+            fobj.write(f"{versionfile_source} export-subst\n")
         files.append(".gitattributes")
     run_command(GITS, ["add", "--"] + files)
 
@@ -1192,30 +1328,23 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {
-                "version": dirname[len(parentdir_prefix) :],
-                "full-revisionid": None,
-                "dirty": False,
-                "error": None,
-                "date": None,
-            }
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
-        )
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
 SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.21) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -1237,15 +1366,13 @@ def versions_from_file(filename):
     try:
         with open(filename) as f:
             contents = f.read()
-    except EnvironmentError:
+    except OSError:
         raise NotThisMethod("unable to read _version.py")
-    mo = re.search(
-        r"version_json = '''\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
-    )
+    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
+                   contents, re.M | re.S)
     if not mo:
-        mo = re.search(
-            r"version_json = '''\r\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
-        )
+        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
+                       contents, re.M | re.S)
     if not mo:
         raise NotThisMethod("no version_json in _version.py")
     return json.loads(mo.group(1))
@@ -1254,7 +1381,8 @@ def versions_from_file(filename):
 def write_to_version_file(filename, versions):
     """Write the given version number to the given _version.py file."""
     os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": "))
+    contents = json.dumps(versions, sort_keys=True,
+                          indent=1, separators=(",", ": "))
     with open(filename, "w") as f:
         f.write(SHORT_VERSION_PY % contents)
 
@@ -1286,25 +1414,74 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces):
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver):
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces):
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version+1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0.post0.dev%d" % pieces["distance"]
     return rendered
 
 
@@ -1335,12 +1512,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
+def render_pep440_post_branch(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
 def render_pep440_old(pieces):
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -1400,23 +1606,25 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {
-            "version": "unknown",
-            "full-revisionid": pieces.get("long"),
-            "dirty": None,
-            "error": pieces["error"],
-            "date": None,
-        }
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
 
     if not style or style == "default":
         style = "pep440"  # the default
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -1426,13 +1634,9 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
 
 
 class VersioneerBadRootError(Exception):
@@ -1455,9 +1659,8 @@ def get_versions(verbose=False):
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
     verbose = verbose or cfg.verbose
-    assert (
-        cfg.versionfile_source is not None
-    ), "please set versioneer.versionfile_source"
+    assert cfg.versionfile_source is not None, \
+        "please set versioneer.versionfile_source"
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)
@@ -1511,13 +1714,9 @@ def get_versions(verbose=False):
     if verbose:
         print("unable to compute version")
 
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None, "error": "unable to compute version",
+            "date": None}
 
 
 def get_version():
@@ -1525,8 +1724,12 @@ def get_version():
     return get_versions()["version"]
 
 
-def get_cmdclass():
-    """Get the custom setuptools/distutils subclasses used by Versioneer."""
+def get_cmdclass(cmdclass=None):
+    """Get the custom setuptools/distutils subclasses used by Versioneer.
+
+    If the package uses a different cmdclass (e.g. one from numpy), it
+    should be provide as an argument.
+    """
     if "versioneer" in sys.modules:
         del sys.modules["versioneer"]
         # this fixes the "python setup.py develop" case (also 'install' and
@@ -1540,9 +1743,9 @@ def get_cmdclass():
         # parent is protected against the child's "import versioneer". By
         # removing ourselves from sys.modules here, before the child build
         # happens, we protect the child from the parent's versioneer too.
-        # Also see https://github.com/warner/python-versioneer/issues/52
+        # Also see https://github.com/python-versioneer/python-versioneer/issues/52
 
-    cmds = {}
+    cmds = {} if cmdclass is None else cmdclass.copy()
 
     # we add "version" to both distutils and setuptools
     from distutils.core import Command
@@ -1566,7 +1769,6 @@ def run(self):
             print(" date: %s" % vers.get("date"))
             if vers["error"]:
                 print(" error: %s" % vers["error"])
-
     cmds["version"] = cmd_version
 
     # we override "build_py" in both distutils and setuptools
@@ -1585,7 +1787,9 @@ def run(self):
     #  setup.py egg_info -> ?
 
     # we override different "build_py" commands for both environments
-    if "setuptools" in sys.modules:
+    if 'build_py' in cmds:
+        _build_py = cmds['build_py']
+    elif "setuptools" in sys.modules:
         from setuptools.command.build_py import build_py as _build_py
     else:
         from distutils.command.build_py import build_py as _build_py
@@ -1599,15 +1803,41 @@ def run(self):
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
             if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
+                target_versionfile = os.path.join(self.build_lib,
+                                                  cfg.versionfile_build)
                 print("UPDATING %s" % target_versionfile)
                 write_to_version_file(target_versionfile, versions)
-
     cmds["build_py"] = cmd_build_py
 
+    if 'build_ext' in cmds:
+        _build_ext = cmds['build_ext']
+    elif "setuptools" in sys.modules:
+        from setuptools.command.build_ext import build_ext as _build_ext
+    else:
+        from distutils.command.build_ext import build_ext as _build_ext
+
+    class cmd_build_ext(_build_ext):
+        def run(self):
+            root = get_root()
+            cfg = get_config_from_root(root)
+            versions = get_versions()
+            _build_ext.run(self)
+            if self.inplace:
+                # build_ext --inplace will only build extensions in
+                # build/lib<..> dir with no _version.py to write to.
+                # As in place builds will already have a _version.py
+                # in the module dir, we do not need to write one.
+                return
+            # now locate _version.py in the new build/ directory and replace
+            # it with an updated value
+            target_versionfile = os.path.join(self.build_lib,
+                                              cfg.versionfile_build)
+            print("UPDATING %s" % target_versionfile)
+            write_to_version_file(target_versionfile, versions)
+    cmds["build_ext"] = cmd_build_ext
+
     if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
         from cx_Freeze.dist import build_exe as _build_exe
-
         # nczeczulin reports that py2exe won't like the pep440-style string
         # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
         # setup(console=[{
@@ -1628,25 +1858,18 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(
-                        LONG
-                        % {
-                            "DOLLAR": "$",
-                            "STYLE": cfg.style,
-                            "TAG_PREFIX": cfg.tag_prefix,
-                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        }
-                    )
-
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
         cmds["build_exe"] = cmd_build_exe
         del cmds["build_py"]
 
-    if "py2exe" in sys.modules:  # py2exe enabled?
-        try:
-            from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
-        except ImportError:
-            from py2exe.build_exe import py2exe as _py2exe  # py2
+    if 'py2exe' in sys.modules:  # py2exe enabled?
+        from py2exe.distutils_buildexe import py2exe as _py2exe
 
         class cmd_py2exe(_py2exe):
             def run(self):
@@ -1661,21 +1884,19 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(
-                        LONG
-                        % {
-                            "DOLLAR": "$",
-                            "STYLE": cfg.style,
-                            "TAG_PREFIX": cfg.tag_prefix,
-                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        }
-                    )
-
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
         cmds["py2exe"] = cmd_py2exe
 
     # we override different "sdist" commands for both environments
-    if "setuptools" in sys.modules:
+    if 'sdist' in cmds:
+        _sdist = cmds['sdist']
+    elif "setuptools" in sys.modules:
         from setuptools.command.sdist import sdist as _sdist
     else:
         from distutils.command.sdist import sdist as _sdist
@@ -1698,10 +1919,8 @@ def make_release_tree(self, base_dir, files):
             # updated value
             target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
             print("UPDATING %s" % target_versionfile)
-            write_to_version_file(
-                target_versionfile, self._versioneer_generated_versions
-            )
-
+            write_to_version_file(target_versionfile,
+                                  self._versioneer_generated_versions)
     cmds["sdist"] = cmd_sdist
 
     return cmds
@@ -1744,25 +1963,28 @@ def make_release_tree(self, base_dir, files):
 
 """
 
-INIT_PY_SNIPPET = """
+OLD_SNIPPET = """
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
 """
 
+INIT_PY_SNIPPET = """
+from . import {0}
+__version__ = {0}.get_versions()['version']
+"""
+
 
 def do_setup():
-    """Main VCS-independent setup function for installing Versioneer."""
+    """Do main VCS-independent setup function for installing Versioneer."""
     root = get_root()
     try:
         cfg = get_config_from_root(root)
-    except (
-        EnvironmentError,
-        configparser.NoSectionError,
-        configparser.NoOptionError,
-    ) as e:
-        if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
+    except (OSError, configparser.NoSectionError,
+            configparser.NoOptionError) as e:
+        if isinstance(e, (OSError, configparser.NoSectionError)):
+            print("Adding sample versioneer config to setup.cfg",
+                  file=sys.stderr)
             with open(os.path.join(root, "setup.cfg"), "a") as f:
                 f.write(SAMPLE_CONFIG)
         print(CONFIG_ERROR, file=sys.stderr)
@@ -1771,28 +1993,31 @@ def do_setup():
     print(" creating %s" % cfg.versionfile_source)
     with open(cfg.versionfile_source, "w") as f:
         LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(
-            LONG
-            % {
-                "DOLLAR": "$",
-                "STYLE": cfg.style,
-                "TAG_PREFIX": cfg.tag_prefix,
-                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                "VERSIONFILE_SOURCE": cfg.versionfile_source,
-            }
-        )
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
+        f.write(LONG % {"DOLLAR": "$",
+                        "STYLE": cfg.style,
+                        "TAG_PREFIX": cfg.tag_prefix,
+                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        })
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
+                       "__init__.py")
     if os.path.exists(ipy):
         try:
             with open(ipy, "r") as f:
                 old = f.read()
-        except EnvironmentError:
+        except OSError:
             old = ""
-        if INIT_PY_SNIPPET not in old:
+        module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0]
+        snippet = INIT_PY_SNIPPET.format(module)
+        if OLD_SNIPPET in old:
+            print(" replacing boilerplate in %s" % ipy)
+            with open(ipy, "w") as f:
+                f.write(old.replace(OLD_SNIPPET, snippet))
+        elif snippet not in old:
             print(" appending to %s" % ipy)
             with open(ipy, "a") as f:
-                f.write(INIT_PY_SNIPPET)
+                f.write(snippet)
         else:
             print(" %s unmodified" % ipy)
     else:
@@ -1811,7 +2036,7 @@ def do_setup():
                 if line.startswith("include "):
                     for include in line.split()[1:]:
                         simple_includes.add(include)
-    except EnvironmentError:
+    except OSError:
         pass
     # That doesn't cover everything MANIFEST.in can do
     # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
@@ -1824,10 +2049,8 @@ def do_setup():
     else:
         print(" 'versioneer.py' already in MANIFEST.in")
     if cfg.versionfile_source not in simple_includes:
-        print(
-            " appending versionfile_source ('%s') to MANIFEST.in"
-            % cfg.versionfile_source
-        )
+        print(" appending versionfile_source ('%s') to MANIFEST.in" %
+              cfg.versionfile_source)
         with open(manifest_in, "a") as f:
             f.write("include %s\n" % cfg.versionfile_source)
     else:

From f766804af5cc5d30d9b5e2dc84e6716f27f60934 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 Dec 2021 14:36:34 -0500
Subject: [PATCH 119/347] Add numpy back in as a general dependency.

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 92fa48536f..edc1538e9f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,4 +3,5 @@ mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3
 mkdocs-macros-plugin
+numpy
 tools/schemacode/

From 181df00a3510c8a21d848679dca2e4a8d23b0d38 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 17 Dec 2021 19:10:49 -0500
Subject: [PATCH 120/347] Apply suggestions from code review

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 .github/workflows/schemacode_ci.yml | 5 ++++-
 tools/schemacode/setup.cfg          | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index e654a2218e..edc003dc62 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -2,6 +2,9 @@ name: "schemacode_ci"
 
 on:
   push:
+    paths:
+      - 'tools/schemacode/**'
+      - 'src/schema/**'
     branches:
       - "master"
   pull_request:
@@ -31,7 +34,7 @@ jobs:
         fail-fast: false
         matrix:
             os: ["ubuntu-latest"]
-            python-version: ["3.8"]
+            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     defaults:
       run:
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
index 59d4889d92..2d42c7a46f 100644
--- a/tools/schemacode/setup.cfg
+++ b/tools/schemacode/setup.cfg
@@ -16,6 +16,7 @@ classifiers =
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
 
 [options]
 python_requires = >=3.6

From 2557616c52fa8499571e4a7b3c8c0b4e534c282a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 17 Dec 2021 19:17:41 -0500
Subject: [PATCH 121/347] Add path restriction to pull requests too.

---
 .github/workflows/schemacode_ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index edc003dc62..d883519ee4 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -2,14 +2,17 @@ name: "schemacode_ci"
 
 on:
   push:
-    paths:
-      - 'tools/schemacode/**'
-      - 'src/schema/**'
     branches:
       - "master"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
   pull_request:
     branches:
       - "*"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
 
 jobs:
   check_skip:

From e19f1031bca9736e457a4bc36f10b6fab57e72e3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 17 Dec 2021 19:44:51 -0500
Subject: [PATCH 122/347] Add license badge.

---
 tools/schemacode/README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/schemacode/README.md b/tools/schemacode/README.md
index 0781fd5e8d..ad8cccb51d 100644
--- a/tools/schemacode/README.md
+++ b/tools/schemacode/README.md
@@ -2,4 +2,5 @@
 
 A Python library for working with the BIDS schema.
 
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 [![codecov](https://codecov.io/gh/bids-standard/bids-specification/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-specification)

From cc5ed8e3dd12398fd261db00c5615cd8ebc7d242 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:11:03 -0500
Subject: [PATCH 123/347] Try out linting job.

---
 .github/workflows/schemacode_ci.yml | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index d883519ee4..e830c167e2 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -29,7 +29,7 @@ jobs:
           commit-filter: "[skip ci];[ci skip];[skip github]"
           commit-filter-separator: ";"
 
-  latest:
+  run_tests:
     needs: check_skip
     if: ${{ needs.check_skip.outputs.skip == 'false' }}
     runs-on: ${{ matrix.os }}
@@ -68,3 +68,18 @@ jobs:
       - name: "Upload coverage to CodeCov"
         uses: codecov/codecov-action@v1
         if: success()
+
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Set up Python environment
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.8"
+      - name: Flake8 Lint
+        uses: py-actions/flake8@v2
+        with:
+          path: "tools/schemacode/"

From a71a323f25135ba3640066c74d3629298bd308a3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:11:30 -0500
Subject: [PATCH 124/347] Fix name.

---
 .github/workflows/schemacode_ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index e830c167e2..37e5fc965a 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -71,7 +71,7 @@ jobs:
 
   flake8-lint:
     runs-on: ubuntu-latest
-    name: Lint
+    name: Lint schemacode
     steps:
       - name: Check out source repository
         uses: actions/checkout@v2

From ce53a66197808a5d178ccd2de963f8b890bb0512 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:16:16 -0500
Subject: [PATCH 125/347] Don't use the flake8 action.

---
 .github/workflows/schemacode_ci.yml | 20 ++++++++++++++------
 tools/schemacode/setup.cfg          |  7 ++++---
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 37e5fc965a..8779e7a653 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -75,11 +75,19 @@ jobs:
     steps:
       - name: Check out source repository
         uses: actions/checkout@v2
+
       - name: Set up Python environment
-        uses: actions/setup-python@v1
-        with:
-          python-version: "3.8"
-      - name: Flake8 Lint
-        uses: py-actions/flake8@v2
+        uses: actions/setup-python@v2
         with:
-          path: "tools/schemacode/"
+          python-version: "3.7"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[tests]
+
+      - name: "Run flake8"
+        shell: bash {0}
+        run: |
+          flake8 ./tools/schemacode/
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
index 2d42c7a46f..5b8b09a0f0 100644
--- a/tools/schemacode/setup.cfg
+++ b/tools/schemacode/setup.cfg
@@ -60,10 +60,11 @@ parentdir_prefix =
 
 [flake8]
 max-line-length = 99
-exclude=*build/
-ignore = E203,E402,W503
+exclude = *build/
+ignore = E203,E402,E722,W503
 per-file-ignores =
-    */__init__.py:F401
+    */__init__.py : F401
+docstring-convention = numpy
 
 [tool:pytest]
 log_cli = true

From 712a1f624f4bf7d04713240cec2204780c9d22ce Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:20:33 -0500
Subject: [PATCH 126/347] Change working directory to use config.

---
 .github/workflows/schemacode_ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 8779e7a653..51f0334e5a 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -88,6 +88,7 @@ jobs:
           python -m pip install -e ./tools/schemacode[tests]
 
       - name: "Run flake8"
+        working-directory: ./tools/schemacode/
         shell: bash {0}
         run: |
-          flake8 ./tools/schemacode/
+          flake8 .

From cf9b6b7b5d483d2cb4e9e36f3d81c47e7460648d Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:23:59 -0500
Subject: [PATCH 127/347] Run black on versioneer files.

---
 tools/schemacode/schemacode/_version.py | 154 ++++++++------
 tools/schemacode/versioneer.py          | 266 ++++++++++++++----------
 2 files changed, 245 insertions(+), 175 deletions(-)

diff --git a/tools/schemacode/schemacode/_version.py b/tools/schemacode/schemacode/_version.py
index 537930fbb8..773b0f3174 100644
--- a/tools/schemacode/schemacode/_version.py
+++ b/tools/schemacode/schemacode/_version.py
@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -59,17 +58,18 @@ class NotThisMethod(Exception):
 
 def register_vcs_handler(vcs, method):  # decorator
     """Create decorator to mark a method as the handler of a VCS."""
+
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
+
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
@@ -77,10 +77,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
-                                       stdout=subprocess.PIPE,
-                                       stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+            process = subprocess.Popen(
+                [command] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
             break
         except OSError:
             e = sys.exc_info()[1]
@@ -115,15 +118,21 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
         rootdirs.append(root)
         root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -182,7 +191,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
+    tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -191,7 +200,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = {r for r in refs if re.search(r'\d', r)}
+        tags = {r for r in refs if re.search(r"\d", r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -199,24 +208,31 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
+            r = ref[len(tag_prefix) :]
             # Filter out refs that exactly match prefix or that don't start
             # with a number once the prefix is stripped (mostly a concern
             # when prefix is '')
-            if not re.match(r'\d', r):
+            if not re.match(r"\d", r):
                 continue
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -233,8 +249,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         GITS = ["git.cmd", "git.exe"]
         TAG_PREFIX_REGEX = r"\*"
 
-    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                   hide_stderr=True)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -242,11 +257,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match",
-                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
-                              cwd=root)
+    describe_out, rc = runner(
+        GITS,
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s%s" % (tag_prefix, TAG_PREFIX_REGEX),
+        ],
+        cwd=root,
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -261,8 +284,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
-    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
-                             cwd=root)
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root)
     # --abbrev-ref was added in git-1.6.3
     if rc != 0 or branch_name is None:
         raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
@@ -302,17 +324,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
         # tag
@@ -321,10 +342,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix)
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -373,8 +393,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -403,8 +422,7 @@ def render_pep440_branch(pieces):
         rendered = "0"
         if pieces["branch"] != "master":
             rendered += ".dev0"
-        rendered += "+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -432,7 +450,7 @@ def render_pep440_pre(pieces):
             tag_version, post_version = pep440_split_post(pieces["closest-tag"])
             rendered = tag_version
             if post_version is not None:
-                rendered += ".post%d.dev%d" % (post_version+1, pieces["distance"])
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
             else:
                 rendered += ".post0.dev%d" % (pieces["distance"])
         else:
@@ -565,11 +583,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -593,9 +613,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
 
 
 def get_versions():
@@ -609,8 +633,7 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
     except NotThisMethod:
         pass
 
@@ -619,13 +642,16 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for _ in cfg.versionfile_source.split('/'):
+        for _ in cfg.versionfile_source.split("/"):
             root = os.path.dirname(root)
     except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree",
-                "date": None}
+        return {
+            "version": "0+unknown",
+            "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to find root of source tree",
+            "date": None,
+        }
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -639,6 +665,10 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
diff --git a/tools/schemacode/versioneer.py b/tools/schemacode/versioneer.py
index b4cd1d6c7c..2da2029331 100644
--- a/tools/schemacode/versioneer.py
+++ b/tools/schemacode/versioneer.py
@@ -1,4 +1,3 @@
-
 # Version: 0.21
 
 """The Versioneer - like a rocketeer, but for versions.
@@ -309,11 +308,13 @@ def get_root():
         setup_py = os.path.join(root, "setup.py")
         versioneer_py = os.path.join(root, "versioneer.py")
     if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = ("Versioneer was unable to run the project root directory. "
-               "Versioneer requires setup.py to be executed from "
-               "its immediate directory (like 'python setup.py COMMAND'), "
-               "or in a way that lets it use sys.argv[0] to find the root "
-               "(like 'python path/to/setup.py COMMAND').")
+        err = (
+            "Versioneer was unable to run the project root directory. "
+            "Versioneer requires setup.py to be executed from "
+            "its immediate directory (like 'python setup.py COMMAND'), "
+            "or in a way that lets it use sys.argv[0] to find the root "
+            "(like 'python path/to/setup.py COMMAND')."
+        )
         raise VersioneerBadRootError(err)
     try:
         # Certain runtime workflows (setup.py install/develop in a setuptools
@@ -326,8 +327,10 @@ def get_root():
         me_dir = os.path.normcase(os.path.splitext(my_path)[0])
         vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
         if me_dir != vsr_dir:
-            print("Warning: build in %s is using versioneer.py from %s"
-                  % (os.path.dirname(my_path), versioneer_py))
+            print(
+                "Warning: build in %s is using versioneer.py from %s"
+                % (os.path.dirname(my_path), versioneer_py)
+            )
     except NameError:
         pass
     return root
@@ -372,15 +375,16 @@ class NotThisMethod(Exception):
 
 def register_vcs_handler(vcs, method):  # decorator
     """Create decorator to mark a method as the handler of a VCS."""
+
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         HANDLERS.setdefault(vcs, {})[method] = f
         return f
+
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
@@ -388,10 +392,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
-                                       stdout=subprocess.PIPE,
-                                       stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+            process = subprocess.Popen(
+                [command] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
             break
         except OSError:
             e = sys.exc_info()[1]
@@ -414,7 +421,9 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     return stdout, process.returncode
 
 
-LONG_VERSION_PY['git'] = r'''
+LONG_VERSION_PY[
+    "git"
+] = r'''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -1116,7 +1125,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
+    tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -1125,7 +1134,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = {r for r in refs if re.search(r'\d', r)}
+        tags = {r for r in refs if re.search(r"\d", r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -1133,24 +1142,31 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
+            r = ref[len(tag_prefix) :]
             # Filter out refs that exactly match prefix or that don't start
             # with a number once the prefix is stripped (mostly a concern
             # when prefix is '')
-            if not re.match(r'\d', r):
+            if not re.match(r"\d", r):
                 continue
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -1167,8 +1183,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         GITS = ["git.cmd", "git.exe"]
         TAG_PREFIX_REGEX = r"\*"
 
-    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                   hide_stderr=True)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -1176,11 +1191,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match",
-                                     "%s%s" % (tag_prefix, TAG_PREFIX_REGEX)],
-                              cwd=root)
+    describe_out, rc = runner(
+        GITS,
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s%s" % (tag_prefix, TAG_PREFIX_REGEX),
+        ],
+        cwd=root,
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -1195,8 +1218,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
-    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
-                             cwd=root)
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root)
     # --abbrev-ref was added in git-1.6.3
     if rc != 0 or branch_name is None:
         raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
@@ -1236,17 +1258,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
         # tag
@@ -1255,10 +1276,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix)
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -1331,15 +1351,21 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
         rootdirs.append(root)
         root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -1368,11 +1394,9 @@ def versions_from_file(filename):
             contents = f.read()
     except OSError:
         raise NotThisMethod("unable to read _version.py")
-    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
-                   contents, re.M | re.S)
+    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S)
     if not mo:
-        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
-                       contents, re.M | re.S)
+        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S)
     if not mo:
         raise NotThisMethod("no version_json in _version.py")
     return json.loads(mo.group(1))
@@ -1381,8 +1405,7 @@ def versions_from_file(filename):
 def write_to_version_file(filename, versions):
     """Write the given version number to the given _version.py file."""
     os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True,
-                          indent=1, separators=(",", ": "))
+    contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": "))
     with open(filename, "w") as f:
         f.write(SHORT_VERSION_PY % contents)
 
@@ -1414,8 +1437,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -1444,8 +1466,7 @@ def render_pep440_branch(pieces):
         rendered = "0"
         if pieces["branch"] != "master":
             rendered += ".dev0"
-        rendered += "+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -1473,7 +1494,7 @@ def render_pep440_pre(pieces):
             tag_version, post_version = pep440_split_post(pieces["closest-tag"])
             rendered = tag_version
             if post_version is not None:
-                rendered += ".post%d.dev%d" % (post_version+1, pieces["distance"])
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
             else:
                 rendered += ".post0.dev%d" % (pieces["distance"])
         else:
@@ -1606,11 +1627,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -1634,9 +1657,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
 
 
 class VersioneerBadRootError(Exception):
@@ -1659,8 +1686,7 @@ def get_versions(verbose=False):
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
     verbose = verbose or cfg.verbose
-    assert cfg.versionfile_source is not None, \
-        "please set versioneer.versionfile_source"
+    assert cfg.versionfile_source is not None, "please set versioneer.versionfile_source"
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)
@@ -1714,9 +1740,13 @@ def get_versions(verbose=False):
     if verbose:
         print("unable to compute version")
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None, "error": "unable to compute version",
-            "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
 
 
 def get_version():
@@ -1769,6 +1799,7 @@ def run(self):
             print(" date: %s" % vers.get("date"))
             if vers["error"]:
                 print(" error: %s" % vers["error"])
+
     cmds["version"] = cmd_version
 
     # we override "build_py" in both distutils and setuptools
@@ -1787,8 +1818,8 @@ def run(self):
     #  setup.py egg_info -> ?
 
     # we override different "build_py" commands for both environments
-    if 'build_py' in cmds:
-        _build_py = cmds['build_py']
+    if "build_py" in cmds:
+        _build_py = cmds["build_py"]
     elif "setuptools" in sys.modules:
         from setuptools.command.build_py import build_py as _build_py
     else:
@@ -1803,14 +1834,14 @@ def run(self):
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
             if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib,
-                                                  cfg.versionfile_build)
+                target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
                 print("UPDATING %s" % target_versionfile)
                 write_to_version_file(target_versionfile, versions)
+
     cmds["build_py"] = cmd_build_py
 
-    if 'build_ext' in cmds:
-        _build_ext = cmds['build_ext']
+    if "build_ext" in cmds:
+        _build_ext = cmds["build_ext"]
     elif "setuptools" in sys.modules:
         from setuptools.command.build_ext import build_ext as _build_ext
     else:
@@ -1830,14 +1861,15 @@ def run(self):
                 return
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
-            target_versionfile = os.path.join(self.build_lib,
-                                              cfg.versionfile_build)
+            target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
             print("UPDATING %s" % target_versionfile)
             write_to_version_file(target_versionfile, versions)
+
     cmds["build_ext"] = cmd_build_ext
 
     if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
         from cx_Freeze.dist import build_exe as _build_exe
+
         # nczeczulin reports that py2exe won't like the pep440-style string
         # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
         # setup(console=[{
@@ -1858,17 +1890,21 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["build_exe"] = cmd_build_exe
         del cmds["build_py"]
 
-    if 'py2exe' in sys.modules:  # py2exe enabled?
+    if "py2exe" in sys.modules:  # py2exe enabled?
         from py2exe.distutils_buildexe import py2exe as _py2exe
 
         class cmd_py2exe(_py2exe):
@@ -1884,18 +1920,22 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["py2exe"] = cmd_py2exe
 
     # we override different "sdist" commands for both environments
-    if 'sdist' in cmds:
-        _sdist = cmds['sdist']
+    if "sdist" in cmds:
+        _sdist = cmds["sdist"]
     elif "setuptools" in sys.modules:
         from setuptools.command.sdist import sdist as _sdist
     else:
@@ -1919,8 +1959,8 @@ def make_release_tree(self, base_dir, files):
             # updated value
             target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
             print("UPDATING %s" % target_versionfile)
-            write_to_version_file(target_versionfile,
-                                  self._versioneer_generated_versions)
+            write_to_version_file(target_versionfile, self._versioneer_generated_versions)
+
     cmds["sdist"] = cmd_sdist
 
     return cmds
@@ -1980,11 +2020,9 @@ def do_setup():
     root = get_root()
     try:
         cfg = get_config_from_root(root)
-    except (OSError, configparser.NoSectionError,
-            configparser.NoOptionError) as e:
+    except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e:
         if isinstance(e, (OSError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg",
-                  file=sys.stderr)
+            print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
             with open(os.path.join(root, "setup.cfg"), "a") as f:
                 f.write(SAMPLE_CONFIG)
         print(CONFIG_ERROR, file=sys.stderr)
@@ -1993,15 +2031,18 @@ def do_setup():
     print(" creating %s" % cfg.versionfile_source)
     with open(cfg.versionfile_source, "w") as f:
         LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(LONG % {"DOLLAR": "$",
-                        "STYLE": cfg.style,
-                        "TAG_PREFIX": cfg.tag_prefix,
-                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        })
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
-                       "__init__.py")
+        f.write(
+            LONG
+            % {
+                "DOLLAR": "$",
+                "STYLE": cfg.style,
+                "TAG_PREFIX": cfg.tag_prefix,
+                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                "VERSIONFILE_SOURCE": cfg.versionfile_source,
+            }
+        )
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
     if os.path.exists(ipy):
         try:
             with open(ipy, "r") as f:
@@ -2049,8 +2090,7 @@ def do_setup():
     else:
         print(" 'versioneer.py' already in MANIFEST.in")
     if cfg.versionfile_source not in simple_includes:
-        print(" appending versionfile_source ('%s') to MANIFEST.in" %
-              cfg.versionfile_source)
+        print(" appending versionfile_source ('%s') to MANIFEST.in" % cfg.versionfile_source)
         with open(manifest_in, "a") as f:
             f.write("include %s\n" % cfg.versionfile_source)
     else:

From e4d3f0881f507118fcb6a234586c06e33b154ef6 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 18 Dec 2021 11:29:52 -0500
Subject: [PATCH 128/347] Fix linting issue.

---
 tools/schemacode/schemacode/render.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index 47f44a2113..b1de890e60 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -379,7 +379,7 @@ def make_entity_table(schema, tablefmt="github", **kwargs):
     def _remove_numeric_suffixes(string):
         import re
 
-        suffix_str = re.findall("\((.+)\)", string)
+        suffix_str = re.findall(r"\\((.+)\\)", string)
         # The "Format" row should be skipped
         if not suffix_str:
             return string

From 1839b58900abafe3f39fc09b81bd1f0214951d24 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 20 Dec 2021 09:51:19 +1100
Subject: [PATCH 129/347] Common principles: Harmonize "file name" ->
 "filename"

Resolves #946 with #962.

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 859fb3547a..7abbc1f26f 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -549,7 +549,7 @@ for more information.
     1.  The metadata and the data filenames possess the same suffix;
     1.  The metadata filename does not include any entity absent from the data filename.
 
-1.  A metadata file MUST NOT have a file name that would be otherwise applicable
+1.  A metadata file MUST NOT have a filename that would be otherwise applicable
     to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
     location in the directory structure as per rule 2.1.
 

From 01aa790fa0c11d285f91ef7e0bd8beaf93f4529c Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 20 Dec 2021 11:42:52 +1100
Subject: [PATCH 130/347] 02-common-principles.md: Formatting fixes for #946

---
 src/02-common-principles.md | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 7abbc1f26f..57525b605c 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -559,16 +559,18 @@ for more information.
 1.  If multiple metadata files are applicable to a given data file:
 
     1.  For [tabular files](#tabular-files) and other simple metadata files
-        (e.g. [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
+        (for instance, [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
         only the file lowest in the filesystem hierarchy SHALL be treated as being
         associated with that data file.
 
     1.  For [JSON files](#key-value-files-dictionaries):
+
         1.  Files are loaded from the top of the directory hierarchy downwards,
             such that values from the top level are inherited by all data files
             at lower levels to which it is applicable unless overridden
             by a value for the same key present in another metadata file at a lower level
             (though it is RECOMMENDED to minimise the extent of such overrides).
+
         1.  There is no notion of "unsetting" a key/value pair.
 
 Corollaries:
@@ -577,6 +579,7 @@ Corollaries:
     MUST be defined in or below the directory corresponding to that participant / session;
     similarly, a metadata file that is applicable to multiple participants / sessions
     MUST NOT be placed within a directory corresponding to only one such participant / session.
+
 1.  It is permissible for a single metadata file to be applicable to multiple data
     files at that level of the hierarchy or below. Where such metadata content is consistent
     across multiple data files, it is RECOMMENDED to store metadata in this
@@ -592,9 +595,9 @@ Example 1: Demonstration of inheritance principle
             "sub-01_task-rest_acq-longtr_bold.nii.gz": "",
             "sub-01_task-rest_acq-longtr_bold.json": "",
             }
-        }
-    }
+        },
     "task-rest_bold.json": "",
+    }
 ) }}
 
 Contents of file "task-rest_bold.json":
@@ -602,7 +605,7 @@ Contents of file "task-rest_bold.json":
 {{ MACROS___make_metadata_table(
    {
         "EchoTime": 40.0,
-        "RepetitionTime", 1000.0
+        "RepetitionTime": 1000.0,
    }
 ) }}
 
@@ -610,7 +613,7 @@ Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
 
 {{ MACROS___make_metadata_table(
    {
-        "RepetitionTime", 3000.0
+        "RepetitionTime": 3000.0,
    }
 ) }}
 

From e349630fef782f27a1f63c42e68bb21aae10150f Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Mon, 20 Dec 2021 02:13:08 -0800
Subject: [PATCH 131/347] [FIX] Reword front page (#958)

* [FIX] Reword front page.

* Use the word "standard" to describe what this is.

* Update src/index.md

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* Update src/index.md

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/index.md | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/index.md b/src/index.md
index cfe83401e7..91f3aa6e44 100644
--- a/src/index.md
+++ b/src/index.md
@@ -1,9 +1,17 @@
 # The Brain Imaging Data Structure
 
-This resource defines the Brain Imaging Data Structure (BIDS) specification, including the core specification as well as many modality-specific extensions.
+The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to
+organize and describe data.
 
-To get started, [check out the introduction](01-introduction.md). If you'd like
-more information on how to adapt your own datasets to match the BIDS
-specification, we recommend exploring the [BIDS Starter Kit](https://bids-standard.github.io/bids-starter-kit/)
+This document defines the BIDS specification, which provides many details
+to help implement the standard. It includes the core specification as well as many extensions
+to specific brain imaging modalities, and increasingly also to other kinds of
+data.
 
-For an overview of the BIDS ecosystem, visit the [BIDS homepage](https://bids.neuroimaging.io).  The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.3686061).
+If BIDS is new to you, and you would like to learn more about how to adapt your
+own datasets to match the BIDS specification, we recommend exploring the
+[BIDS Starter Kit](https://bids-standard.github.io/bids-starter-kit/).
+Alternatively, to get started please read [the introduction to the specification](01-introduction.md).
+
+For an overview of the BIDS ecosystem, visit the [BIDS homepage](https://bids.neuroimaging.io).
+The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.3686061).

From b026112a3d6c6b5a7d046d9b853e210127083ec4 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 20 Dec 2021 11:21:04 +0100
Subject: [PATCH 132/347] add macro doc from hackmd

---
 macros_doc.md | 310 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 310 insertions(+)
 create mode 100644 macros_doc.md

diff --git a/macros_doc.md b/macros_doc.md
new file mode 100644
index 0000000000..119197cb5d
--- /dev/null
+++ b/macros_doc.md
@@ -0,0 +1,310 @@
+# Using MkDocs macros in the BIDS specification
+
+## What are macros and why use them?
+
+A macro is a rule or pattern that specifies how an input should be mapped to
+output. Macros are very useful for standardizing the output format for items
+such as tables. You might already be familiar with using macros from other tools
+such as Excel.
+
+MkDocs (the tool we use to turn the markdown version of the specification into
+HTML pages) supports macros. In the BIDS specification document, we use these
+macros to standarize the format of items such as tables and examples.
+
+Increasingly, parts of the BIDS specification are being formalized into a
+"schema" so that requirements in the specification can be automatically checked
+by validators. Several of the macros incorporate information from the schema to
+assure consistency.
+
+Table of macros here: | Name | Purpose | Uses schema | Link to example of use |
+| ---- | ------- | ----------- | ---------------------- |
+
+## When should I use a macro?
+
+Most typo corrections and minor changes to the BIDS specification do not require
+you to use macros. Even adding a table may not require you to use macros unless
+the table falls into one of the categories listed in the macros table.
+
+If you want to add content with a macro and need help, do not hesitate to
+contact a member of the bids-maintainers for help.
+
+Nope. No need to learn how to program to use those macros. But some macros
+require some specific "input", so you will just need to know what input to give
+it. In many cases, it will be just a metadata term whose definition or
+description should be displayed somewhere in the specification.
+
+Once you have given the macro its input, it usually knows where to look for the
+rest of the info it should use to do the rest of its work.
+
+The only exception to this is when you want to add new content. Say you want to
+add a completely new piece of metadata to the specification. In that case, you
+will need to create the input for the macro to be able to do its job. For that,
+you will need to update the schema itself.
+
+## How to
+
+Say you want to edit the content of table of the `Reconstruction` section for
+the PET page.
+
+The HTML version of the this section is here:
+
+https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/09-positron-emission-tomography.html#reconstruction
+
+In the markdown document, it is here:
+
+https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/09-positron-emission-tomography.md#reconstruction
+
+GitHub's way of directly rendering markdown documents makes it a bit harder to
+read, so if you opened the markdown document in your code editor it would look
+like this.
+
+```python
+#### Reconstruction
+
+{{ MACROS___make_metadata_table(
+   {
+      "AcquisitionMode": "REQUIRED",
+      "ImageDecayCorrected": "REQUIRED",
+      "ImageDecayCorrectionTime": "REQUIRED",
+      "ReconMethodName": "REQUIRED",
+      "ReconMethodParameterLabels": "REQUIRED",
+      "ReconMethodParameterUnits": "REQUIRED",
+      "ReconMethodParameterValues": "REQUIRED",
+      "ReconFilterType": "REQUIRED",
+      "ReconFilterSize": "REQUIRED",
+      "AttenuationCorrection": "REQUIRED",
+      "ReconMethodImplementationVersion": "RECOMMENDED",
+      "AttenuationCorrectionMethodReference": "RECOMMENDED",
+      "ScaleFactor": "RECOMMENDED",
+      "ScatterFraction": "RECOMMENDED",
+      "DecayCorrectionFactor": "RECOMMENDED",
+      "DoseCalibrationFactor": "RECOMMENDED",
+      "PromptRate": "RECOMMENDED",
+      "RandomRate": "RECOMMENDED",
+      "SinglesRate": "RECOMMENDED",
+   }
+) }}
+```
+
+---
+
+**HINT:** if you want to see the "raw" content of a file on Github you can
+always press the `raw` button that is on the top right of the document you are
+browsing on Github.
+
+---
+
+This section calls the macro `make_metadata_table` to create the table when
+building the HTML version of that page.
+
+The macro will create the different columns of the table:
+
+- Key name
+- Requirement level
+- Data type
+- Description
+
+A general description of that Macro call would look like this:
+
+```python
+{{ MACROS___make_metadata_table(
+   {
+      "TermToRender": "REQUIREMENT_LEVEL plus anything else after", "Extra content you want to append after the description of that term."
+   }
+) }}
+```
+
+To know what to put in the different columns, the macro will go and look into
+the `metadata.yaml` file in the BIDS schema and find the entry that correspond
+to the term you want to add.
+
+https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml
+
+And in the above example, all the information about `AcquisitionMode` would be
+read from that section:
+
+https://github.com/bids-standard/bids-specification/blob/05f7ce1ae9cc72b087b57c39183e36afcf37cb00/src/schema/objects/metadata.yaml#L20
+
+If you had to write the markdown equivalent of the general example for the Macro
+call above it would give a table that would look like this:
+
+| Key name     | Requirement level                          | Data type | Description                                  |
+| ------------ | ------------------------------------------ | --------- | -------------------------------------------- |
+| TermToRender | REQUIREMENT_LEVEL plus anything else after | string    | whatever description was in the metadata.yml |
+
+### Modifying a term in the table
+
+So if you want to change the content of what will appear in the HTML table, you
+need to edit this `metadata.yml` file.
+
+If you wanted to add some extra content to that table, but without modifying the
+definition in the schema, then you could just add some extra content into the
+macro call.
+
+```python
+#### Reconstruction
+
+{{ MACROS___make_metadata_table(
+   {
+      "AcquisitionMode": "REQUIRED", "But only when the acquisition was done on a full moon."
+
+       ...
+```
+
+### Why would you NOT want to modify the content of the yml file directly ?
+
+Well the same term can be used in different parts of the BIDS specification and
+some details that might apply to, say, PET might not apply to how the term is
+used for MRI. So we can use the schema for the common part and add extra content
+where necessary in the macro call.
+
+So always better to check if that term is not used somewhere else before making
+a change in the yml file. When in doubt add the change directly in the Macro
+call and ask the BIDS maintainers for help.
+
+### Adding a new term to the table
+
+Say you wanted to add a new term `MoonPhase` to the table, on the second row.
+You would do it like this. But this would only work if the `metadata.yml` file
+contains an entry for `MoonPhase`. If this is the case because the term already
+exist and is used somewhere in the BIDS specification, you are in luck and you
+can just stop there.
+
+```python
+#### Reconstruction
+
+{{ MACROS___make_metadata_table(
+   {
+      "AcquisitionMode": "REQUIRED",
+      "MoonPhase": "OPTIONAL",
+      "ImageDecayCorrected": "REQUIRED",
+      "ImageDecayCorrectionTime": "REQUIRED",
+
+      ...
+
+   }
+) }}
+```
+
+If the term does not exist, you need to add it. `YML` files have a fairly strict
+syntax where spaces and indentation matter a lot. You can a mini intro to YML
+files in the Turing way:
+https://the-turing-way.netlify.app/reproducible-research/renv/renv-yaml.html
+
+In practice, you should try to use a code editor that tells you when your syntax
+is wrong.
+
+## Why use macros at all?
+
+> Seriously why did you have to make it so complicated just to have pretty
+> tables? Are Macros that necessary ? Couldn't we just have everything in
+> Markdown?
+
+In principle we could, and before we started working on the schema that's
+exactly what we did. But there are several good reasons to use macros.
+
+When a definition gets repeated in different places, we could just copy-paste
+it. But when you start having several copies of that definition, if you have to
+modify it, you then need to edit several files and never forget any of them. So
+this becomes very error prone.
+
+So it becomes better to have one central place for that definition and grab that
+definition every time we need to reuse it.
+
+In practice this applies the DRY principle ("Don't Repeat Yourself") to the
+specification:
+
+> "Every piece of knowledge must have a single, unambiguous, authoritative
+> representation within a system".
+
+https://en.wikipedia.org/wiki/Don%27t_repeat_yourself
+
+Having one centralized place where we put all our definitions can be useful when
+we want other tools (the BIDS validator, bids-matlab...) to use the content of
+the specification.
+
+This is where the BIDS schema (those .yml files we talked about above) comes in
+as it is meant to be a machine readable version of the specification.
+
+And so to avoid having to maintain the SAME definition in both the schema and
+specification, we started using macros to generate the specification from the
+schema.
+
+## Anything else I need to know if I need to insert a new macro call?
+
+One nice thing for the people who will come after you (or yourself in 6 months
+when you get back to the document you just edited) is to leave a comment before
+the macro to quickly explain what it does and where to find more information
+about it.
+
+<!-- - [ ] TODO for maintainers: actually add those comments in the current
+      specification. -->
+
+It could for example look like this:
+
+```markdown
+<!--
+This block generates a metadata table.
+The definitions of these fields can be found in src/schema/...
+and a guide for editing at <link>.
+-->
+
+
+{{ MACROS___make_metadata_table(
+   {
+      "AcquisitionMode": "REQUIRED",
+      "MoonPhase": "OPTIONAL",
+      "ImageDecayCorrected": "REQUIRED",
+      "ImageDecayCorrectionTime": "REQUIRED",
+
+      ...
+
+   }
+) }}
+
+```
+
+## Should I create a macro if I need a new kind of table?
+
+As a rule of thumb, no.
+
+Unless it is clear that this kind of table will reappear many times in the
+future in the specification. But this is usually hard to predict so better start
+with a table in Markdown.
+
+If later we see that the same type of table keeps reoccuring the specification
+we could create a macro to generate them.
+
+## What macros are available? What can we use macros for?
+
+All the macros we use are in here:
+https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py
+
+Some of the main ones and what they do:
+
+- create the filename templates for each valid combination of datatype / suffix
+  / extension
+- create a table of definition, format... for each of the (1) metadata terms
+  that goes into a specific JSON, (2) valid suffixes for a given modality, and
+  (3) valid columns that can go into a specific TSV file.
+- create the entity table in the appendix that list for each datatype / suffix,
+  which entity is required
+- format the folder / file trees example in a systematic manner
+- Create the Entities appendix page, which contains the definitions and other
+  relevant information for valid BIDS entities.
+- ...
+
+Under the hood the macros themselves call some more python code that is in the
+`tools` folder:
+
+https://github.com/bids-standard/bids-specification/tree/master/tools
+
+---
+
+Macro section in the CONTRIBUTING.md
+
+https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#using-macros
+
+The official MkDocs documentation for the `macros` plugin:
+
+https://mkdocs-macros-plugin.readthedocs.io/en/latest/

From 98ca3fa8795a2ad29910cc54327c3cedb8f84906 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 20 Dec 2021 11:23:24 +0100
Subject: [PATCH 133/347] ci: store artifacts of build_docs mkdocs job

---
 .circleci/config.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1b72ae5b15..f4cc26dd65 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -18,6 +18,9 @@ jobs:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
           paths: site
+      - store_artifacts:
+          path: ~/project/site/
+          destination: dev_docs
 
   linkchecker:
     docker:

From 7f3b35d7f440e755a3e58d339a43368c7ae37e2f Mon Sep 17 00:00:00 2001
From: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
Date: Mon, 20 Dec 2021 13:27:37 -0500
Subject: [PATCH 134/347] Apply suggestions from code review

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/04-modality-specific-files/10-microscopy.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a3ecf69d63..cb4e4bc762 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -37,12 +37,12 @@ The OME-TIFF file allows for multi-page TIFF files to store multiple image plane
 multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
 file’s header.
 
-The BIDS standard accepts microscopy data in different file formats to accommodate datasets
+The BIDS standard accepts microscopy data in a number of file formats to accommodate datasets
 stored in 2D image formats and whole-slide imaging formats, to accommodate lossless and lossy
 compression, and to avoid unnecessary conversions of the original data from a non-tiled to a
 tiled format, or vice-versa.
 
-For BIDS, Microscopy raw data MUST be stored in one of the following formats:
+Microscopy raw data MUST be stored in one of the following formats:
 
 -   [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
 
@@ -89,7 +89,7 @@ Microscopy data currently support the following imaging modalities:
 
 In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))
 can refer to all the acquisitions between the start and the end of an imaging experiment
-for ex vivo imaging or a subject lab visit for biopsy procedure and/or in vivo imaging.
+for ex vivo imaging, or a subject lab visit for biopsy procedure and/or in vivo imaging.
 Consistent with other data types in BIDS, the session entity is optional.
 
 The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRED for

From 7ba50a6c4544cd4e5a8cb2ba31ca30407f6da3f2 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Tue, 21 Dec 2021 09:42:56 +1100
Subject: [PATCH 135/347] Inheritance principle: Fix JSON formatting

---
 src/02-common-principles.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 57525b605c..f8e01b582d 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -602,20 +602,20 @@ Example 1: Demonstration of inheritance principle
 
 Contents of file "task-rest_bold.json":
 
-{{ MACROS___make_metadata_table(
-   {
-        "EchoTime": 40.0,
-        "RepetitionTime": 1000.0,
-   }
-) }}
+```JSON
+{
+    "EchoTime": 40.0,
+    "RepetitionTime": 1000.0
+}
+```
 
 Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
 
-{{ MACROS___make_metadata_table(
-   {
-        "RepetitionTime": 3000.0,
-   }
-) }}
+```JSON
+{
+    "RepetitionTime": 3000.0
+}
+```
 
 When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
 metadata file `task-rest_bold.json` is read; file

From 21b772582fe412ff3676dd3f32c1b64b9c6a1846 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 21 Dec 2021 02:04:43 -0800
Subject: [PATCH 136/347] [DATALAD RUNCMD] RF: harmonize 'file name' into
 'filename' (#962)

Text is using both 'file name' and 'filename' pretty much to the equal amount
ATM (see git grep outputs below).  Code uses 'filename', and wikipedia has
https://en.wikipedia.org/wiki/Filename and prefers to use 'filename' in it. So
I decided to harmonize  into  'filename'.

	$> git grep  'file name' | grep '\.md' | grep -v MACRO | nl
		 1	src/02-common-principles.md:1.  **File extension** - a portion of the file name after the left-most
		 2	src/02-common-principles.md:are compulsory. For example a particular file name format is required when
		 3	src/02-common-principles.md:saved under a particular file name specified in the standard. This standard
		 4	src/02-common-principles.md:A file name consists of a chain of *entities*, or key-value pairs, a *suffix* and an
		 5	src/02-common-principles.md:`subject`, the file name MUST begin with the string `sub-<label>_ses-<label>`.
		 6	src/02-common-principles.md:If the `session` level is omitted in the folder structure, the file name MUST begin
		 7	src/02-common-principles.md:key/value pair MUST also be included as part of the file names themselves.
		 8	src/02-common-principles.md:produces a human readable file name, such as `sub-01_task-rest_eeg.edf`.
		 9	src/02-common-principles.md:It is evident from the file name alone that the file contains resting state
		10	src/02-common-principles.md:Entities within a file name MUST be unique.
		11	src/02-common-principles.md:For example, the following file name is not valid because it uses the `acq`
		12	src/02-common-principles.md:label, but must be included in file names (similarly to other key names).
		13	src/02-common-principles.md:meaning of file names and setting requirements on their contents or metadata.
		14	src/02-common-principles.md:to suppress warnings or provide interpretations of your file names.
		15	src/03-modality-agnostic-files.md:This file is REQUIRED if `sample-<label>` is present in any file name within the dataset.
		16	src/04-modality-specific-files/05-task-events.md:Where `<matches>` corresponds to task file name. For example:
		17	src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md:In the template file names, the `<matches>` part corresponds to task file name
		18	src/05-derivatives/02-common-data-types.md:is used to prevent clashing with the original file name.
		19	src/06-longitudinal-and-multi-site-studies.md:and [file names](02-common-principles.md#file-name-structure)
		20	src/99-appendices/03-hed.md:screen or the file name of the stimulus image.
		21	src/99-appendices/03-hed.md:       "LongName": "Stimulus file name",
		22	src/99-appendices/04-entity-table.md:[file name structure](../02-common-principles.md#file-name-structure),
		23	src/99-appendices/06-meg-file-formats.md:that not only the file names, but also the internal file pointers will be
		24	src/99-appendices/09-entities.md:[file name structure](../02-common-principles.md#file-name-structure).
		25	src/CHANGES.md:-   \[FIX] Clarify use of session entity in file names [#532](https://github.com/bids-standard/bids-specification/pull/532) ([Moo-Marc](https://github.com/Moo-Marc))
		26	src/CHANGES.md:-   \[FIX] Specify marker file names for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
		27	src/CHANGES.md:-   Added missing `sub-<participant_label>` in behavioral data file names.
		28	src/pregh-changes.md:-   Added missing `sub-<participant_label>` in behavioral data file names.

	$> git grep 'filename' | grep '\.md' | grep -v MACRO | nl
		 1	CONTRIBUTING.md:Make sure that all filename format templates, entity tables, and entity definitions are correct
		 2	src/02-common-principles.md:(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
		 3	src/03-modality-agnostic-files.md:      "filename": ("REQUIRED", "There MUST be exactly one row for each file."),
		 4	src/03-modality-agnostic-files.md:filename	acq_time
		 5	src/04-modality-specific-files/02-magnetoencephalography.md:which saves the MEG sensor coil positions in a separate file with two possible filename extensions  (`.sqd`, `.mrk`).
		 6	src/05-derivatives/01-introduction.md:    status. Any modification of raw files must use a modified filename that does
		 7	src/05-derivatives/01-introduction.md:    not conflict with the raw filename. Further, any files created as part of a
		 8	src/05-derivatives/01-introduction.md:    derivative dataset must not match a permissible filename of a valid raw
		 9	src/05-derivatives/01-introduction.md:    dataset. Stated equivalently, if any filename in a derivative dataset has a
		10	src/05-derivatives/01-introduction.md:-   Each Derivatives filename MUST be of the form:
		11	src/05-derivatives/01-introduction.md:    `source_entities` MUST be the entire source filename, with the omission of
		12	src/05-derivatives/01-introduction.md:    the source suffix and extension. One exception to this rule is filename
		13	src/05-derivatives/01-introduction.md:-   There is no prohibition against identical filenames in different derived
		14	src/05-derivatives/03-imaging.md:filename.
		15	src/99-appendices/04-entity-table.md:specification, and establishes a common order within a filename.
		16	src/99-appendices/08-coordinate-systems.md:The `scanner` coordinate system is implicit and assumed by default if the derivative filename does not define **any** `space-<label>`.
		17	src/99-appendices/11-qmri.md:filenames will remain the same; however, the optional metadata (third column) may
		18	src/CHANGES.md:-   \[SCHEMA] Use macro for filename templates in file collections appendix [#787](https://github.com/bids-standard/bids-specification/pull/787) ([tsalo](https://github.com/tsalo))
		19	src/CHANGES.md:-   \[FIX] Accidentally swapped Neuromag/Elekta/MEGIN cross-talk & fine-calibration filename extensions [#621](https://github.com/bids-standard/bids-specification/pull/621) ([hoechenberger](https://github.com/hoechenberger))
		20	src/CHANGES.md:-   \[INFRA] SCHEMA: Declare entities by concept names, add entity field for filename components [#616](https://github.com/bids-standard/bids-specification/pull/616) ([effigies](https://github.com/effigies))
		21	src/CHANGES.md:-   \[FIX] Common principles: Fix filename in inheritance principle [#261](https://github.com/bids-standard/bids-specification/pull/261) ([Lestropie](https://github.com/Lestropie))
		22	src/CHANGES.md:-   \[FIX] Example for IntendedFor was missing session indicator in the filename [#129](https://github.com/bids-standard/bids-specification/pull/129) ([yarikoptic](https://github.com/yarikoptic))
		23	src/schema/README.md:the entity tables, entity definitions, filename templates, and metadata tables.
		24	src/schema/README.md:-   `entities.yaml`: Entities (key/value pairs in folder and filenames).
		25	src/schema/README.md:This file contains a dictionary in which each entity (key/value pair in filenames) is defined.
		26	src/schema/README.md:they appear in filenames _and_ their full names.
		27	src/schema/README.md:For example, the key for the "Contrast Enhancing Agent" entity, which appears in filenames as `ce-<label>`,
		28	src/schema/README.md:since many entities (such as `ce`) have very short filename elements.
		29	src/schema/README.md:The `entity` field is the entity as it appears in filenames. For example, the `entity` for `ceagent` is `ce`.
		30	src/schema/README.md:Given that all entities appear in filenames, they should all be strings and the `type` field should always be `string`.
		31	src/schema/README.md:For example, `run` should have an index, so a valid key-value pair in a filename would be `run-01`.
		32	src/schema/README.md:Keys are the filenames (without file extensions),
		33	src/schema/README.md:-   `datatypes/*.yaml`: Files in the `datatypes` folder contain information about valid filenames within a given datatype.
		34	src/schema/README.md:    Each dictionary contains a list of suffixes, entities, and file extensions which may constitute a valid BIDS filename.
		35	src/schema/README.md:-   `entities.yaml`: This file simply defines the order in which entities, when present, MUST appear in filenames.
		36	src/schema/README.md:Each dictionary corresponds to a group of suffixes that have the same rules regarding filenames.
		37	src/schema/README.md:**NOTE**: The order in which entities appear in these dictionaries does not reflect how they should appear in filenames.
		38	src/schema/README.md:This file contains a list of entities in the order in which they must appear in filenames.
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "bash -c 'git grep -l '\"'\"'file name'\"'\"' | grep '\"'\"'\\.md'\"'\"' | grep -v MACRO | xargs sed -i -e '\"'\"'s,file name,filename,g'\"'\"''",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 src/02-common-principles.md                   | 28 +++++++++----------
 src/03-modality-agnostic-files.md             |  2 +-
 .../05-task-events.md                         |  2 +-
 ...logical-and-other-continuous-recordings.md |  2 +-
 src/05-derivatives/02-common-data-types.md    |  2 +-
 src/06-longitudinal-and-multi-site-studies.md |  2 +-
 src/99-appendices/03-hed.md                   |  4 +--
 src/99-appendices/04-entity-table.md          |  2 +-
 src/99-appendices/06-meg-file-formats.md      |  2 +-
 src/99-appendices/09-entities.md              |  2 +-
 src/CHANGES.md                                |  6 ++--
 src/pregh-changes.md                          |  2 +-
 12 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index e29d0b96ed..337705235c 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -118,7 +118,7 @@ misunderstanding we clarify them here.
     the final `_`), right before the **File extension**, for example, it is `eeg` in
     `sub-05_task-matchingpennies_eeg.vhdr`.
 
-1.  **File extension** - a portion of the file name after the left-most
+1.  **File extension** - a portion of the filename after the left-most
     period (`.`) preceded by any other alphanumeric. For example, `.gitignore` does
     not have a file extension, but the file extension of `test.nii.gz` is `.nii.gz`.
     Note that the left-most period is included in the file extension.
@@ -133,10 +133,10 @@ misunderstanding we clarify them here.
 
 The following standard describes a way of arranging data and writing down
 metadata for a subset of neuroimaging experiments. Some aspects of the standard
-are compulsory. For example a particular file name format is required when
+are compulsory. For example a particular filename format is required when
 storing structural scans. Some aspects are regulated but optional. For example a
 T2 volume does not need to be included, but when it is available it should be
-saved under a particular file name specified in the standard. This standard
+saved under a particular filename specified in the standard. This standard
 aspires to describe a majority of datasets, but acknowledges that there will be
 cases that do not fit. In such cases one can include additional files and
 subfolders to the existing folder structure following common sense. For example
@@ -149,13 +149,13 @@ specification.
 
 ## File name structure
 
-A file name consists of a chain of *entities*, or key-value pairs, a *suffix* and an
+A filename consists of a chain of *entities*, or key-value pairs, a *suffix* and an
 *extension*.
 Two prominent examples of entities are `subject` and `session`.
 
 For a data file that was collected in a given `session` from a given
-`subject`, the file name MUST begin with the string `sub-<label>_ses-<label>`.
-If the `session` level is omitted in the folder structure, the file name MUST begin
+`subject`, the filename MUST begin with the string `sub-<label>_ses-<label>`.
+If the `session` level is omitted in the folder structure, the filename MUST begin
 with the string `sub-<label>`, without `ses-<label>`.
 
 Note that `sub-<label>` corresponds to the `subject` entity because it has
@@ -169,19 +169,19 @@ be added for all subjects if at least one subject in the dataset has more than
 one session.
 If a `/ses-<label>` subfolder is included as part of the directory hierarchy,
 then the same [`ses-<label>`](./99-appendices/09-entities.md#ses)
-key/value pair MUST also be included as part of the file names themselves.
+key/value pair MUST also be included as part of the filenames themselves.
 Acquisition time of session can
 be defined in the [sessions file](03-modality-agnostic-files.md#sessions-file).
 
 A chain of entities, followed by a suffix, connected by underscores (`_`)
-produces a human readable file name, such as `sub-01_task-rest_eeg.edf`.
-It is evident from the file name alone that the file contains resting state
+produces a human readable filename, such as `sub-01_task-rest_eeg.edf`.
+It is evident from the filename alone that the file contains resting state
 data from subject `01`.
 The suffix `eeg` and the extension `.edf` depend on the imaging modality and
 the data format and indicate further details of the file's contents.
 
-Entities within a file name MUST be unique.
-For example, the following file name is not valid because it uses the `acq`
+Entities within a filename MUST be unique.
+For example, the following filename is not valid because it uses the `acq`
 entity twice:
 `sub-01_acq-laser_acq-uneven_electrodes.tsv`
 
@@ -658,7 +658,7 @@ of `<index>`es.
 Please note that a given label or index is distinct from the "prefix"
 it refers to. For example `sub-01` refers to the `sub` entity (a
 subject) with the label `01`. The `sub-` prefix is not part of the subject
-label, but must be included in file names (similarly to other key names).
+label, but must be included in filenames (similarly to other key names).
 
 ## Uniform Resource Indicator
 
@@ -816,10 +816,10 @@ For example, an ASSET calibration scan might be named
 
 Non-standard files and directories should be named with care.
 Future BIDS efforts may standardize new entities and suffixes, changing the
-meaning of file names and setting requirements on their contents or metadata.
+meaning of filenames and setting requirements on their contents or metadata.
 Validation and parsing tools MAY treat the presence of non-standard files and
 directories as an error, so consult the details of these tools for mechanisms
-to suppress warnings or provide interpretations of your file names.
+to suppress warnings or provide interpretations of your filenames.
 
 <!-- Link Definitions -->
 
diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 1788f1911f..68bf8550cf 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -259,7 +259,7 @@ samples.json
 ```
 
 The purpose of this file is to describe properties of samples, indicated by the `sample` entity.
-This file is REQUIRED if `sample-<label>` is present in any file name within the dataset.
+This file is REQUIRED if `sample-<label>` is present in any filename within the dataset.
 Each sample MUST be described by one and only one row.
 
 {{ MACROS___make_columns_table(
diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md
index 6fe334e0ff..5188a8c1ae 100644
--- a/src/04-modality-specific-files/05-task-events.md
+++ b/src/04-modality-specific-files/05-task-events.md
@@ -20,7 +20,7 @@ sub-<label>/[ses-<label>]
         <matches>_events.json
 ```
 
-Where `<matches>` corresponds to task file name. For example:
+Where `<matches>` corresponds to task filename. For example:
 `sub-control01_task-nback`.
 
 Each task events file REQUIRES a corresponding task data file.
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
index ce443f1a07..3bf43c7532 100644
--- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
@@ -24,7 +24,7 @@ For the template directory name, `<datatype>` can correspond to any data
 recording modality, for example `func`, `anat`, `dwi`, `meg`, `eeg`, `ieeg`,
 or `beh`.
 
-In the template file names, the `<matches>` part corresponds to task file name
+In the template filenames, the `<matches>` part corresponds to task filename
 before the suffix.
 For example for the file `sub-control01_task-nback_run-1_bold.nii.gz`,
 `<matches>` would correspond to `sub-control01_task-nback_run-1`.
diff --git a/src/05-derivatives/02-common-data-types.md b/src/05-derivatives/02-common-data-types.md
index e03d88ca14..9dbe604706 100644
--- a/src/05-derivatives/02-common-data-types.md
+++ b/src/05-derivatives/02-common-data-types.md
@@ -26,7 +26,7 @@ share the following (non-required) ones:
 Preprocessed `bold` NIfTI file in the original coordinate space of the original run.
 The location of the file in the original datasets is encoded in the `RawSources` metadata,
 and [`_desc-<label>`](../99-appendices/09-entities.md#desc)
-is used to prevent clashing with the original file name.
+is used to prevent clashing with the original filename.
 
 {{ MACROS___make_filetree_example(
    {
diff --git a/src/06-longitudinal-and-multi-site-studies.md b/src/06-longitudinal-and-multi-site-studies.md
index c617812bc8..568c80c9c7 100644
--- a/src/06-longitudinal-and-multi-site-studies.md
+++ b/src/06-longitudinal-and-multi-site-studies.md
@@ -1,7 +1,7 @@
 # Longitudinal and multi-site studies
 
 Multiple sessions (visits) are encoded by adding an extra layer of directories
-and [file names](02-common-principles.md#file-name-structure)
+and [filenames](02-common-principles.md#file-name-structure)
 in the form of a session (for example `ses-<label>`) and
 with a [`*_sessions.tsv` file](03-modality-agnostic-files.md#sessions-file).
 
diff --git a/src/99-appendices/03-hed.md b/src/99-appendices/03-hed.md
index 1526c1b036..0466cb7870 100644
--- a/src/99-appendices/03-hed.md
+++ b/src/99-appendices/03-hed.md
@@ -104,7 +104,7 @@ Example: An accompanying `*_events.json` sidecar describing the `mycodes` catego
 
 Each column of `*_events.tsv` containing non-categorical values usually represents a
 particular type of data, for example the `speed` of a stimulus object across the
-screen or the file name of the stimulus image.
+screen or the filename of the stimulus image.
 These variables could be annotated in the HED column of `*_events.tsv`.
 However, that approach requires repeating the values appearing in the individual
 columns in the HED column.
@@ -155,7 +155,7 @@ Example: An accompanying `*_events.json` sidecar describing both categorical and
        "HED": "Attribute/Response start delay/# ms, Action/Button press"
    },
    "stim_file": {
-       "LongName": "Stimulus file name",
+       "LongName": "Stimulus filename",
        "Description": "Relative path of the stimulus image file",
        "HED": "Attribute/File/#"
    }
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 5dfd86d018..1afd0771a9 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -10,7 +10,7 @@ Entity formats indicate whether the value is alphanumeric
 (`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure),
+[filename structure](../02-common-principles.md#file-name-structure),
 while entity definitions are in [Appendix IX](09-entities.md).
 
 <!--
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 1f5abc039f..7036eb32a0 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -187,7 +187,7 @@ Each of these files has an internal pointer to the next file.
 This is important when renaming these split recordings to the BIDS convention.
 Instead of a simple renaming, files should be read in and saved under their new
 names with dedicated tools like [MNE](https://mne.tools), which will ensure
-that not only the file names, but also the internal file pointers will be
+that not only the filenames, but also the internal file pointers will be
 updated.
 
 It is RECOMMENDED that FIFF files with multiple parts use the `split-<index>`
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index b72e06e9a3..64d9700033 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -4,7 +4,7 @@ This section compiles the entities (key-value pairs) described throughout this
 specification, and describes each.
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure).
+[filename structure](../02-common-principles.md#file-name-structure).
 
 The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT
 be specified for a given file type, is specified in the [Entity Table](04-entity-table.md).
diff --git a/src/CHANGES.md b/src/CHANGES.md
index 41ad4f92aa..9684d8a8ab 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -188,7 +188,7 @@
 -   \[FIX] clarify that \<physio|stim>.json is REQUIRED [#542](https://github.com/bids-standard/bids-specification/pull/542) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Replace all non-breaking spaces with vanilla spaces [#536](https://github.com/bids-standard/bids-specification/pull/536) ([nicholst](https://github.com/nicholst))
 -   \[FIX] Clarify indices are nonnegative integers. [#535](https://github.com/bids-standard/bids-specification/pull/535) ([nicholst](https://github.com/nicholst))
--   \[FIX] Clarify use of session entity in file names [#532](https://github.com/bids-standard/bids-specification/pull/532) ([Moo-Marc](https://github.com/Moo-Marc))
+-   \[FIX] Clarify use of session entity in filenames [#532](https://github.com/bids-standard/bids-specification/pull/532) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[ENH] Add the ability of users to specify an explicit HED.xml schema for validation. [#527](https://github.com/bids-standard/bids-specification/pull/527) ([VisLab](https://github.com/VisLab))
 -   \[FIX] clarify that scans.json is allowed and recommended [#523](https://github.com/bids-standard/bids-specification/pull/523) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] add copyright holder to license.  [#521](https://github.com/bids-standard/bids-specification/pull/521) ([sappelhoff](https://github.com/sappelhoff))
@@ -342,7 +342,7 @@
 -   \[FIX] Clarify continuous recording metadata fields [#167](https://github.com/bids-standard/bids-specification/pull/167) ([effigies](https://github.com/effigies))
 -   \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisgorgo](https://github.com/chrisgorgo))
--   \[FIX] Specify marker file names for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
+-   \[FIX] Specify marker filenames for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
 ## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
@@ -461,7 +461,7 @@
 -   Added `InversionTime` metadata key.
 -   Clarification on the source vs raw language.
 -   Added `trial_type` column to the event files.
--   Added missing `sub-<participant_label>` in behavioral data file names.
+-   Added missing `sub-<participant_label>` in behavioral data filenames.
 -   Added ability to store stimuli files.
 -   Clarified the language describing allowed subject labels.
 -   Added quantitative proton density maps.
diff --git a/src/pregh-changes.md b/src/pregh-changes.md
index 6351057aa6..da91e7f2e5 100644
--- a/src/pregh-changes.md
+++ b/src/pregh-changes.md
@@ -39,7 +39,7 @@
 -   Added `InversionTime` metadata key.
 -   Clarification on the source vs raw language.
 -   Added `trial_type` column to the event files.
--   Added missing `sub-<participant_label>` in behavioral data file names.
+-   Added missing `sub-<participant_label>` in behavioral data filenames.
 -   Added ability to store stimuli files.
 -   Clarified the language describing allowed subject labels.
 -   Added quantitative proton density maps.

From 7bc7ad5a5dfcd54f985257e1bd148de854b1aeb8 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Wed, 5 Jan 2022 17:18:44 +1100
Subject: [PATCH 137/347] Inheritance principle: Minor changes and formatting

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/02-common-principles.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index f8e01b582d..1b1cd42561 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -550,18 +550,18 @@ for more information.
     1.  The metadata filename does not include any entity absent from the data filename.
 
 1.  A metadata file MUST NOT have a filename that would be otherwise applicable
-    to some data file based on rules 2.2 and 2.3 but is made inapplicable based on its
-    location in the directory structure as per rule 2.1.
+    to some data file based on rules 2.b and 2.c but is made inapplicable based on its
+    location in the directory structure as per rule 2.a.
 
 1.  There MUST NOT be multiple metadata files applicable to a data file at one level
     of the directory hierarchy.
 
-1.  If multiple metadata files are applicable to a given data file:
+1.  If multiple metadata files satisfy criteria 2.a-c above:
 
     1.  For [tabular files](#tabular-files) and other simple metadata files
-        (for instance, [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information),
-        only the file lowest in the filesystem hierarchy SHALL be treated as being
-        associated with that data file.
+        (for instance, [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information)),
+        accessing metadata associated with a data file MUST consider only the
+        applicable file that is lowest in the filesystem hierarchy.
 
     1.  For [JSON files](#key-value-files-dictionaries):
 
@@ -600,7 +600,7 @@ Example 1: Demonstration of inheritance principle
     }
 ) }}
 
-Contents of file "task-rest_bold.json":
+Contents of file `task-rest_bold.json`:
 
 ```JSON
 {
@@ -609,7 +609,7 @@ Contents of file "task-rest_bold.json":
 }
 ```
 
-Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
+Contents of file `sub-01/func/sub-01_task-rest_acq-longtr_bold.json`:
 
 ```JSON
 {
@@ -620,13 +620,13 @@ Contents of file "sub-01/func/sub-01_task-rest_acq-longtr_bold.json":
 When reading image `sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz`, only
 metadata file `task-rest_bold.json` is read; file
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.json` is inapplicable as it contains
-entity "`acq-longtr`" that is absent from the image path (rule 2.3). When reading image
+entity "`acq-longtr`" that is absent from the image path (rule 2.c). When reading image
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
 `task-rest_bold.json` at the top level is read first, followed by file
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2.1);
-the value for field "`RepetitionTime`" is therefore overridden to the value 3000.0.
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.b.i);
+the value for field "`RepetitionTime`" is therefore overridden to the value `3000.0`.
 The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
-absence in the metadata file at the lower level (rule 5.2.2).
+absence in the metadata file at the lower level (rule 5.b.ii).
 
 Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
 

From adeeeedb9072ce18f5b3b405fdf2f6ac8fe57400 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 5 Jan 2022 12:32:30 -0500
Subject: [PATCH 138/347] Apply @effigies' suggestions

Thanks for the suggestions!

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 tools/schemacode/schemacode/render.py |  2 +-
 tools/schemacode/schemacode/schema.py | 42 +++++++++------------------
 2 files changed, 14 insertions(+), 30 deletions(-)

diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index b1de890e60..db802d8db9 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -379,7 +379,7 @@ def make_entity_table(schema, tablefmt="github", **kwargs):
     def _remove_numeric_suffixes(string):
         import re
 
-        suffix_str = re.findall(r"\\((.+)\\)", string)
+        suffix_str = re.findall(r"\((.+)\)", string)
         # The "Format" row should be skipped
         if not suffix_str:
             return string
diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 805a4f5177..d3975ab59a 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -78,39 +78,23 @@ def load_schema(schema_path):
     schema["rules"] = {}
 
     # Load object definitions. All are present in single files.
-    object_group_files = sorted(glob(str(objects_dir / "*.yaml")))
-    for object_group_file in object_group_files:
-        group_name = op.splitext(op.basename(object_group_file))[0]
-        lgr.debug(f"Loading {group_name} objects.")
-        with open(object_group_file, "r") as fo:
-            dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
-            dict_ = dereference_yaml(dict_, dict_)
-            schema["objects"][group_name] = dict_
+    for object_group_file in sorted(objects_dir.glob("*.yaml")):
+        lgr.debug(f"Loading {object_group_file.stem} objects.")
+        dict_ = yaml.safe_load(object_group_file.read_text())
+        schema["objects"][object_group_file.stem] = dereference_yaml(dict_, dict_)
 
     # Grab single-file rule groups
-    rule_group_files = sorted(glob(str(rules_dir / "*.yaml")))
-    rule_group_folders = sorted(glob(str(rules_dir / "*")))
-    rule_group_folders = [f for f in rule_group_folders if op.isdir(f)]
-    for rule_group_file in rule_group_files:
-        group_name = op.splitext(op.basename(rule_group_file))[0]
-        lgr.debug(f"Loading {group_name} rules.")
-        with open(rule_group_file, "r") as fo:
-            dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
-            dict_ = dereference_yaml(dict_, dict_)
-            schema["rules"][group_name] = dict_
+    for rule_group_file in sorted(rules_dir.glob("*.yaml")):
+        lgr.debug(f"Loading {rule_group_file.stem} rules.")
+        dict_ = yaml.safe_load(rule_group_file.read_text())
+        schema["rules"][rule_group_file.stem] = dereference_yaml(dict_, dict_)
 
     # Load folders of rule subgroups.
-    for rule_group_folder in rule_group_folders:
-        group_name = op.basename(rule_group_folder)
-        rule_subgroup_files = sorted(glob(op.join(rule_group_folder, "*.yaml")))
-        schema["rules"][group_name] = {}
-        for rule_subgroup_file in rule_subgroup_files:
-            subgroup_name = op.splitext(op.basename(rule_subgroup_file))[0]
-            lgr.debug(f"Loading {subgroup_name} rules.")
-            with open(rule_subgroup_file, "r") as fo:
-                dict_ = yaml.load(fo, Loader=yaml.SafeLoader)
-                dict_ = dereference_yaml(dict_, dict_)
-                schema["rules"][group_name][subgroup_name] = dict_
+    for rule_group_file in sorted(rules_dir.glob("*/*.yaml")):
+        rule = schema["rules"].setdefault(rule_group_file.parent.name, {})
+        lgr.debug(f"Loading {rule_group_file.stem} rules.")
+        dict_ = yaml.safe_load(rule_group_file.read_text())
+        rule[rule_group_file.stem] = dereference_yaml(dict_, dict_)
 
     return schema
 

From 97794d56b45ec6b3ffa61ad6a670d17382ae7fdc Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 5 Jan 2022 12:34:15 -0500
Subject: [PATCH 139/347] Remove unused imports.

---
 tools/schemacode/schemacode/schema.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index d3975ab59a..9203eaa921 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -1,9 +1,7 @@
 """Schema loading- and processing-related functions."""
 import logging
 import os
-import os.path as op
 from copy import deepcopy
-from glob import glob
 from pathlib import Path
 
 import yaml

From febae4fb9b2c9f055dc1392e0283c85f05618de0 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 5 Jan 2022 17:44:49 +0000
Subject: [PATCH 140/347] [DOC] Auto-generate changelog entry for PR #892

---
 src/CHANGES.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 9684d8a8ab..15de82bd56 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,8 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[FIX] harmonize 'file name' into 'filename' [#962](https://github.com/bids-standard/bids-specification/pull/962) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] Reword front page [#958](https://github.com/bids-standard/bids-specification/pull/958) ([arokem](https://github.com/arokem))
 -   \[MAINT] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies))
 -   \[FIX] Entity table: Clarify meaning of empty cells [#955](https://github.com/bids-standard/bids-specification/pull/955) ([Lestropie](https://github.com/Lestropie))
 -   \[MISC] Add Eric Earl as a Maintainer [#953](https://github.com/bids-standard/bids-specification/pull/953) ([ericearl](https://github.com/ericearl))
@@ -28,6 +30,7 @@
 -   \[FIX] small typo in json example [#897](https://github.com/bids-standard/bids-specification/pull/897) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] tiny speedup of building PDF by moving `re.compile\(\)` outside of a loop [#896](https://github.com/bids-standard/bids-specification/pull/896) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[INFRA] Document \*.webm video files as binary [#895](https://github.com/bids-standard/bids-specification/pull/895) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[SCHEMA] Reorganize schema code into a package [#892](https://github.com/bids-standard/bids-specification/pull/892) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Clarify shifting dates RECOMMENDED, add example EDF [#891](https://github.com/bids-standard/bids-specification/pull/891) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix draft rendering css on mobile or when browser window is narrow [#889](https://github.com/bids-standard/bids-specification/pull/889) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Add an animated BIDS logo [#886](https://github.com/bids-standard/bids-specification/pull/886) ([adswa](https://github.com/adswa))

From fc604ef586d3bd055339349d5cbfe64d20ef27de Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Tue, 11 Jan 2022 13:36:01 +1100
Subject: [PATCH 141/347] Inheritance principle: No unsetting as corollary

The rule regarding the fact that it is not possible to "unset" a key-value pair from a JSON file from higher in the filesystem hierarchy is here moved to the "corollaries" section. This is because this behaviour is a natural consequence of loading consecutive JSON files using a simple merge operation, and the absence of an equivalent to Python' "None" in the JSON specification.
---
 src/02-common-principles.md | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 57525b605c..5dfefb49f4 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -563,15 +563,12 @@ for more information.
         only the file lowest in the filesystem hierarchy SHALL be treated as being
         associated with that data file.
 
-    1.  For [JSON files](#key-value-files-dictionaries):
-
-        1.  Files are loaded from the top of the directory hierarchy downwards,
-            such that values from the top level are inherited by all data files
-            at lower levels to which it is applicable unless overridden
-            by a value for the same key present in another metadata file at a lower level
-            (though it is RECOMMENDED to minimise the extent of such overrides).
-
-        1.  There is no notion of "unsetting" a key/value pair.
+    1.  For [JSON files](#key-value-files-dictionaries), key-values are loaded
+        from files from the top of the directory hierarchy downwards, such that
+        key-values from the top level are inherited by all data files at lower
+        levels to which it is applicable unless overridden by a value for the
+        same key present in another metadata file at a lower level
+        (though it is RECOMMENDED to minimise the extent of such overrides).
 
 Corollaries:
 
@@ -585,6 +582,11 @@ Corollaries:
     across multiple data files, it is RECOMMENDED to store metadata in this
     way, rather than duplicating that metadata content across multiple metadata files.
 
+1.  Where multiple applicable JSON files are loaded as per rule 5.2, key-values can
+    only be overwritten by files lower in the filesystem hierarchy; the absence of
+    a key-value in a later file does not imply the "unsetting" of that field
+    (and indeed there is no notion of such).
+
 Example 1: Demonstration of inheritance principle
 
 {{ MACROS___make_filetree_example(
@@ -623,10 +625,10 @@ metadata file `task-rest_bold.json` is read; file
 entity "`acq-longtr`" that is absent from the image path (rule 2.3). When reading image
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
 `task-rest_bold.json` at the top level is read first, followed by file
-`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2.1);
+`sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.2);
 the value for field "`RepetitionTime`" is therefore overridden to the value 3000.0.
 The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
-absence in the metadata file at the lower level (rule 5.2.2).
+absence in the metadata file at the lower level (rule 5.2; corollary 3).
 
 Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
 

From 2590d0ac82a8689ceb861187d7a7ad360eded60e Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Thu, 13 Jan 2022 10:52:59 +1100
Subject: [PATCH 142/347] Inheritance principle: Rephrase corollary RE:
 unsetting

---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 5dfefb49f4..6e1b7251d8 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -585,7 +585,7 @@ Corollaries:
 1.  Where multiple applicable JSON files are loaded as per rule 5.2, key-values can
     only be overwritten by files lower in the filesystem hierarchy; the absence of
     a key-value in a later file does not imply the "unsetting" of that field
-    (and indeed there is no notion of such).
+    (indeed removal of existing fields is not possible).
 
 Example 1: Demonstration of inheritance principle
 

From ed19ddd46b03c253f0aac40aa3db05225db0b17b Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 13 Jan 2022 09:37:18 -0500
Subject: [PATCH 143/347] Update BIDS-examples link and remove commented lines

---
 src/04-modality-specific-files/10-microscopy.md | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index cb4e4bc762..efb1542c52 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -7,14 +7,9 @@ Please see [Citing BIDS](../01-introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
-<!---
-The following link is temporary and points to the bep031 branch of bids-examples,
-update to 'https://github.com/bids-standard/bids-examples' when examples are merged.
--->
 Microscopy datasets formatted using this specification are available on the
-[BIDS examples repository](https://github.com/neuropoly/bids-examples/tree/bep031)
-(`micr_SEM` and `micr_SPIM`) and can be used for practical guidance when curating
-a new dataset.
+[BIDS examples repository](https://github.com/bids-standard/bids-examples#microscopy-datasets)
+and can be used for practical guidance when curating a new dataset.
 
 Further Microscopy datasets are available:
 

From 8062d19b5923fc015b03fa554ff08c8b92f20e35 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 13 Jan 2022 10:35:23 -0500
Subject: [PATCH 144/347] Add "samples" to
 src/schema/objects/top_level_files.yaml

---
 src/schema/objects/top_level_files.yaml | 31 +++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 12e1823472..88c9204d58 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_files.yaml
@@ -77,3 +77,34 @@ participants:
 
     Throughout BIDS you can indicate missing values with `n/a` (for "not
     available").
+
+samples:
+  name: Sample Information
+  description: |
+    The purpose of this file is to describe properties of samples, indicated by the `sample` entity.
+    This file is REQUIRED if `sample-<label>` is present in any file name within the dataset.
+    If this file exists, it MUST contain the three following columns:
+
+    -   `sample_id`: MUST consist of `sample-<label>` values identifying one row
+        for each sample
+
+    -   `participant_id`: MUST consist of `sub-<label>`
+
+    -   `sample_type`: MUST consist of sample type values, either `cell line`, `in vitro differentiated cells`,
+        `primary cell`, `cell-free sample`, `cloning host`, `tissue`, `whole organisms`, `organoid` or
+        `technical sample` from [ENCODE Biosample Type](https://www.encodeproject.org/profiles/biosample_type)
+
+    Other optional columns MAY be used to describe the samples.
+    Each sample MUST be described by one and only one row.
+
+    Commonly used *optional* columns in `samples.tsv` files are `pathology` and
+    `derived_from`. We RECOMMEND to make use of these columns, and in case that
+    you do use them, we RECOMMEND to use the following values for them:
+
+    -   `pathology`: string value describing the pathology of the sample or type of control.
+        When different from `healthy`, pathology SHOULD be specified in `samples.tsv`.
+        The pathology MAY instead be specified in [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file)
+        in case it changes over time.
+
+    -   `derived_from`: `sample-<label>` key/value pair from which a sample is derived from,
+        for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`)

From 5a58d60cf7966f98431ac6e004c56d028a41bbd2 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Thu, 13 Jan 2022 10:42:11 -0500
Subject: [PATCH 145/347] Formatting in src/schema/objects/top_level_files.yaml

---
 src/schema/objects/top_level_files.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 88c9204d58..0277d43fbd 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_files.yaml
@@ -103,8 +103,8 @@ samples:
 
     -   `pathology`: string value describing the pathology of the sample or type of control.
         When different from `healthy`, pathology SHOULD be specified in `samples.tsv`.
-        The pathology MAY instead be specified in [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file)
-        in case it changes over time.
+        The pathology MAY instead be specified in
+        [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file) in case it changes over time.
 
     -   `derived_from`: `sample-<label>` key/value pair from which a sample is derived from,
         for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`)

From 6405a2b1d7ad3e1221cc71e4afcc617378dcf46d Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 17 Jan 2022 14:46:29 +0100
Subject: [PATCH 146/347] update steering group composition (#976)

---
 DECISION-MAKING.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index 3250390561..f52f7e2763 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -20,6 +20,12 @@ BIDS governance.
 | Melanie Ganz ([@melanieganz](https://github.com/melanieganz))                |
 | Robert Oostenveld ([@robertoostenveld](https://github.com/robertoostenveld)) |
 | Russell Poldrack ([@poldrack](https://github.com/poldrack))                  |
+| Ariel Rokem ([@arokem](https://github.com/arokem))            |
+
+#### Past steering group members
+
+| Name                                                                         |
+|------------------------------------------------------------------------------|
 | Kirstie Whitaker ([@KirstieJane](https://github.com/KirstieJane))            |
 
 ### Maintainers Group

From b0b144b1003dc4c2dee9f9a1a1a943b08238402a Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Mon, 17 Jan 2022 09:16:18 -0500
Subject: [PATCH 147/347] Fix link to sessions file in
 src/schema/objects/top_level_files.yaml

---
 src/schema/objects/top_level_files.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 0277d43fbd..79eab838c0 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_files.yaml
@@ -104,7 +104,7 @@ samples:
     -   `pathology`: string value describing the pathology of the sample or type of control.
         When different from `healthy`, pathology SHOULD be specified in `samples.tsv`.
         The pathology MAY instead be specified in
-        [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file) in case it changes over time.
+        [Sessions files](../03-modality-agnostic-files.md#sessions-file) in case it changes over time.
 
     -   `derived_from`: `sample-<label>` key/value pair from which a sample is derived from,
         for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`)

From 0fdf5adb793f3aa1b22d2686c45be260d4927c90 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Tue, 18 Jan 2022 18:54:25 +0000
Subject: [PATCH 148/347] [DOC] Auto-generate changelog entry for PR #881

---
 src/CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 15de82bd56..a3cc4bfb12 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[DOC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] harmonize 'file name' into 'filename' [#962](https://github.com/bids-standard/bids-specification/pull/962) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Reword front page [#958](https://github.com/bids-standard/bids-specification/pull/958) ([arokem](https://github.com/arokem))
 -   \[MAINT] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies))
@@ -35,6 +36,7 @@
 -   \[INFRA] fix draft rendering css on mobile or when browser window is narrow [#889](https://github.com/bids-standard/bids-specification/pull/889) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Add an animated BIDS logo [#886](https://github.com/bids-standard/bids-specification/pull/886) ([adswa](https://github.com/adswa))
 -   \[SCHEMA] Consolidate schema files by term type [#883](https://github.com/bids-standard/bids-specification/pull/883) ([tsalo](https://github.com/tsalo))
+-   \[ENH] BEP031: Microscopy [#881](https://github.com/bids-standard/bids-specification/pull/881) ([mariehbourget](https://github.com/mariehbourget))
 -   \[INFRA] jQuery 3.4.1 → 3.6.0 [#875](https://github.com/bids-standard/bids-specification/pull/875) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[INFRA] Add "codespell" tool to CI checks to catch typos sooner [#873](https://github.com/bids-standard/bids-specification/pull/873) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[INFRA] Several style fixes (Flake8) for Python code in the repo [#872](https://github.com/bids-standard/bids-specification/pull/872) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))

From 6dfc9d4a5a85da3cd1d7097f7c93f95de7469888 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 10:41:36 +0100
Subject: [PATCH 149/347] Apply suggestions from code review

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 macros_doc.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/macros_doc.md b/macros_doc.md
index 119197cb5d..0219b4d51b 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -27,6 +27,8 @@ the table falls into one of the categories listed in the macros table.
 
 If you want to add content with a macro and need help, do not hesitate to
 contact a member of the bids-maintainers for help.
+To do this, you can either mention an individual maintainer by their GitHub
+username or mention the whole team (`@bids-standard/maintainers`).
 
 Nope. No need to learn how to program to use those macros. But some macros
 require some specific "input", so you will just need to know what input to give
@@ -58,7 +60,7 @@ GitHub's way of directly rendering markdown documents makes it a bit harder to
 read, so if you opened the markdown document in your code editor it would look
 like this.
 
-```python
+```markdown
 #### Reconstruction
 
 {{ MACROS___make_metadata_table(

From 5f34a8edffdca949b36c1c2b5a2357736d9e9f23 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 10:48:45 +0100
Subject: [PATCH 150/347] remove macro doc from CONTRIBUTING.md

---
 CONTRIBUTING.md | 77 ++-----------------------------------------------
 1 file changed, 3 insertions(+), 74 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index cef99f9fa8..bd49034b93 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -225,81 +225,10 @@ That would look like this:
 ## Using macros
 
 We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
-to render parts of the BIDS specification from the BIDS schema.
-Macros make it easy to achieve a consistent style throughout the specification,
-and changing a given macro will automatically change all appropriate paragraphs in the specification.
-
-For example, all tables on BIDS metadata are generated via macros that make use of data in the
-[yaml files](src/schema/metadata) in the [schema](src/schema/README.md).
-
-These macros are written in Python
-(see the folders [tools/schemacode](tools/schemacode) and [tools/mkdocs_macros_bids](tools/mkdocs_macros_bids)),
-and are called directly in the Markdown document where you want the output of the macro to be inserted.
-
-For example:
-
-```Text
-{{ MACROS___make_metadata_table(
-   {
-      "SamplingFrequency": "REQUIRED",
-      "StartTime": "RECOMMENDED, but REQUIRED for sparse sequences",
-   }
-) }}
-```
-
-This macro will create a table for the "SamplingFrequency" and "StartTime" metadata,
-filling the table with the content specified in their respective yaml files
-(see [SamplingFrequency.yaml](src/schema/metadata/SamplingFrequency.yaml) and [StartTime.yaml](src/schema/metadata/StartTime.yaml)).
-
-Some of the content created by the macro can be specified in the macro call itself, as opposed to in the yaml files.
-Here the `"REQUIRED"`, `"RECOMMENDED, but REQUIRED for sparse sequences"`
-specify the content of the requirement level column for each piece of metadata.
-
-This macro also allows you to append extra content to the description of that metadata
-by specifying it in the macro call:
-
-```Text
-{{ MACROS___make_metadata_table(
-   {
-      "SamplingFrequency": ("REQUIRED", "This extra content will be added to the description")
-      "StartTime": "RECOMMENDED, but REQUIRED for sparse sequences",
-   }
-) }}
-```
-
-### Writing folder content examples
-
-We also use macros to have a consistent style to render the examples of folder contents.
-
-These code for these macros are in the folder [tools/schemacode](tools/schemacode).
-
-To insert examples in the code you have make calls to the macro like this:
-
-```
-{{ MACROS___make_filetree_example(
-
-   {
-   "sub-01": {
-      "func": {
-         "sub-control01_task-nback_bold.json": "",
-         },
-      }
-   }
-
-) }}
-```
-
-And this will be turned into this.
-
-```Text
-└─ sub-01/
-   └─ func/
-      └─ sub-control01_task-nback_bold.json
-```
+to standardize how some aspects of the BIDS specification are rendered in HTML.
 
-When you have complex files and folder structure, we suggest you use this
-[Jupyter notebook](tools/filetree_example.ipynb) for sandboxing your example
-before you insert the macro call into the markdown document.
+<!-- TODO update link once we know we have found a final home for that doc -->
+We have dedicated documentation for [this](./macro_doc.md).
 
 ## Building the specification using mkdocs
 

From edad914a416376e5dedf285dce3c1549369b27b4 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 10:55:12 +0100
Subject: [PATCH 151/347] add links to documentation for mkdocs, theme and
 macros

---
 macros_doc.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/macros_doc.md b/macros_doc.md
index 0219b4d51b..f726603692 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -301,6 +301,12 @@ Under the hood the macros themselves call some more python code that is in the
 
 https://github.com/bids-standard/bids-specification/tree/master/tools
 
+
+## Links and references
+
+- [documentation for mkdocs](https://www.mkdocs.org) and how to install it locally,
+- [documentation for the material theme](https://squidfunk.github.io/mkdocs-material/) we use.
+- [documentation for the `macros` plugin](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
 ---
 
 Macro section in the CONTRIBUTING.md

From 0eb8aea97be0c334448e91cd1a2e2a16bafce0ab Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 11:10:46 +0100
Subject: [PATCH 152/347] incorporate content from CONTRIBUTING to the new
 macro doc

---
 macros_doc.md | 114 ++++++++++++++++++++++++++++++++++----------------
 1 file changed, 77 insertions(+), 37 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index f726603692..81d78a0194 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -1,5 +1,14 @@
 # Using MkDocs macros in the BIDS specification
 
+We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
+to standardize how some aspects of the BIDS specification are rendered in HTML.
+Macros make it easy to achieve a consistent style throughout the specification,
+and changing a given macro will automatically change all appropriate paragraphs in the specification.
+
+Below you will find answers to frequently asked questions regarding macros.
+
+<!-- TODO add TOC -->
+
 ## What are macros and why use them?
 
 A macro is a rule or pattern that specifies how an input should be mapped to
@@ -9,16 +18,37 @@ such as Excel.
 
 MkDocs (the tool we use to turn the markdown version of the specification into
 HTML pages) supports macros. In the BIDS specification document, we use these
-macros to standarize the format of items such as tables and examples.
+macros to standardize the format of items such as tables and examples.
 
 Increasingly, parts of the BIDS specification are being formalized into a
 "schema" so that requirements in the specification can be automatically checked
-by validators. Several of the macros incorporate information from the schema to
+by validators. Several of the macros incorporate information from this schema to
 assure consistency.
 
-Table of macros here: | Name | Purpose | Uses schema | Link to example of use |
+## What macros are available? What can we use macros for?
+
+All the macros we use are in listed in this [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
+
+Some of the main ones and what they do:
+
+| Name | Purpose | Uses schema | Link to example of use |
 | ---- | ------- | ----------- | ---------------------- |
 
+- create the filename templates for each valid combination of datatype / suffix
+  / extension
+- create a table of definition, format... for each of the (1) metadata terms
+  that goes into a specific JSON, (2) valid suffixes for a given modality, and
+  (3) valid columns that can go into a specific TSV file.
+- create the entity table in the appendix that list for each datatype / suffix,
+  which entity is required
+- format the folder / file trees example in a systematic manner
+- Create the Entities appendix page, which contains the definitions and other
+  relevant information for valid BIDS entities.
+- ...
+
+Under the hood the macros themselves call some more python code that is in the
+[`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
+
 ## When should I use a macro?
 
 Most typo corrections and minor changes to the BIDS specification do not require
@@ -43,7 +73,43 @@ add a completely new piece of metadata to the specification. In that case, you
 will need to create the input for the macro to be able to do its job. For that,
 you will need to update the schema itself.
 
-## How to
+## How-To and Examples
+
+### Writing folder content examples
+
+We also use macros to have a consistent style to render the examples of folder contents.
+
+These code for these macros are in the folder [tools/schemacode](tools/schemacode).
+
+To insert examples in the code you have make calls to the macro like this:
+
+```
+{{ MACROS___make_filetree_example(
+
+   {
+   "sub-01": {
+      "func": {
+         "sub-control01_task-nback_bold.json": "",
+         },
+      }
+   }
+
+) }}
+```
+
+And this will be turned into this.
+
+```Text
+└─ sub-01/
+   └─ func/
+      └─ sub-control01_task-nback_bold.json
+```
+
+When you have complex files and folder structure, we suggest you use this
+[Jupyter notebook](tools/filetree_example.ipynb) for sandboxing your example
+before you insert the macro call into the markdown document.
+
+### Generating tables
 
 Say you want to edit the content of table of the `Reconstruction` section for
 the PET page.
@@ -134,7 +200,7 @@ call above it would give a table that would look like this:
 | ------------ | ------------------------------------------ | --------- | -------------------------------------------- |
 | TermToRender | REQUIREMENT_LEVEL plus anything else after | string    | whatever description was in the metadata.yml |
 
-### Modifying a term in the table
+#### Modifying a term in the table
 
 So if you want to change the content of what will appear in the HTML table, you
 need to edit this `metadata.yml` file.
@@ -153,7 +219,7 @@ macro call.
        ...
 ```
 
-### Why would you NOT want to modify the content of the yml file directly ?
+#### Why would you NOT want to modify the content of the yml file directly ?
 
 Well the same term can be used in different parts of the BIDS specification and
 some details that might apply to, say, PET might not apply to how the term is
@@ -164,7 +230,7 @@ So always better to check if that term is not used somewhere else before making
 a change in the yml file. When in doubt add the change directly in the Macro
 call and ask the BIDS maintainers for help.
 
-### Adding a new term to the table
+#### Adding a new term to the table
 
 Say you wanted to add a new term `MoonPhase` to the table, on the second row.
 You would do it like this. But this would only work if the `metadata.yml` file
@@ -277,42 +343,16 @@ with a table in Markdown.
 If later we see that the same type of table keeps reoccuring the specification
 we could create a macro to generate them.
 
-## What macros are available? What can we use macros for?
-
-All the macros we use are in here:
-https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py
-
-Some of the main ones and what they do:
-
-- create the filename templates for each valid combination of datatype / suffix
-  / extension
-- create a table of definition, format... for each of the (1) metadata terms
-  that goes into a specific JSON, (2) valid suffixes for a given modality, and
-  (3) valid columns that can go into a specific TSV file.
-- create the entity table in the appendix that list for each datatype / suffix,
-  which entity is required
-- format the folder / file trees example in a systematic manner
-- Create the Entities appendix page, which contains the definitions and other
-  relevant information for valid BIDS entities.
-- ...
-
-Under the hood the macros themselves call some more python code that is in the
-`tools` folder:
-
-https://github.com/bids-standard/bids-specification/tree/master/tools
-
-
 ## Links and references
 
 - [documentation for mkdocs](https://www.mkdocs.org) and how to install it locally,
 - [documentation for the material theme](https://squidfunk.github.io/mkdocs-material/) we use.
 - [documentation for the `macros` plugin](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
----
 
-Macro section in the CONTRIBUTING.md
 
-https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#using-macros
 
-The official MkDocs documentation for the `macros` plugin:
 
-https://mkdocs-macros-plugin.readthedocs.io/en/latest/
+
+
+
+

From 5aeb272ee9dd3f6498ef2d863ab5f02f77c7ae69 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:10:35 +0100
Subject: [PATCH 153/347] add TOC

---
 macros_doc.md | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/macros_doc.md b/macros_doc.md
index 81d78a0194..27a8f53e59 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -7,7 +7,22 @@ and changing a given macro will automatically change all appropriate paragraphs
 
 Below you will find answers to frequently asked questions regarding macros.
 
-<!-- TODO add TOC -->
+- [Using MkDocs macros in the BIDS specification](#using-mkdocs-macros-in-the-bids-specification)
+   - [What are macros and why use them?](#what-are-macros-and-why-use-them)
+   - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros)
+   - [What macros are available? What can we use macros for?](#what-macros-are-available-what-can-we-use-macros-for)
+   - [When should I use a macro?](#when-should-i-use-a-macro)
+   - [Do I need learn how to code in Python to use those macros?](#do-i-need-learn-how-to-code-in-python-to-use-those-macros)
+   - [Why use macros at all?](#why-use-macros-at-all)
+   - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call)
+   - [How-To and Examples](#how-to-and-examples)
+      - [Writing folder content examples](#writing-folder-content-examples)
+      - [Generating tables](#generating-tables)
+         - [Modifying a term in the table](#modifying-a-term-in-the-table)
+         - [Why would you NOT want to modify the content of the yml file directly ?](#why-would-you-not-want-to-modify-the-content-of-the-yml-file-directly-)
+         - [Adding a new term to the table](#adding-a-new-term-to-the-table)
+         - [Should I create a macro if I need a new kind of table?](#should-i-create-a-macro-if-i-need-a-new-kind-of-table)
+   - [Links and references](#links-and-references)
 
 ## What are macros and why use them?
 

From 94f308539068e178adfcfb89bb122a5256c9f104 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:11:09 +0100
Subject: [PATCH 154/347] add doc about input types required by the macros

---
 macros_doc.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/macros_doc.md b/macros_doc.md
index 27a8f53e59..000f510c08 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -35,7 +35,16 @@ MkDocs (the tool we use to turn the markdown version of the specification into
 HTML pages) supports macros. In the BIDS specification document, we use these
 macros to standardize the format of items such as tables and examples.
 
-Increasingly, parts of the BIDS specification are being formalized into a
+## What kind of input information are required by macros?
+
+It will depend for each macro.
+
+For some of them, all the inputs will be directly available in the markdown document
+where you have put the call to the macro.
+
+Other macros will need to be pointed to some external input (like a metadata term) 
+that they are supposed to help rendering. 
+For example, parts of the BIDS specification are formalized into a
 "schema" so that requirements in the specification can be automatically checked
 by validators. Several of the macros incorporate information from this schema to
 assure consistency.

From 0272e0546914bba459f9b75568bb08f8c780e43a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:11:26 +0100
Subject: [PATCH 155/347] add table of available macros

---
 macros_doc.md | 29 ++++++++++++-----------------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 000f510c08..0fac18160c 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -51,26 +51,21 @@ assure consistency.
 
 ## What macros are available? What can we use macros for?
 
-All the macros we use are in listed in this [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
-
-Some of the main ones and what they do:
+All the macros we use are in listed in this 
+[python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
 
 | Name | Purpose | Uses schema | Link to example of use |
 | ---- | ------- | ----------- | ---------------------- |
-
-- create the filename templates for each valid combination of datatype / suffix
-  / extension
-- create a table of definition, format... for each of the (1) metadata terms
-  that goes into a specific JSON, (2) valid suffixes for a given modality, and
-  (3) valid columns that can go into a specific TSV file.
-- create the entity table in the appendix that list for each datatype / suffix,
-  which entity is required
-- format the folder / file trees example in a systematic manner
-- Create the Entities appendix page, which contains the definitions and other
-  relevant information for valid BIDS entities.
-- ...
-
-Under the hood the macros themselves call some more python code that is in the
+| make_filename_template | Generate a filename template from the schema, based on specific filters. | Yes | |
+| make_entity_table | Generate an entity table from the schema, based on specific filters. | Yes |  |
+| make_entity_definitions | Generate definitions and other relevant information for entities in the specification.  | Yes |  |
+| make_glossary |  | yes |  |
+| make_suffix_table | Generate a markdown table of suffix information. | yes |  |
+| make_metadata_table | Generate a markdown table of metadata field information. | Yes |  |
+| make_columns_table | Generate a markdown table of TSV column information. | Yes |  |
+| make_filetree_example | Generate a filetree snippet from example content. | Yes |  |
+
+Note that under the hood the macros themselves call some more python code that is in the
 [`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
 
 ## When should I use a macro?

From a8bc09aa4c5bf1496932019a42e4a37835f93748 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:11:49 +0100
Subject: [PATCH 156/347] reorder sections

---
 macros_doc.md | 162 ++++++++++++++++++++++++--------------------------
 1 file changed, 79 insertions(+), 83 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 0fac18160c..725c08a464 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -79,6 +79,8 @@ contact a member of the bids-maintainers for help.
 To do this, you can either mention an individual maintainer by their GitHub
 username or mention the whole team (`@bids-standard/maintainers`).
 
+## Do I need learn how to code in Python to use those macros?
+
 Nope. No need to learn how to program to use those macros. But some macros
 require some specific "input", so you will just need to know what input to give
 it. In many cases, it will be just a metadata term whose definition or
@@ -89,8 +91,75 @@ rest of the info it should use to do the rest of its work.
 
 The only exception to this is when you want to add new content. Say you want to
 add a completely new piece of metadata to the specification. In that case, you
-will need to create the input for the macro to be able to do its job. For that,
-you will need to update the schema itself.
+will need to create the input for the macro to be able to do its job.
+
+## Why use macros at all?
+
+> Seriously why did you have to make it so complicated just to have pretty
+> tables? Are macros that necessary ? Couldn't we just have everything in
+> Markdown?
+
+In principle we could, and before we started working on the schema that's
+exactly what we did. But there are several good reasons to use macros.
+
+When a definition gets repeated in different places, we could just copy-paste
+it. But when you start having several copies of that definition, if you have to
+modify it, you then need to edit several files and never forget any of them. So
+this becomes very error prone.
+
+So it becomes better to have one central place for that definition and grab that
+definition every time we need to reuse it.
+
+In practice this applies the 
+[DRY principle ("Don't Repeat Yourself")](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself) 
+to the specification:
+
+> "Every piece of knowledge must have a single, unambiguous, authoritative
+> representation within a system".
+
+Having one centralized place where we put all our definitions can be useful when
+we want other tools (the BIDS validator, bids-matlab...) to use the content of
+the specification.
+
+This is where the BIDS schema (those .yml files we talked about above) comes in
+as it is meant to be a machine readable version of the specification.
+
+And so to avoid having to maintain the SAME definition in both the schema and
+specification, we started using macros to generate the specification from the
+schema.
+
+## Anything else I need to know if I need to insert a new macro call?
+
+One nice thing for the people who will come after you (or yourself in 6 months
+when you get back to the document you just edited) is to leave a comment before
+the macro to quickly explain what it does and where to find more information
+about it.
+
+<!-- - [ ] TODO for maintainers: actually add those comments in the current
+      specification. -->
+
+It could for example look like this:
+
+```markdown
+<!--
+This block generates a metadata table.
+The definitions of these fields can be found in src/schema/...
+and a guide for editing at <link>.
+-->
+
+{{ MACROS___make_metadata_table(
+   {
+      "AcquisitionMode": "REQUIRED",
+      "MoonPhase": "OPTIONAL",
+      "ImageDecayCorrected": "REQUIRED",
+      "ImageDecayCorrectionTime": "REQUIRED",
+
+      ...
+
+   }
+) }}
+
+```
 
 ## How-To and Examples
 
@@ -191,7 +260,7 @@ The macro will create the different columns of the table:
 - Data type
 - Description
 
-A general description of that Macro call would look like this:
+A general description of that macro call would look like this:
 
 ```python
 {{ MACROS___make_metadata_table(
@@ -201,18 +270,15 @@ A general description of that Macro call would look like this:
 ) }}
 ```
 
-To know what to put in the different columns, the macro will go and look into
-the `metadata.yaml` file in the BIDS schema and find the entry that correspond
-to the term you want to add.
-
-https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml
+To know what to put in the different columns, the macro will go and look into the 
+[`metadata.yaml`](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml) 
+file in the BIDS schema and find the entry that correspond to the term you want to add.
 
 And in the above example, all the information about `AcquisitionMode` would be
-read from that section:
+read from [that section](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml#L20).
 
-https://github.com/bids-standard/bids-specification/blob/05f7ce1ae9cc72b087b57c39183e36afcf37cb00/src/schema/objects/metadata.yaml#L20
 
-If you had to write the markdown equivalent of the general example for the Macro
+If you had to write the markdown equivalent of the general example for the macro
 call above it would give a table that would look like this:
 
 | Key name     | Requirement level                          | Data type | Description                                  |
@@ -246,7 +312,7 @@ used for MRI. So we can use the schema for the common part and add extra content
 where necessary in the macro call.
 
 So always better to check if that term is not used somewhere else before making
-a change in the yml file. When in doubt add the change directly in the Macro
+a change in the yml file. When in doubt add the change directly in the macro
 call and ask the BIDS maintainers for help.
 
 #### Adding a new term to the table
@@ -281,77 +347,7 @@ https://the-turing-way.netlify.app/reproducible-research/renv/renv-yaml.html
 In practice, you should try to use a code editor that tells you when your syntax
 is wrong.
 
-## Why use macros at all?
-
-> Seriously why did you have to make it so complicated just to have pretty
-> tables? Are Macros that necessary ? Couldn't we just have everything in
-> Markdown?
-
-In principle we could, and before we started working on the schema that's
-exactly what we did. But there are several good reasons to use macros.
-
-When a definition gets repeated in different places, we could just copy-paste
-it. But when you start having several copies of that definition, if you have to
-modify it, you then need to edit several files and never forget any of them. So
-this becomes very error prone.
-
-So it becomes better to have one central place for that definition and grab that
-definition every time we need to reuse it.
-
-In practice this applies the DRY principle ("Don't Repeat Yourself") to the
-specification:
-
-> "Every piece of knowledge must have a single, unambiguous, authoritative
-> representation within a system".
-
-https://en.wikipedia.org/wiki/Don%27t_repeat_yourself
-
-Having one centralized place where we put all our definitions can be useful when
-we want other tools (the BIDS validator, bids-matlab...) to use the content of
-the specification.
-
-This is where the BIDS schema (those .yml files we talked about above) comes in
-as it is meant to be a machine readable version of the specification.
-
-And so to avoid having to maintain the SAME definition in both the schema and
-specification, we started using macros to generate the specification from the
-schema.
-
-## Anything else I need to know if I need to insert a new macro call?
-
-One nice thing for the people who will come after you (or yourself in 6 months
-when you get back to the document you just edited) is to leave a comment before
-the macro to quickly explain what it does and where to find more information
-about it.
-
-<!-- - [ ] TODO for maintainers: actually add those comments in the current
-      specification. -->
-
-It could for example look like this:
-
-```markdown
-<!--
-This block generates a metadata table.
-The definitions of these fields can be found in src/schema/...
-and a guide for editing at <link>.
--->
-
-
-{{ MACROS___make_metadata_table(
-   {
-      "AcquisitionMode": "REQUIRED",
-      "MoonPhase": "OPTIONAL",
-      "ImageDecayCorrected": "REQUIRED",
-      "ImageDecayCorrectionTime": "REQUIRED",
-
-      ...
-
-   }
-) }}
-
-```
-
-## Should I create a macro if I need a new kind of table?
+#### Should I create a macro if I need a new kind of table?
 
 As a rule of thumb, no.
 

From 793ff70b5711b91dfedd5dba662ed811da67583a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:12:21 +0100
Subject: [PATCH 157/347] auto lint

---
 macros_doc.md | 100 ++++++++++++++++++++++++--------------------------
 1 file changed, 47 insertions(+), 53 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 725c08a464..32947301e5 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -3,7 +3,8 @@
 We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
 to standardize how some aspects of the BIDS specification are rendered in HTML.
 Macros make it easy to achieve a consistent style throughout the specification,
-and changing a given macro will automatically change all appropriate paragraphs in the specification.
+and changing a given macro will automatically change all appropriate paragraphs
+in the specification.
 
 Below you will find answers to frequently asked questions regarding macros.
 
@@ -39,33 +40,33 @@ macros to standardize the format of items such as tables and examples.
 
 It will depend for each macro.
 
-For some of them, all the inputs will be directly available in the markdown document
-where you have put the call to the macro.
+For some of them, all the inputs will be directly available in the markdown
+document where you have put the call to the macro.
 
-Other macros will need to be pointed to some external input (like a metadata term) 
-that they are supposed to help rendering. 
-For example, parts of the BIDS specification are formalized into a
-"schema" so that requirements in the specification can be automatically checked
-by validators. Several of the macros incorporate information from this schema to
-assure consistency.
+Other macros will need to be pointed to some external input (like a metadata
+term) that they are supposed to help rendering. For example, parts of the BIDS
+specification are formalized into a "schema" so that requirements in the
+specification can be automatically checked by validators. Several of the macros
+incorporate information from this schema to assure consistency.
 
 ## What macros are available? What can we use macros for?
 
-All the macros we use are in listed in this 
+All the macros we use are in listed in this
 [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
 
-| Name | Purpose | Uses schema | Link to example of use |
-| ---- | ------- | ----------- | ---------------------- |
-| make_filename_template | Generate a filename template from the schema, based on specific filters. | Yes | |
-| make_entity_table | Generate an entity table from the schema, based on specific filters. | Yes |  |
-| make_entity_definitions | Generate definitions and other relevant information for entities in the specification.  | Yes |  |
-| make_glossary |  | yes |  |
-| make_suffix_table | Generate a markdown table of suffix information. | yes |  |
-| make_metadata_table | Generate a markdown table of metadata field information. | Yes |  |
-| make_columns_table | Generate a markdown table of TSV column information. | Yes |  |
-| make_filetree_example | Generate a filetree snippet from example content. | Yes |  |
-
-Note that under the hood the macros themselves call some more python code that is in the
+| Name                    | Purpose                                                                                | Uses schema | Link to example of use |
+| ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ---------------------- |
+| make_filename_template  | Generate a filename template from the schema, based on specific filters.               | Yes         |                        |
+| make_entity_table       | Generate an entity table from the schema, based on specific filters.                   | Yes         |                        |
+| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes         |                        |
+| make_glossary           |                                                                                        | yes         |                        |
+| make_suffix_table       | Generate a markdown table of suffix information.                                       | yes         |                        |
+| make_metadata_table     | Generate a markdown table of metadata field information.                               | Yes         |                        |
+| make_columns_table      | Generate a markdown table of TSV column information.                                   | Yes         |                        |
+| make_filetree_example   | Generate a filetree snippet from example content.                                      | Yes         |                        |
+
+Note that under the hood the macros themselves call some more python code that
+is in the
 [`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
 
 ## When should I use a macro?
@@ -75,9 +76,9 @@ you to use macros. Even adding a table may not require you to use macros unless
 the table falls into one of the categories listed in the macros table.
 
 If you want to add content with a macro and need help, do not hesitate to
-contact a member of the bids-maintainers for help.
-To do this, you can either mention an individual maintainer by their GitHub
-username or mention the whole team (`@bids-standard/maintainers`).
+contact a member of the bids-maintainers for help. To do this, you can either
+mention an individual maintainer by their GitHub username or mention the whole
+team (`@bids-standard/maintainers`).
 
 ## Do I need learn how to code in Python to use those macros?
 
@@ -110,8 +111,8 @@ this becomes very error prone.
 So it becomes better to have one central place for that definition and grab that
 definition every time we need to reuse it.
 
-In practice this applies the 
-[DRY principle ("Don't Repeat Yourself")](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself) 
+In practice this applies the
+[DRY principle ("Don't Repeat Yourself")](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself)
 to the specification:
 
 > "Every piece of knowledge must have a single, unambiguous, authoritative
@@ -147,27 +148,24 @@ The definitions of these fields can be found in src/schema/...
 and a guide for editing at <link>.
 -->
 
-{{ MACROS___make_metadata_table(
-   {
-      "AcquisitionMode": "REQUIRED",
-      "MoonPhase": "OPTIONAL",
-      "ImageDecayCorrected": "REQUIRED",
-      "ImageDecayCorrectionTime": "REQUIRED",
+{{ MACROS\_\_\_make_metadata_table( { "AcquisitionMode": "REQUIRED",
+"MoonPhase": "OPTIONAL", "ImageDecayCorrected": "REQUIRED",
+"ImageDecayCorrectionTime": "REQUIRED",
 
       ...
 
-   }
-) }}
-
+} ) }}
 ```
 
 ## How-To and Examples
 
 ### Writing folder content examples
 
-We also use macros to have a consistent style to render the examples of folder contents.
+We also use macros to have a consistent style to render the examples of folder
+contents.
 
-These code for these macros are in the folder [tools/schemacode](tools/schemacode).
+These code for these macros are in the folder
+[tools/schemacode](tools/schemacode).
 
 To insert examples in the code you have make calls to the macro like this:
 
@@ -270,13 +268,15 @@ A general description of that macro call would look like this:
 ) }}
 ```
 
-To know what to put in the different columns, the macro will go and look into the 
-[`metadata.yaml`](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml) 
-file in the BIDS schema and find the entry that correspond to the term you want to add.
+To know what to put in the different columns, the macro will go and look into
+the
+[`metadata.yaml`](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml)
+file in the BIDS schema and find the entry that correspond to the term you want
+to add.
 
 And in the above example, all the information about `AcquisitionMode` would be
-read from [that section](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml#L20).
-
+read from
+[that section](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/metadata.yaml#L20).
 
 If you had to write the markdown equivalent of the general example for the macro
 call above it would give a table that would look like this:
@@ -360,14 +360,8 @@ we could create a macro to generate them.
 
 ## Links and references
 
-- [documentation for mkdocs](https://www.mkdocs.org) and how to install it locally,
-- [documentation for the material theme](https://squidfunk.github.io/mkdocs-material/) we use.
+- [documentation for mkdocs](https://www.mkdocs.org) and how to install it
+  locally,
+- [documentation for the material theme](https://squidfunk.github.io/mkdocs-material/)
+  we use.
 - [documentation for the `macros` plugin](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
-
-
-
-
-
-
-
-

From 5413b0aeb4c562d81d36e4973310ec7ba3cfea6d Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 19 Jan 2022 12:17:28 +0100
Subject: [PATCH 158/347] update filetree macro example

---
 macros_doc.md | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 32947301e5..5d5123b865 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -161,13 +161,16 @@ and a guide for editing at <link>.
 
 ### Writing folder content examples
 
-We also use macros to have a consistent style to render the examples of folder
-contents.
+One of the simplest macro we use helps us create consistent "file tree" examples
+that would look like this in the final document:
 
-These code for these macros are in the folder
-[tools/schemacode](tools/schemacode).
+```Text
+└─ sub-01/
+   └─ func/
+      └─ sub-control01_task-nback_bold.json
+```
 
-To insert examples in the code you have make calls to the macro like this:
+To do this get this output, your macro call would look like this:
 
 ```
 {{ MACROS___make_filetree_example(
@@ -183,14 +186,6 @@ To insert examples in the code you have make calls to the macro like this:
 ) }}
 ```
 
-And this will be turned into this.
-
-```Text
-└─ sub-01/
-   └─ func/
-      └─ sub-control01_task-nback_bold.json
-```
-
 When you have complex files and folder structure, we suggest you use this
 [Jupyter notebook](tools/filetree_example.ipynb) for sandboxing your example
 before you insert the macro call into the markdown document.

From 4bf68b9d0bc09e61879e9196e2e48e1471e0fa2a Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Wed, 19 Jan 2022 17:42:32 +0100
Subject: [PATCH 159/347] customize footer on html spec (#975)

* add socials

* fix

* fix link
---
 LICENSE                                   |  2 +-
 mkdocs.yml                                | 11 ++-
 theme_customizations/partials/footer.html | 99 -----------------------
 3 files changed, 11 insertions(+), 101 deletions(-)
 delete mode 100644 theme_customizations/partials/footer.html

diff --git a/LICENSE b/LICENSE
index d4466ac392..d591978380 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 Attribution 4.0 International
 
-Copyright (c) 2020, BIDS Contributors.
+Copyright (c) 2018-2022, BIDS Contributors.
 
 =======================================================================
 
diff --git a/mkdocs.yml b/mkdocs.yml
index 0f37932c70..d7867faea3 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -2,11 +2,20 @@ site_name: Brain Imaging Data Structure v1.6.1-dev
 site_url: https://bids-specification.readthedocs.io/en/stable/
 theme:
     name: material
-    custom_dir: theme_customizations/
     favicon: images/favicon.png
     logo: images/logo.png
     features:
       - navigation.sections
+copyright: Copyright &copy; 2018-2022, BIDS Contributors - <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>
+extra:
+    generator: false
+    social:
+      - icon: fontawesome/brands/twitter
+        link: https://twitter.com/BIDSstandard/
+      - icon: fontawesome/brands/github
+        link: https://github.com/bids-standard/bids-specification/
+      - icon: fontawesome/brands/google
+        link: https://groups.google.com/g/bids-discussion
 extra_javascript:
     - js/jquery-3.6.0.min.js
 markdown_extensions:
diff --git a/theme_customizations/partials/footer.html b/theme_customizations/partials/footer.html
deleted file mode 100644
index b28c19183a..0000000000
--- a/theme_customizations/partials/footer.html
+++ /dev/null
@@ -1,99 +0,0 @@
-<!--
-  Copyright (c) 2016-2019 Martin Donath <martin.donath@squidfunk.com>
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy
-  of this software and associated documentation files (the "Software"), to
-  deal in the Software without restriction, including without limitation the
-  rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-  sell copies of the Software, and to permit persons to whom the Software is
-  furnished to do so, subject to the following conditions:
-
-  The above copyright notice and this permission notice shall be included in
-  all copies or substantial portions of the Software.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
-  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-  IN THE SOFTWARE.
--->
-
-{%- import "partials/language.html" as lang with context -%}
-
-<!-- Application footer -->
-<footer class="md-footer">
-
-  <!-- Link to previous and/or next page -->
-  {%- if page.previous_page or page.next_page -%}
-    <div class="md-footer-nav">
-      <nav class="md-footer-nav__inner md-grid">
-
-        <!-- Link to previous page -->
-        {%- if page.previous_page -%}
-          <a href="{{ page.previous_page.url | url }}"
-              title="{{ page.previous_page.title }}"
-              class="md-flex md-footer-nav__link md-footer-nav__link--prev"
-              rel="prev">
-            <div class="md-flex__cell md-flex__cell--shrink">
-              <i class="md-icon md-icon--arrow-back
-                    md-footer-nav__button"></i>
-            </div>
-            <div class="md-flex__cell md-flex__cell--stretch
-                  md-footer-nav__title">
-              <span class="md-flex__ellipsis">
-                <span class="md-footer-nav__direction">
-                  {{- lang.t("footer.previous") -}}
-                </span>
-                {{- page.previous_page.title -}}
-              </span>
-            </div>
-          </a>
-        {%- endif -%}
-
-        <!-- Link to next page -->
-        {%- if page.next_page -%}
-          <a href="{{ page.next_page.url | url }}"
-              title="{{ page.next_page.title }}"
-              class="md-flex md-footer-nav__link md-footer-nav__link--next"
-              rel="next">
-            <div class="md-flex__cell md-flex__cell--stretch
-                  md-footer-nav__title">
-              <span class="md-flex__ellipsis">
-                <span class="md-footer-nav__direction">
-                  {{- lang.t("footer.next") -}}
-                </span>
-                {{- page.next_page.title -}}
-              </span>
-            </div>
-            <div class="md-flex__cell md-flex__cell--shrink">
-              <i class="md-icon md-icon--arrow-forward
-                    md-footer-nav__button"></i>
-            </div>
-          </a>
-        {%- endif -%}
-      </nav>
-    </div>
-  {%- endif -%}
-
-  <!-- Further information -->
-  <div class="md-footer-meta md-typeset">
-    <div class="md-footer-meta__inner md-grid">
-
-      <!-- Copyright and theme information -->
-      <div class="md-footer-copyright">
-        {%- if config.copyright -%}
-          <div class="md-footer-copyright__highlight">
-            {{- config.copyright -}}
-          </div>
-        {%- endif -%}
-        See the source code and discussion page on
-        <a href="https://github.com/bids-standard/bids-specification">GitHub</a>
-      </div>
-
-      <!-- Social links -->
-      {%- include "partials/social.html" -%}
-    </div>
-  </div>
-</footer>

From d611689a270d8a90981e7b715c697a769305d8c0 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Fri, 21 Jan 2022 10:32:38 +0100
Subject: [PATCH 160/347] [INFRA] Fix linkchecker (#982)

* ignore failing urls

* forgot \

* also ignore DOI

* Update .circleci/config.yml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* remove comment

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .circleci/config.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 272ffdb56c..db88083e9a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -48,9 +48,11 @@ jobs:
               # failures for local file:/// -- yoh found no better way,
               linkchecker -t 1 --check-extern \
                 --ignore-url 'file:///.*' \
-                --ignore-url https://fonts.gstatic.com \
-                --ignore-url "https://github.com/bids-standard/bids-specification/(pull|tree)/.*" \
-                --ignore-url "https://github.com/[^/]*" \
+                --ignore-url 'https://fonts.gstatic.com' \
+                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
+                --ignore-url 'https://github.com/[^/]*' \
+                --ignore-url 'https://doi.org/.*' \
+                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

From cbb745f5171f93003b56b46cafd4af1c44a074e8 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 22 Jan 2022 16:39:53 +0100
Subject: [PATCH 161/347] add microscopy to modalities in schema

---
 src/schema/objects/modalities.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/schema/objects/modalities.yaml b/src/schema/objects/modalities.yaml
index 56b083425d..089ba49c5d 100644
--- a/src/schema/objects/modalities.yaml
+++ b/src/schema/objects/modalities.yaml
@@ -24,3 +24,7 @@ pet:
   name: Positron Emission Tomography
   description: |
     Data acquired with PET.
+micr:
+  name: Microscopy
+  description: |
+    Data acquired with a microscope.
\ No newline at end of file

From 17ca52dfdf8127c72071affb0356b30de45abc26 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 23 Jan 2022 08:41:29 +0100
Subject: [PATCH 162/347] add extra line at EOF

---
 src/schema/objects/modalities.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/modalities.yaml b/src/schema/objects/modalities.yaml
index 089ba49c5d..be32d324a4 100644
--- a/src/schema/objects/modalities.yaml
+++ b/src/schema/objects/modalities.yaml
@@ -27,4 +27,4 @@ pet:
 micr:
   name: Microscopy
   description: |
-    Data acquired with a microscope.
\ No newline at end of file
+    Data acquired with a microscope.

From e5f8f2a205dc1a9a306b053248de79b25fe19d60 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 23 Jan 2022 08:53:49 +0100
Subject: [PATCH 163/347] update definition acq_time for sessions.tsv

---
 src/03-modality-agnostic-files.md |  4 ++--
 src/schema/objects/columns.yaml   | 12 +-----------
 2 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 68bf8550cf..0de7ee068a 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file.
 {{ MACROS___make_columns_table(
    {
       "filename": ("REQUIRED", "There MUST be exactly one row for each file."),
-      "acq_time": "OPTIONAL",
+      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical.")
    }
 ) }}
 
@@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip
 {{ MACROS___make_columns_table(
    {
       "session_id": ("REQUIRED", "There MUST be exactly one row for each session."),
-      "acq_time": "OPTIONAL",
+      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired.")
       "pathology": "RECOMMENDED",
    }
 ) }}
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index ee658ffbbd..9e13fc4394 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -17,18 +17,8 @@ acq_time:
     Furthermore, if this header is provided, the acquisition times of all files that
     belong to a recording MUST be identical.
 
-    Datetime should be expressed as described in [Units](/02-common-principles.html#units).
+    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
 
-    For anonymization purposes all dates within one subject should be shifted by a randomly
-    chosen (but consistent across all recordings) number of days.
-    This way relative timing would be preserved, but chances of identifying a person based
-    on the date and time of their scan would be decreased.
-    Dates that are shifted for anonymization purposes SHOULD be set to the year 1925 or earlier
-    to clearly distinguish them from unmodified data.
-    Note that some data formats do not support arbitrary recording dates.
-    For example, the [EDF](https://www.edfplus.info/)
-    data format can only contain recording dates after 1985.
-    Shifting dates is RECOMMENDED, but not required.
   type: string
   format: datetime
 age:

From e767a83af5c5bb827123b5bfebfae0e68c151d63 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 23 Jan 2022 08:57:23 +0100
Subject: [PATCH 164/347] simplify acq_time definition from schema to make it
 common to scans and sessions TSVs

---
 src/schema/objects/columns.yaml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 9e13fc4394..776a6334e6 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -12,13 +12,7 @@ abbreviation:
   type: string
 acq_time:
   name: acq_time
-  description: |
-    Acquisition time refers to when the first data point in each run was acquired.
-    Furthermore, if this header is provided, the acquisition times of all files that
-    belong to a recording MUST be identical.
-
-    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
-
+  description: Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
   type: string
   format: datetime
 age:

From ffcc6eef7003648ea0e18af1de582ebac9fb7ef2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 23 Jan 2022 09:48:15 +0100
Subject: [PATCH 165/347] add missing coma

---
 src/03-modality-agnostic-files.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 0de7ee068a..d1cac29292 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file.
 {{ MACROS___make_columns_table(
    {
       "filename": ("REQUIRED", "There MUST be exactly one row for each file."),
-      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical.")
+      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical."),
    }
 ) }}
 
@@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip
 {{ MACROS___make_columns_table(
    {
       "session_id": ("REQUIRED", "There MUST be exactly one row for each session."),
-      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired.")
+      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired."),
       "pathology": "RECOMMENDED",
    }
 ) }}

From f8882915a55613b26d60d1789a75da037c8dd63a Mon Sep 17 00:00:00 2001
From: VisLab <1189050+VisLab@users.noreply.github.com>
Date: Sun, 23 Jan 2022 09:03:17 -0600
Subject: [PATCH 166/347] [FIX] Update HED appendix to comply with current HED
 version (#970)

* First pass at revision of Appendix III to update to HED-3G

* Updated the Appendix III description of HED versioning

* Updated the markdown format

* Fixed lint errors in the HED.md

* Minor syntax changes

* Added more detail about column inheritance.

* Got rid of e.g.

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* A few minor rewordings for recommendations

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Corrected confusion about lower directories

* Added a link to the hed-examples repository in hed-standard on GitHub

* apply "uncontroversial" suggestions

* remove trailing whitespace

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update src/99-appendices/03-hed.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/03-modality-agnostic-files.md |   6 +-
 src/99-appendices/03-hed.md       | 320 ++++++++++++++----------------
 2 files changed, 152 insertions(+), 174 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 68bf8550cf..d12ccad3cf 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -36,7 +36,7 @@ Example:
 ```JSON
 {
   "Name": "The mother of all experiments",
-  "BIDSVersion": "1.4.0",
+  "BIDSVersion": "1.6.0",
   "DatasetType": "raw",
   "License": "CC0",
   "Authors": [
@@ -57,7 +57,7 @@ Example:
     "Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
   ],
   "DatasetDOI": "doi:10.0.2.3/dfjj.10",
-  "HEDVersion": "7.1.1"
+  "HEDVersion": "8.0.0"
 }
 ```
 
@@ -94,7 +94,7 @@ Example:
 ```JSON
 {
   "Name": "FMRIPREP Outputs",
-  "BIDSVersion": "1.4.0",
+  "BIDSVersion": "1.6.0",
   "DatasetType": "derivative",
   "GeneratedBy": [
     {
diff --git a/src/99-appendices/03-hed.md b/src/99-appendices/03-hed.md
index 0466cb7870..bb217322a5 100644
--- a/src/99-appendices/03-hed.md
+++ b/src/99-appendices/03-hed.md
@@ -3,120 +3,47 @@
 Hierarchical Event Descriptors (HED) are a controlled vocabulary of terms describing
 events in a machine-actionable form so that algorithms can use the information without
 manual recoding.
-HED was originally developed with EEG in mind, but is applicable to
-all behavioral experiments.
-
-Each level of a hierarchical tag is delimited with a forward slash (`/`).
-A HED string contains one or more HED tags separated by commas (`,`).
-Parentheses (brackets, `()`) group tags and enable specification of multiple items
-and their attributes in a single **HED string** (see section 2.4 in
-[HED Tagging Strategy Guide](https://www.hedtags.org/hed-docs/HEDTaggingStrategyGuide.pdf)).
-For more information about HED and tools available to validate and match HED
-strings, please visit [www.hedtags.org](https://www.hedtags.org).
-Since dedicated fields already exist for the overall task classification in the
-sidecar JSON files (`CogAtlasID` and `CogPOID`), HED tags from the `Paradigm`
-HED subcategory should not be used to annotate events.
-
-## Annotating each event
-
-There are several ways to associate HED annotations with events within the BIDS
-framework.
-The most direct way is to use the `HED` column of the `*_events.tsv`
-file to annotate events.
-
-Example: An `*_events.tsv` annotated using HED tags for individual events.
-
-```Text
-onset  duration  HED
-1.1    n/a       Event/Category/Experimental stimulus, Event/Label/CrossFix,  Sensory presentation/Visual, Item/Object/2D Shape/Cross
-1.3    n/a       Event/Category/Participant response, Event/Label/ButtonPress, Action/Button press
-...
-```
-
-The direct approach requires that each line in the events file be annotated.
-Since there are typically thousands of events in each experiment,
-this method of annotation is not convenient unless the annotations are
-automatically generated.
-Usually annotations that appear in the `HED` column are specific to each individual event.
-Information that is common to groups of events can be annotated by category.
-Numerical values associated with each event can be annotated by value type.
-Annotating by category and by value greatly reduces the effort required to HED tag
-data and improves the clarity for data users.
-
-## Annotating events by categories
-
-In many experiments, the event instances fall into a much smaller number of
-categories, and often these categories are labeled with numerical codes or short names.
-This categorical information usually corresponds to one or more columns in `*_events.tsv`
-representing categorical values.
-Instead of tagging this information for each individual event,
-you can assign HED tags for each distinct categorical value
-in an accompanying `*_events.json` sidecar and allow the analysis tools to make
-the association with individual event instances during analysis.
-The column name in the `*_events.tsv` identifies the type of categorical variable.
-The following `*_events.tsv` file has one categorical variable called `mycodes` that
-takes on three possible values: `Fixation`, `Button`, and `Target`.
-
-Example: An `*_events.tsv` containing the `mycodes` categorical column.
-
-```Text
-onset  duration  mycodes
-1.1    n/a       Fixation
-1.3    n/a       Button
-1.8    n/a       Target
-...
-
-```
-
-Example: An accompanying `*_events.json` sidecar describing the `mycodes` categorical variable.
-
-```JSON
-{
-   "mycodes": {
-       "LongName": "Local event type names",
-       "Description": "Main types of events that comprise a trial",
-       "Levels": {
-          "Fixation": "Fixation cross is displayed",
-          "Target": "Target image appears",
-          "Button": "Subject presses a button"
-       },
-       "HED": {
-           "Fixation": "Event/Category/Experimental stimulus, Event/Label/CrossFix,
-               Event/Description/A cross appears at screen center to serve as a fixation point,
-               Sensory presentation/Visual, Item/Object/2D Shape/Cross,
-               Attribute/Visual/Fixation point, Attribute/Visual/Rendering type/Screen,
-               Attribute/Location/Screen/Center",
-           "Target": "Event/Label/TargetImage, Event/Category/Experimental stimulus,
-               Event/Description/A white airplane as the RSVP target superimposed on a satellite image is displayed.,
-               Item/Object/Vehicle/Aircraft/Airplane, Participant/Effect/Cognitive/Target,
-               Sensory presentation/Visual/Rendering type/Screen/2D),
-               (Item/Natural scene/Aerial/Satellite,
-               Sensory presentation/Visual/Rendering type/Screen/2D)",
-           "Button": "Event/Category/Participant response, Event/Label/PressButton,
-               Event/Description/The participant presses the button as soon as the target is visible,
-               Action/Button press"
-        }
-   }
-}
-```
-
-## Annotating events by value type
-
-Each column of `*_events.tsv` containing non-categorical values usually represents a
-particular type of data, for example the `speed` of a stimulus object across the
-screen or the filename of the stimulus image.
-These variables could be annotated in the HED column of `*_events.tsv`.
-However, that approach requires repeating the values appearing in the individual
-columns in the HED column.
-A better approach is to annotate the type of value contained in each of these
-columns in the `*_events.json` sidecar.
-Value variables are annotated in a manner similar to categorical values,
-except that the HED string must contain exactly one `#` specifying a placeholder
-for the actual column values.
-Tools are responsible for substituting the actual column values for the `#` during analysis.
-
-Example: An `*_events.tsv` containing a categorical column (`trial_type`) and two value
-columns (`response_time` and `stim_file`).
+HED annotation can be used to describe any experimental events by combining
+information from the dataset's `_events.tsv` files and `_events.json` sidecars.
+
+## HED annotations and vocabulary
+
+A HED annotation consists of terms selected from a controlled
+hierarchical vocabulary (the HED schema).
+Individual terms are comma-separated and may be grouped using parentheses to indicate
+association.
+See [https://www.hedtags.org/display_hed.html](https://www.hedtags.org/display_hed.html)
+to view the HED schema and the
+[HED documentation](https://hed-specification.readthedocs.io/en/latest/index.html)
+for additional resources.
+
+Starting with HED version 8.0.0, HED allows users to annotate using individual
+terms or partial paths in the HED vocabulary (for example `Red` or `Visual-presentation`)
+rather than the full paths in the HED hierarchy (
+`Property/Sensory-property/Sensory-attribute/Visual-attribute/Color/CSS-color/Red-color/Red`
+or
+`Property/Sensory-property/Sensory-presentation/Visual-presentation`).
+
+HED specific tools MUST treat the short and long HED tag forms interchangeably,
+converting between the forms when necessary, based on the HED schema.
+Examples of test datasets using the various forms can be found in
+[hed-examples/datasets](https://github.com/hed-standard/hed-examples/tree/main/datasets)
+on GitHub.
+**Using the short form for tags is strongly RECOMMENDED whenever possible**.
+
+## Annotating events
+
+Event-related data in BIDS appears in tab-separated value (`events.tsv`)
+files in various places in the dataset hierarchy
+(see [Events](../04-modality-specific-files/05-task-events.md)).
+
+`events.tsv` files MUST have `onset` and `duration` columns.
+Dataset curators MAY also include additional columns and define their
+meanings in associated JSON sidecar files (`events.json`).
+
+Example: An excerpt from an `events.tsv` file containing three columns
+(`trial_type`, `response_time`, and `stim_file`) in addition to
+the required `onset` and `duration` columns.
 
 ```Text
 onset  duration  trial_type  response_time stim_file
@@ -124,86 +51,137 @@ onset  duration  trial_type  response_time stim_file
 5.6    0.6       stop        1.739         images/blue_square.jpg
 ```
 
-Example: An accompanying `*_events.json` sidecar describing both categorical and value columns.
+The `trial_type` column in the above example contains a limited number of distinct
+values (`go` and `stop`).
+This type of column is referred to as a *categorical* column,
+and the column's meaning can be annotated by assigning HED tags to describe
+each of these distinct values.
+The JSON sidecar provides a [JSON object](https://www.json.org/json-en.html) of annotations for these categorical values.
+That is, the object is a dictionary mapping the categorical values to corresponding HED annotations.
+
+In contrast, the `response_time` and `stim_file` columns could potentially contain
+distinct values in every row.
+These columns are referred to as *value* columns and are annotated by creating
+a HED tag string to describe a general pattern for these values.
+The HED annotation for a value column must include a `#` placeholder,
+which dedicated HED tools MUST replace by the actual column value when the annotations
+are assembled for analysis.
+
+Example: An accompanying `events.json` sidecar describing both categorical and
+value columns of the previous example.
+The `duration` column is also annotated as a value column.
 
 ```JSON
 {
-   "trial_type": {
-       "LongName": "Event category",
-       "Description": "Indicator of type of action that is expected",
-       "Levels": {
-          "go": "A red square is displayed to indicate starting",
-          "stop": "A blue square is displayed to indicate stopping",
-       },
-       "HED": {
-          "go": "Event/Category/Experimental stimulus, Event/Label/RedSquare,
-          Event/Description/A red square is displayed to indicate starting,
-          Sensory presentation/Visual, Item/Object/2D Shape/Square,
-          Attribute/Visual/Color/Red, Attribute/Visual/Rendering type/Screen,
-          Attribute/Location/Screen/Center",
-          "stop": "Event/Category/Experimental stimulus, Event/Label/BlueSquare,
-          Event/Description/A blue square is displayed to indicate stopping,
-          Sensory presentation/Visual, Item/Object/2D Shape/Square,
-          Attribute/Visual/Color/Blue, Attribute/Visual/Rendering type/Screen,
-          Attribute/Location/Screen/Center",
+  "Duration": {
+    "LongName": "Image duration",
+    "Description": "Duration of the image presentations",
+    "Units": "s",
+    "HED": "Duration/# s"
+  },
+  "trial_type": {
+    "LongName": "Event category",
+    "Description": "Indicator of type of action that is expected",
+    "Levels": {
+      "go": "A red square is displayed to indicate starting",
+      "stop": "A blue square is displayed to indicate stopping"
+    },
+    "HED": {
+          "go": "Sensory-event, Visual-presentation, ((Square, Blue),(Computer-screen, Center-of))",
+          "stop": "Sensory-event, Visual-presentation, ((Square, Blue), (Computer-screen, Center-of))"
        }
    },
    "response_time": {
        "LongName": "Response time after stimulus",
        "Description": "Time from stimulus presentation until subject presses button",
        "Units": "ms",
-       "HED": "Attribute/Response start delay/# ms, Action/Button press"
+       "HED": "(Delay/# ms, Agent-action, (Experiment-participant, (Press, Mouse-button))),"
    },
    "stim_file": {
        "LongName": "Stimulus filename",
        "Description": "Relative path of the stimulus image file",
-       "HED": "Attribute/File/#"
+       "HED": "Pathname/#"
    }
 }
 ```
 
-## Best practices
-
-Most studies will have event categorical variables and value variables that
-are common across many of the datasets in the study.
-You should try to annotate these columns in a `*_events.json` sidecar
-as high in the study hierarchy as possible to avoid duplicate annotations.
-Annotations that can be placed in sidecars are preferred to those placed
-directly in the HED column, because they are simpler, more compact, and
-less prone to inconsistent annotation.
-Downstream tools should not distinguish between tags specified using
-the explicit HED column and the categorical specifications, but should
-form the union before analysis.
-Further, the [inheritance principle](../02-common-principles.md#the-inheritance-principle)
-applies, so the data dictionaries can appear higher in the BIDS hierarchy.
-
-You should try to annotate in as much detail as possible.
-The HED path structure makes it easy for analysis tools to extract tags
-at different levels of detail: For example a user can consider extracting
-events associated with 2D shapes for stimuli, ignoring the particular
-color or shape details for the stimuli.
-
-## HED schema and HED versions
+Dedicated HED tools MUST assemble an annotation for each event by concatenating the
+annotations for each column.
+
+Example: The fully assembled annotation for the first event in the above
+`events.tsv` file with onset `1.2` (the first row) is:
+
+```Text
+Duration/0.6 s, Sensory-event, Visual-presentation,
+((Square, Blue), (Computer-screen, Center-of)),
+(Delay/1.435 ms, Agent-action,
+(Experiment-participant, (Press, Mouse-button))),
+Pathname/images/red_square.jpg
+```
+
+## Annotation using the `HED` column
+
+Another tagging strategy is to annotate individual events directly by
+including a `HED` column in the `events.tsv` file.
+This approach is necessary when each event has annotations that are unique
+and do not fit into a standard set of patterns.
+
+Some acquisition or presentation software systems directly
+write annotations during the experiment, and these MAY also be placed in the
+`HED` column of the `events.tsv` file.
+
+Dedicated HED tools that assemble the full annotation for events treat MUST not distinguish
+between HED annotations extracted from `_events.json` sidecars and those
+appearing in the `HED` column of `_events.tsv` files.
+The HED strings from all sources are concatenated to form the final
+event annotations.
+
+Annotations placed in sidecars are the RECOMMENDED way
+to annotate data using HED.
+These annnotations are preferred to those placed
+directly in the `HED` column, because they are simpler, more compact,
+more easily edited, and less prone to inconsistencies.
+
+## HED and the BIDS inheritance principle
+
+Most studies have event files whose columns contain categorical and
+numerical values that are similar across the recordings in the study.
+If possible, users should annotate these columns in a single
+`events.json` sidecar placed at the top level in the dataset.
+
+If some recordings in the dataset have a column whose values deviate from a
+standard pattern, then the annotations for that column MUST be placed in
+sidecars located deeper in the dataset directory hierarchy.
+According to the BIDS [Inheritance Principle](../02-common-principles.md#the-inheritance-principle),
+once a column key in a sidecar (that is, the column name found in the `events.tsv` files) is set,
+information about that column cannot be overridden by a sidecar appearing in a directory
+closer to the dataset root.
+
+## HED schema versions
 
 The HED vocabulary is specified by a HED schema,
 which delineates the allowed HED path strings.
-By default, BIDS uses the latest HED schema available in the
-[hed-specification](https://github.com/hed-standard/hed-specification/tree/master/hedxml) repository
-maintained by the hed-standard group.
+The version of HED used in tagging a dataset should be provided in the `HEDVersion`
+field of the `dataset_description.json` file located in the dataset root directory.
+This allows for a proper validation of the HED annotations
+(for example using the `bids-validator`).
 
-You can override the default by providing a specific HED version number in the
-`dataset_description.json` file using the `HEDVersion` field.
-The preferred approach is to validate with the latest version (the default),
-but to use the `HEDVersion` field to specify which version was used for later reference.
-
-Example: The following `dataset_description.json` file specifies that
-`HED7.1.1.xml` from the [hed-specification](https://github.com/hed-standard/hed-specification/tree/master/hedxml) repository
-should be used to validate the study event annotations.
+Example: The following `dataset_description.json` file specifies that the
+[`HED8.0.0.xml`](https://github.com/hed-standard/hed-specification/tree/master/hedxml/HED8.0.0.xml)
+file from the `hedxml` directory of the
+[`hed-specification`](https://github.com/hed-standard/hed-specification)
+repository on GitHub should be used to validate the study event annotations.
 
 ```JSON
 {
-  "Name": "The mother of all experiments",
-  "BIDSVersion": "1.4.0",
-  "HEDVersion": "7.1.1"
+  "Name": "A great experiment",
+  "BIDSVersion": "1.6.0",
+  "HEDVersion": "8.0.0"
 }
 ```
+
+If you omit the `HEDVersion` field from the dataset description file,
+any present HED information will be validated using the latest version of the HED schema,
+which is bound to result in problems.
+Hence, it is strongly RECOMMENDED that the `HEDVersion` field be included when using HED
+in a BIDS dataset.

From 5a6757629a1ff5ae2b57cbfbc8e70270beda04f5 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 23 Jan 2022 17:14:01 +0100
Subject: [PATCH 167/347] integrate review comments from @VisLab

---
 macros_doc.md | 165 ++++++++++++++++++++++++++++----------------------
 1 file changed, 93 insertions(+), 72 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 5d5123b865..45d75f990d 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -13,8 +13,7 @@ Below you will find answers to frequently asked questions regarding macros.
    - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros)
    - [What macros are available? What can we use macros for?](#what-macros-are-available-what-can-we-use-macros-for)
    - [When should I use a macro?](#when-should-i-use-a-macro)
-   - [Do I need learn how to code in Python to use those macros?](#do-i-need-learn-how-to-code-in-python-to-use-those-macros)
-   - [Why use macros at all?](#why-use-macros-at-all)
+   - [Do I need learn how to program to use those macros?](#do-i-need-learn-how-to-program-to-use-those-macros)
    - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call)
    - [How-To and Examples](#how-to-and-examples)
       - [Writing folder content examples](#writing-folder-content-examples)
@@ -23,6 +22,7 @@ Below you will find answers to frequently asked questions regarding macros.
          - [Why would you NOT want to modify the content of the yml file directly ?](#why-would-you-not-want-to-modify-the-content-of-the-yml-file-directly-)
          - [Adding a new term to the table](#adding-a-new-term-to-the-table)
          - [Should I create a macro if I need a new kind of table?](#should-i-create-a-macro-if-i-need-a-new-kind-of-table)
+   - [Why use macros at all?](#why-use-macros-at-all)
    - [Links and references](#links-and-references)
 
 ## What are macros and why use them?
@@ -32,42 +32,63 @@ output. Macros are very useful for standardizing the output format for items
 such as tables. You might already be familiar with using macros from other tools
 such as Excel.
 
-MkDocs (the tool we use to turn the markdown version of the specification into
-HTML pages) supports macros. In the BIDS specification document, we use these
+MkDocs (the tool we use to turn the markdown version of the BIDS specification
+into HTML pages) supports macros. In the specification document, we use these
 macros to standardize the format of items such as tables and examples.
 
-## What kind of input information are required by macros?
+The following is an example of a macro used to create consistent "file tree"
+layouts in the documentation. The macro takes a single parameter, the directory
+tree to be displayed in JSON format. If you insert the following in the BIDS
+markdown document:
+
+```python
+{{ MACROS___make_filetree_example(
+
+   {
+   "sub-01": {
+      "func": {
+         "sub-control01_task-nback_bold.json": "",
+         },
+      }
+   }
+
+) }}
+```
+
+The result would be rendered in the specification document as:
 
-It will depend for each macro.
+```bash
+└─ sub-01/
+   └─ func/
+      └─ sub-control01_task-nback_bold.json
+```
+
+## What kind of input information are required by macros?
 
-For some of them, all the inputs will be directly available in the markdown
-document where you have put the call to the macro.
+Some macros only use the arguments you directly supply in the macro call.
 
-Other macros will need to be pointed to some external input (like a metadata
-term) that they are supposed to help rendering. For example, parts of the BIDS
-specification are formalized into a "schema" so that requirements in the
-specification can be automatically checked by validators. Several of the macros
-incorporate information from this schema to assure consistency.
+Other macros use information (such as metadata terms) from external sources, and
+you will need to provide links to this information as part of the call. For
+example, parts of the BIDS specification are formalized into a "schema" so that
+requirements in the specification can be automatically checked by validators.
+Several of the macros incorporate information from this schema to assure
+consistency.
 
 ## What macros are available? What can we use macros for?
 
 All the macros we use are in listed in this
 [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
 
-| Name                    | Purpose                                                                                | Uses schema | Link to example of use |
-| ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ---------------------- |
-| make_filename_template  | Generate a filename template from the schema, based on specific filters.               | Yes         |                        |
-| make_entity_table       | Generate an entity table from the schema, based on specific filters.                   | Yes         |                        |
-| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes         |                        |
-| make_glossary           |                                                                                        | yes         |                        |
-| make_suffix_table       | Generate a markdown table of suffix information.                                       | yes         |                        |
-| make_metadata_table     | Generate a markdown table of metadata field information.                               | Yes         |                        |
-| make_columns_table      | Generate a markdown table of TSV column information.                                   | Yes         |                        |
-| make_filetree_example   | Generate a filetree snippet from example content.                                      | Yes         |                        |
-
-Note that under the hood the macros themselves call some more python code that
-is in the
-[`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
+| Name                    | Purpose                                                                                | Uses schema | Example |
+| ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ------- |
+| make_columns_table      | Generate a markdown table of TSV column information.                                   | Yes         |         |
+| make_entity_table       | Generate an entity table from the schema, based on specific filters.                   | Yes         |         |
+| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes         |         |
+| make_filename_template  | Generate a filename template from the schema, based on specific filters.               | Yes         |         |
+| make_filetree_example   | Generate a filetree snippet from example content.                                      | No          |         |
+| make_glossary           |                                                                                        | Yes         |         |
+| make_metadata_table     | Generate a markdown table of metadata field information.                               | Yes         |         |
+| make_suffix_table       | Generate a markdown table of suffix information.                                       | Yes         |         |
 
 ## When should I use a macro?
 
@@ -80,54 +101,19 @@ contact a member of the bids-maintainers for help. To do this, you can either
 mention an individual maintainer by their GitHub username or mention the whole
 team (`@bids-standard/maintainers`).
 
-## Do I need learn how to code in Python to use those macros?
-
-Nope. No need to learn how to program to use those macros. But some macros
-require some specific "input", so you will just need to know what input to give
-it. In many cases, it will be just a metadata term whose definition or
-description should be displayed somewhere in the specification.
-
-Once you have given the macro its input, it usually knows where to look for the
-rest of the info it should use to do the rest of its work.
-
-The only exception to this is when you want to add new content. Say you want to
-add a completely new piece of metadata to the specification. In that case, you
-will need to create the input for the macro to be able to do its job.
-
-## Why use macros at all?
-
-> Seriously why did you have to make it so complicated just to have pretty
-> tables? Are macros that necessary ? Couldn't we just have everything in
-> Markdown?
-
-In principle we could, and before we started working on the schema that's
-exactly what we did. But there are several good reasons to use macros.
-
-When a definition gets repeated in different places, we could just copy-paste
-it. But when you start having several copies of that definition, if you have to
-modify it, you then need to edit several files and never forget any of them. So
-this becomes very error prone.
-
-So it becomes better to have one central place for that definition and grab that
-definition every time we need to reuse it.
-
-In practice this applies the
-[DRY principle ("Don't Repeat Yourself")](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself)
-to the specification:
-
-> "Every piece of knowledge must have a single, unambiguous, authoritative
-> representation within a system".
+## Do I need learn how to program to use those macros?
 
-Having one centralized place where we put all our definitions can be useful when
-we want other tools (the BIDS validator, bids-matlab...) to use the content of
-the specification.
+Macros don't require programming knowledge to use. You do need to know what
+arguments the macro expects. The examples linked in the above table provide
+useful guidance in this respect.
 
-This is where the BIDS schema (those .yml files we talked about above) comes in
-as it is meant to be a machine readable version of the specification.
+Macros that extract information from the schema also require you to use the
+correct terms in the schema. This process is illustrated in the next section.
 
-And so to avoid having to maintain the SAME definition in both the schema and
-specification, we started using macros to generate the specification from the
-schema.
+Note that under the hood the macros themselves call python code that can be
+found in the
+[`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
+If you are interested in creating a new macro for users, this would be useful.
 
 ## Anything else I need to know if I need to insert a new macro call?
 
@@ -353,6 +339,41 @@ with a table in Markdown.
 If later we see that the same type of table keeps reoccuring the specification
 we could create a macro to generate them.
 
+## Why use macros at all?
+
+> Seriously why did you have to make it so complicated just to have pretty
+> tables? Are macros that necessary ? Couldn't we just have everything in
+> Markdown?
+
+In principle we could, and before we started working on the schema that's
+exactly what we did. But there are several good reasons to use macros.
+
+When a definition gets repeated in different places, we could just copy-paste
+it. But when you start having several copies of that definition, if you have to
+modify it, you then need to edit several files and never forget any of them. So
+this becomes very error prone.
+
+So it becomes better to have one central place for that definition and grab that
+definition every time we need to reuse it.
+
+In practice this applies the
+[DRY principle ("Don't Repeat Yourself")](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself)
+to the specification:
+
+> "Every piece of knowledge must have a single, unambiguous, authoritative
+> representation within a system".
+
+Having one centralized place where we put all our definitions can be useful when
+we want other tools (the BIDS validator, bids-matlab...) to use the content of
+the specification.
+
+This is where the BIDS schema (those .yml files we talked about above) comes in
+as it is meant to be a machine readable version of the specification.
+
+And so to avoid having to maintain the SAME definition in both the schema and
+specification, we started using macros to generate the specification from the
+schema.
+
 ## Links and references
 
 - [documentation for mkdocs](https://www.mkdocs.org) and how to install it

From be1a2ed51c194321c2dbb9e16996aa933e304895 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 24 Jan 2022 14:45:01 +0100
Subject: [PATCH 168/347] new series of updates after reviews

---
 macros_doc.md | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/macros_doc.md b/macros_doc.md
index 45d75f990d..08892cc4b7 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -6,12 +6,11 @@ Macros make it easy to achieve a consistent style throughout the specification,
 and changing a given macro will automatically change all appropriate paragraphs
 in the specification.
 
-Below you will find answers to frequently asked questions regarding macros.
+Below you will find answers to frequently asked questions regarding using macros in the BIDS specification.
 
-- [Using MkDocs macros in the BIDS specification](#using-mkdocs-macros-in-the-bids-specification)
    - [What are macros and why use them?](#what-are-macros-and-why-use-them)
    - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros)
-   - [What macros are available? What can we use macros for?](#what-macros-are-available-what-can-we-use-macros-for)
+   - [What macros are available?](#what-macros-are-available)
    - [When should I use a macro?](#when-should-i-use-a-macro)
    - [Do I need learn how to program to use those macros?](#do-i-need-learn-how-to-program-to-use-those-macros)
    - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call)
@@ -74,7 +73,7 @@ requirements in the specification can be automatically checked by validators.
 Several of the macros incorporate information from this schema to assure
 consistency.
 
-## What macros are available? What can we use macros for?
+## What macros are available?
 
 All the macros we use are in listed in this
 [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
@@ -301,7 +300,7 @@ call and ask the BIDS maintainers for help.
 Say you wanted to add a new term `MoonPhase` to the table, on the second row.
 You would do it like this. But this would only work if the `metadata.yml` file
 contains an entry for `MoonPhase`. If this is the case because the term already
-exist and is used somewhere in the BIDS specification, you are in luck and you
+exists and is used somewhere in the BIDS specification, you are in luck and you
 can just stop there.
 
 ```python
@@ -330,9 +329,7 @@ is wrong.
 
 #### Should I create a macro if I need a new kind of table?
 
-As a rule of thumb, no.
-
-Unless it is clear that this kind of table will reappear many times in the
+As a rule of thumb, no, unless it is clear that this kind of table will reappear many times in the
 future in the specification. But this is usually hard to predict so better start
 with a table in Markdown.
 

From 31d72b343d1986ded2011c6c56d4f3d884e78d89 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Tue, 25 Jan 2022 14:48:15 -0500
Subject: [PATCH 169/347] [FIX] Optionally support echo entity for VFA suffix

Closes: https://github.com/bids-standard/bids-specification/issues/977
---
 src/schema/rules/datatypes/anat.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/datatypes/anat.yaml b/src/schema/rules/datatypes/anat.yaml
index 82d99b44b9..b1a470c2ef 100644
--- a/src/schema/rules/datatypes/anat.yaml
+++ b/src/schema/rules/datatypes/anat.yaml
@@ -105,6 +105,7 @@
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    echo: optional
     flip: required
     part: optional
 

From f544835e0b5b6e39f5ff125b137351034b682e47 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Thu, 27 Jan 2022 10:26:01 +0000
Subject: [PATCH 170/347] [DOC] Auto-generate changelog entry for PR #984

---
 src/CHANGES.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index a3cc4bfb12..89940c4077 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,7 +2,11 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[INFRA] Fix linkchecker [#982](https://github.com/bids-standard/bids-specification/pull/982) ([sappelhoff](https://github.com/sappelhoff))
 -   \[DOC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))
+-   customize footer on html spec [#975](https://github.com/bids-standard/bids-specification/pull/975) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Update HED appendix to comply with current HED version [#970](https://github.com/bids-standard/bids-specification/pull/970) ([VisLab](https://github.com/VisLab))
 -   \[FIX] harmonize 'file name' into 'filename' [#962](https://github.com/bids-standard/bids-specification/pull/962) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Reword front page [#958](https://github.com/bids-standard/bids-specification/pull/958) ([arokem](https://github.com/arokem))
 -   \[MAINT] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies))

From 33cc25a49e716a2d30d212bccd611570c3d2e1da Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 31 Jan 2022 13:52:36 +1100
Subject: [PATCH 171/347] Inheritance principle: Revise EchoTime and
 RepetitionTime exemplar values

---
 src/02-common-principles.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index a234632259..94c14d4467 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -607,8 +607,8 @@ Contents of file `task-rest_bold.json`:
 
 ```JSON
 {
-    "EchoTime": 40.0,
-    "RepetitionTime": 1000.0
+    "EchoTime": 0.040,
+    "RepetitionTime": 1.0
 }
 ```
 
@@ -616,7 +616,7 @@ Contents of file `sub-01/func/sub-01_task-rest_acq-longtr_bold.json`:
 
 ```JSON
 {
-    "RepetitionTime": 3000.0
+    "RepetitionTime": 3.0
 }
 ```
 
@@ -627,7 +627,7 @@ entity "`acq-longtr`" that is absent from the image path (rule 2.c). When readin
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz`, metadata file
 `task-rest_bold.json` at the top level is read first, followed by file
 `sub-01/func/sub-01_task-rest_acq-longtr_bold.json` at the bottom level (rule 5.b);
-the value for field "`RepetitionTime`" is therefore overridden to the value `3000.0`.
+the value for field "`RepetitionTime`" is therefore overridden to the value `3.0`.
 The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
 absence in the metadata file at the lower level (rule 5.b; corollary 3).
 

From 5fe26e15644e71740fcb7efa3a7302053f3bd15a Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 31 Jan 2022 11:36:31 +0100
Subject: [PATCH 172/347] [MISC] add "forward slash" requirement for paths to
 common principles (#867)

* add forward slash path requirement to common principles

* clarify absolute paths and relative paths

* go from must to should
---
 src/02-common-principles.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 0736457e1c..8280542646 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -661,6 +661,20 @@ it refers to. For example `sub-01` refers to the `sub` entity (a
 subject) with the label `01`. The `sub-` prefix is not part of the subject
 label, but must be included in filenames (similarly to other key names).
 
+## Specification of paths
+
+Several metadata fields in BIDS require the specification of paths,
+that is, a string of characters used to uniquely identify a location in a directory structure.
+For example the `IntendedFor` or `AssociatedEmptyroom` metadata fields.
+
+Throughout BIDS all such paths MUST be specified using the slash character (`/`),
+regardless of the operating system that a particular dataset is curated on or used on.
+
+Paths SHOULD NOT be absolute local paths,
+because these might break when a dataset is used on a different machine.
+It is RECOMMENDED that all paths specified in a BIDS dataset are relative paths,
+as specified in the respective descriptions of metadata fields that require the use of paths.
+
 ## Uniform Resource Indicator
 
 A Uniform Resource Indicator (URI) is a string referring to a resource and SHOULD

From 7af3e05dba799b996c3ee6decaf2f1b270fc5a81 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Tue, 1 Feb 2022 11:51:40 +1100
Subject: [PATCH 173/347] Inheritance principle: Use American spelling

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 94c14d4467..818bd2903d 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -569,7 +569,7 @@ for more information.
         key-values from the top level are inherited by all data files at lower
         levels to which it is applicable unless overridden by a value for the
         same key present in another metadata file at a lower level
-        (though it is RECOMMENDED to minimise the extent of such overrides).
+        (though it is RECOMMENDED to minimize the extent of such overrides).
 
 Corollaries:
 

From 525ab87b4d885b17c1b4c1c1fec5885bfc1d234e Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Tue, 1 Feb 2022 11:53:31 +1100
Subject: [PATCH 174/347] Inheritance principle: Fix enumeration
 cross-reference

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 818bd2903d..c599874b3f 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -583,7 +583,7 @@ Corollaries:
     across multiple data files, it is RECOMMENDED to store metadata in this
     way, rather than duplicating that metadata content across multiple metadata files.
 
-1.  Where multiple applicable JSON files are loaded as per rule 5.2, key-values can
+1.  Where multiple applicable JSON files are loaded as per rule 5.b, key-values can
     only be overwritten by files lower in the filesystem hierarchy; the absence of
     a key-value in a later file does not imply the "unsetting" of that field
     (indeed removal of existing fields is not possible).

From 733c53a64ec8b9272984190be194c947cc2cc374 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Tue, 1 Feb 2022 10:30:30 +0100
Subject: [PATCH 175/347] misc wording changes

---
 .../02-magnetoencephalography.md              | 15 ++++++------
 .../03-electroencephalography.md              | 18 +++++++-------
 .../04-intracranial-electroencephalography.md | 24 ++++++++-----------
 3 files changed, 25 insertions(+), 32 deletions(-)

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 77169924e9..22ecf0f8b8 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -218,14 +218,13 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["channels"]) }}
 
-This file is RECOMMENDED as it provides easily searchable information across
-BIDS datasets for example, general curation, response to queries or batch
-analysis.
-To avoid confusion, the channels SHOULD be listed in the order they
-appear in the MEG data file.
-Missing values MUST be indicated with `n/a`.
-
-The columns of the Channels description table stored in `*_channels.tsv` are:
+This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
+For example for general curation, response to queries, or for batch analysis.
+To avoid confusion, the channels SHOULD be listed in the order they appear in the MEG data file.
+Any number of additional columns MAY be added to provide additional information about the channels.
+Missing values MUST be indicated with `"n/a"`.
+
+The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index e6b7178491..71ed7374ef 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -184,15 +184,13 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["channels"]) }}
 
-This file is RECOMMENDED as it provides easily searchable information across
-BIDS datasets for example, general curation, response to queries or batch
-analysis.
-To avoid confusion, the channels SHOULD be listed in the order they
-appear in the EEG data file.
-Any number of additional columns may be added to provide additional information
-about the channels.
-
-Note that electrode positions SHOULD NOT be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).
+This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
+For example for general curation, response to queries, or for batch analysis.
+To avoid confusion, the channels SHOULD be listed in the order they appear in the EEG data file.
+Any number of additional columns MAY be added to provide additional information about the channels.
+
+Note that electrode positions SHOULD NOT be added to this file, but to
+[`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).
 Furthermore, the entries in `*_electrodes.tsv` and `*_channels.tsv` do not have to match exactly,
 as for example in the case of recording a single `EOG` channel from a bipolar referencing scheme
 of two electrodes, or a data channel originating from an auxiliary, non-electrode device.
@@ -200,7 +198,7 @@ That is, in most cases `*_electrodes.tsv` will have more entries than `*_channel
 See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in
 ["Electrodes description"](./03-electroencephalography.md#electrodes-description-_electrodestsv).
 
-The columns of the Channels description table stored in `*_channels.tsv` are:
+The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index 2c2983e8ba..a258492927 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -204,21 +204,17 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["channels"]) }}
 
-A channel represents one time series recorded with the recording system (for
-example, there can be a bipolar channel, recorded from two electrodes or contact
-points on the tissue).
+A channel represents one time series recorded with the recording system
+(for example, there can be a bipolar channel, recorded from two electrodes or contact points on the tissue).
 Although this information can often be extracted from the iEEG recording,
-listing it in a simple `.tsv` document makes it easy to browse or search (for example,
-searching for recordings with a sampling frequency of >=1000 Hz).
-Hence, the channels.tsv is RECOMMENDED.
-Channels SHOULD appear in the table in the same order they do in the iEEG data
-file.
-Any number of additional columns may be provided to provide additional
-information about the channels.
-Note that electrode positions SHOULD NOT be added to this file but to
-`*_electrodes.tsv`.
-
-The columns of the Channels description table stored in `*_channels.tsv` are:
+listing it in a simple `.tsv` document makes it easy to browse or search
+(for example, searching for recordings with a sampling frequency of >=1000 Hz).
+Hence, the `channels.tsv` file is RECOMMENDED.
+Channels SHOULD appear in the table in the same order they do in the iEEG data file.
+Any number of additional columns MAY be provided to provide additional information about the channels.
+Note that electrode positions SHOULD NOT be added to this file but to `*_electrodes.tsv`.
+
+The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 

From c0cacdc7e11d5205d01fabd945a8cb00e303fec0 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Tue, 1 Feb 2022 18:03:21 +0000
Subject: [PATCH 176/347] [DOC] Auto-generate changelog entry for PR #946

---
 src/CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 89940c4077..b72d0cf706 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -14,6 +14,7 @@
 -   \[MISC] Add Eric Earl as a Maintainer [#953](https://github.com/bids-standard/bids-specification/pull/953) ([ericearl](https://github.com/ericearl))
 -   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
 -   \[FIX] Broken hyperlink in entity list file [#949](https://github.com/bids-standard/bids-specification/pull/949) ([Lestropie](https://github.com/Lestropie))
+-   \[FIX] Rewrite inheritance principle [#946](https://github.com/bids-standard/bids-specification/pull/946) ([Lestropie](https://github.com/Lestropie))
 -   \[INFRA] fix "CircleCI redirector" GH-action: remove the 2nd (sanity) check [#944](https://github.com/bids-standard/bids-specification/pull/944) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))
@@ -46,6 +47,7 @@
 -   \[INFRA] Several style fixes (Flake8) for Python code in the repo [#872](https://github.com/bids-standard/bids-specification/pull/872) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] Make subheadings consistent in  06-longitudinal-and-multi-site-studies.md [#870](https://github.com/bids-standard/bids-specification/pull/870) ([guiomar](https://github.com/guiomar))
 -   \[DOC] add Anthony as maintainer [#868](https://github.com/bids-standard/bids-specification/pull/868) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[MISC] add "forward slash" requirement for paths to common principles [#867](https://github.com/bids-standard/bids-specification/pull/867) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Add "ScanRAS" as an accepted coordinate frame for ieeg [#866](https://github.com/bids-standard/bids-specification/pull/866) ([alexrockhill](https://github.com/alexrockhill))
 -   \[INFRA] Add .lgtm.yml file for better usage of LGTM CI tool [#865](https://github.com/bids-standard/bids-specification/pull/865) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] update physio bids name in longitudinal study page examples [#863](https://github.com/bids-standard/bids-specification/pull/863) ([Remi-Gau](https://github.com/Remi-Gau))

From 51e9f1bbc2a4b0f271efd173718492621c282491 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 1 Feb 2022 13:14:29 -0500
Subject: [PATCH 177/347] [ENH] Render valid value restrictions in tables based
 on object definitions in schema (#921)

* Add function.

* Flatten anyOfs of enums.

* Render valid values in metadata tables.

* Add valid values to column tables.

* Drop coverage of certain types.

Dropped types include anyOfs, pattern strings, format strings, and arrays.

* Fix.

* Actually fix?

* Reincorporate changes.

* Run black.

* Remove "allowed values" from field descriptions.

Those values will automatically be rendered from the associated enums.

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/schema/objects/columns.yaml       |  8 ++--
 src/schema/objects/metadata.yaml      | 58 +++++++++---------------
 tools/schemacode/schemacode/render.py | 12 +++++
 tools/schemacode/schemacode/schema.py | 11 +++++
 tools/schemacode/schemacode/utils.py  | 64 +++++++++++++++++++++++++++
 5 files changed, 110 insertions(+), 43 deletions(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index ee658ffbbd..3b4cc655bf 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -127,7 +127,7 @@ handedness:
 hemisphere:
   name: hemisphere
   description: |
-    The hemisphere in which the electrode is placed, one of `['L' or 'R']` (MUST be in upper-case).
+    The hemisphere in which the electrode is placed.
   type: string
   enum:
   - L
@@ -325,8 +325,6 @@ sample_type:
   description: |
     Biosample type defined by
     [ENCODE Biosample Type](https://www.encodeproject.org/profiles/biosample_type).
-    One of: `"cell line"`, `"in vitro differentiated cells"`, `"primary cell"`, `"cell-free sample"`,
-    `"cloning host"`, `"tissue"`, `"whole organisms"`, `"organoid"`, or `"technical sample"`.
   type: string
   enum:
   - cell line
@@ -410,8 +408,8 @@ status:
   name: status
   description: |
     Data quality observed on the channel.
-    Must be one of: `good`, `bad`, or `n/a` (when quality is unknown).
-    A channel is considered `bad` if its data quality is compromised by excessive noise.
+    A channel is considered `"bad"` if its data quality is compromised by excessive noise.
+    If quality is unknown, then a value of `"n/a"` may be used.
     Description of noise type SHOULD be provided in `[status_description]`.
   type: string
   enum:
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index d391384fbd..6fe9ecfc20 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -81,7 +81,6 @@ AnatomicalLandmarkCoordinateUnits:
   name: AnatomicalLandmarkCoordinateUnits
   description: |
     Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -126,7 +125,7 @@ AnatomicalLandmarkCoordinates__mri:
 ArterialSpinLabelingType:
   name: ArterialSpinLabelingType
   description: |
-    `"CASL"`, `"PCASL"`, `"PASL"`.
+    The arterial spin labeling type.
   type: string
   enum:
   - CASL
@@ -311,8 +310,7 @@ BrainLocation:
 CASLType:
   name: CASLType
   description: |
-    Describes if a separate coil is used for labeling:
-    `"single-coil"` or `"double-coil"`.
+    Describes if a separate coil is used for labeling.
   type: string
   enum:
   - single-coil
@@ -425,8 +423,6 @@ ContrastBolusIngredient:
   name: ContrastBolusIngredient
   description: |
     Active ingredient of agent.
-    Values MUST be one of: `"IODINE"`, `"GADOLINIUM"`, `"CARBON DIOXIDE"`,
-    `"BARIUM"`, `"XENON"`.
     Corresponds to DICOM Tag 0018, 1048 `Contrast/Bolus Ingredient`.
   type: string
   enum:
@@ -456,7 +452,6 @@ DatasetType:
   name: DatasetType
   description: |
     The interpretation of the dataset.
-    MUST be one of `"raw"` or `"derivative"`.
     For backwards compatibility, the default value is `"raw"`.
   type: string
   enum:
@@ -560,7 +555,6 @@ DigitizedHeadPointsCoordinateUnits:
   name: DigitizedHeadPointsCoordinateUnits
   description: |
     Units of the coordinates of `DigitizedHeadPointsCoordinateSystem`.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -651,7 +645,6 @@ EEGCoordinateUnits:
   name: EEGCoordinateUnits
   description: |
     Units of the coordinates of `EEGCoordinateSystem`.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -839,7 +832,6 @@ FiducialsCoordinateUnits:
   description: |
     Units in which the coordinates that are  listed in the field
     `FiducialsCoordinateSystem` are represented.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -1083,7 +1075,6 @@ HeadCoilCoordinateUnits:
   name: HeadCoilCoordinateUnits
   description: |
     Units of the coordinates of `HeadCoilCoordinateSystem`.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -1463,12 +1454,12 @@ M0Estimate:
 M0Type:
   name: M0Type
   description: |
-    Describes the presence of M0 information, as either:
-    `"Separate"` when a separate `*_m0scan.nii[.gz]` is present,
-    `"Included"` when an m0scan volume is contained within the current
-    `*_asl.nii[.gz]`,
-    `"Estimate"` when a single whole-brain M0 value is provided, or
-    `"Absent"` when no specific M0 information is present.
+    Describes the presence of M0 information.
+    `"Separate"` means that a separate `*_m0scan.nii[.gz]` is present.
+    `"Included"` means that an m0scan volume is contained within the current
+    `*_asl.nii[.gz]`.
+    `"Estimate"` means that a single whole-brain M0 value is provided.
+    `"Absent"` means that no specific M0 information is present.
   type: string
   enum:
   - Separate
@@ -1505,7 +1496,6 @@ MEGCoordinateUnits:
   name: MEGCoordinateUnits
   description: |
     Units of the coordinates of `MEGCoordinateSystem`.
-    MUST be `"m"`, `"cm"`, or `"mm"`.
   type: string
   enum:
   - m
@@ -1523,7 +1513,6 @@ MEGREFChannelCount:
 MRAcquisitionType:
   name: MRAcquisitionType
   description: |
-    Possible values: `"2D"` or `"3D"`.
     Type of sequence readout.
     Corresponds to DICOM Tag 0018, 0023 `MR Acquisition Type`.
   type: string
@@ -1564,10 +1553,9 @@ MTPulseShape:
   name: MTPulseShape
   description: |
     Shape of the magnetization transfer RF pulse waveform.
-    Accepted values: `"HARD"`, `"GAUSSIAN"`,
-    `"GAUSSHANN"` (gaussian pulse with Hanning window),
-    `"SINC"`, `"SINCHANN"` (sinc pulse with Hanning window),
-    `"SINCGAUSS"` (sinc pulse with Gaussian window), `"FERMI"`.
+    The value `"GAUSSHANN"` refers to a Gaussian pulse with a Hanning window.
+    The value `"SINCHANN"` refers to a sinc pulse with a Hanning window.
+    The value `"SINCGAUSS"` refers to a sinc pulse with a Gaussian window.
   type: string
   enum:
   - HARD
@@ -1807,8 +1795,7 @@ PASLType:
 PCASLType:
   name: PCASLType
   description: |
-    Type the gradient pulses used in the `"control"` condition:
-    `"balanced"` or `"unbalanced"`.
+    The type of gradient pulses used in the `"control"` condition.
   type: string
   enum:
   - balanced
@@ -1886,7 +1873,6 @@ PharmaceuticalName:
 PhaseEncodingDirection:
   name: PhaseEncodingDirection
   description: |
-    Possible values: `"i"`, `"j"`, `"k"`, `"i-"`, `"j-"`, `"k-"`.
     The letters `i`, `j`, `k` correspond to the first, second and third axis of
     the data in the NIFTI file.
     The polarity of the phase encoding is assumed to go from zero index to
@@ -2109,7 +2095,7 @@ RecordingDuration:
 RecordingType:
   name: RecordingType
   description: |
-    Defines whether the recording is `"continuous"`, `"discontinuous"` or
+    Defines whether the recording is `"continuous"`, `"discontinuous"`, or
     `"epoched"`, where `"epoched"` is limited to time windows about events of
     interest (for example, stimulus presentations or subject responses).
   type: string
@@ -2244,8 +2230,6 @@ SampleOrigin:
   name: SampleOrigin
   description: |
     Describes from which tissue the genetic information was extracted.
-    Values MUST be one of `"blood"`, `"saliva"`, `"brain"`, `"csf"`,
-    `"breast milk"`, `"bile"`, `"amniotic fluid"`, `"other biospecimen"`.
   type: string
   enum:
   - blood
@@ -2385,9 +2369,8 @@ SkullStripped:
 SliceEncodingDirection:
   name: SliceEncodingDirection
   description: |
-    Possible values: `"i"`, `"j"`, `"k"`, `"i-"`, `"j-"`, `"k-"`
-    (the axis of the NIfTI data along which slices were acquired,
-    and the direction in which `SliceTiming` is defined with respect to).
+    The axis of the NIfTI data along which slices were acquired,
+    and the direction in which `SliceTiming` is defined with respect to.
     `i`, `j`, `k` identifiers correspond to the first, second and third axis of
     the data in the NIfTI file.
     A `-` sign indicates that the contents of `SliceTiming` are defined in
@@ -2598,7 +2581,6 @@ SpoilingType:
   name: SpoilingType
   description: |
     Specifies which spoiling method(s) are used by a spoiled sequence.
-    Accepted values: `"RF"`, `"GRADIENT"` or `"COMBINED"`.
   type: string
   enum:
   - RF
@@ -2685,8 +2667,6 @@ TissueOrigin:
   name: TissueOrigin
   description: |
     Describes the type of tissue analyzed for `SampleOrigin` `brain`.
-    Values MUST be one of `"gray matter"`, `"white matter"`, `"csf"`,
-    `"meninges"`, `"macrovascular"` or `microvascular`.
   type: string
   enum:
   - gray matter
@@ -2767,8 +2747,10 @@ Type:
   name: Type
   description: |
     Short identifier of the mask.
-    Reserved values: `Brain` - brain mask, `Lesion` - lesion mask,
-    `Face` - face mask, `ROI` - ROI mask
+    The value `"Brain"` refers to a brain mask.
+    The value `"Lesion"` refers to a lesion mask.
+    The value `"Face"` refers to a face mask.
+    The value `"ROI"` refers to a region of interest mask.
   type: string
   enum:
   - Brain
@@ -2963,7 +2945,7 @@ iEEGCoordinateSystemDescription:
 iEEGCoordinateUnits:
   name: iEEGCoordinateUnits
   description: |
-    Units of the `*_electrodes.tsv`, MUST be `"m"`, `"mm"`, `"cm"` or `"pixels"`.
+    Units of the `*_electrodes.tsv`.
     MUST be `"pixels"` if `iEEGCoordinateSystem` is `Pixels`.
   type: string
   enum:
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index 56480f351a..ea4f0fd1f9 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -507,6 +507,12 @@ def make_metadata_table(schema, field_info, tablefmt="github"):
         type_string = utils.resolve_metadata_type(metadata_schema[field])
 
         description = metadata_schema[field]["description"] + " " + description_addendum
+
+        # Try to add info about valid values
+        valid_values_str = utils.describe_valid_values(metadata_schema[field])
+        if valid_values_str:
+            description += "\n\n\n\n" + valid_values_str
+
         # A backslash before a newline means continue a string
         description = description.replace("\\\n", "")
         # Two newlines should be respected
@@ -576,6 +582,12 @@ def make_columns_table(schema, column_info, tablefmt="github"):
         type_string = utils.resolve_metadata_type(column_schema[field])
 
         description = column_schema[field]["description"] + " " + description_addendum
+
+        # Try to add info about valid values
+        valid_values_str = utils.describe_valid_values(column_schema[field])
+        if valid_values_str:
+            description += "\n\n\n\n" + valid_values_str
+
         # A backslash before a newline means continue a string
         description = description.replace("\\\n", "")
         # Two newlines should be respected
diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 9203eaa921..1748c3a5aa 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -37,6 +37,17 @@ def dereference_yaml(schema, struct):
 
         struct = {key: dereference_yaml(schema, val) for key, val in struct.items()}
 
+        # For the rare case of multiple sets of valid values (enums) from multiple references,
+        # anyOf is used. Here we try to flatten our anyOf of enums into a single enum list.
+        if "anyOf" in struct.keys():
+            if all("enum" in obj for obj in struct["anyOf"]):
+                all_enum = [v["enum"] for v in struct["anyOf"]]
+                all_enum = [item for sublist in all_enum for item in sublist]
+
+                struct.pop("anyOf")
+                struct["type"] = "string"
+                struct["enum"] = all_enum
+
     elif isinstance(struct, list):
         struct = [dereference_yaml(schema, item) for item in struct]
 
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 7505b2e000..6d2cfcabe5 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -197,3 +197,67 @@ def resolve_metadata_type(definition):
         string = "unknown"
 
     return string
+
+
+def describe_valid_values(definition):
+    """Build a sentence describing valid values for an object from its definition.
+
+    This only covers booleans, enums, integers, and numbers.
+    Currently uncovered are anyOfs, arrays, and objects.
+
+    Parameters
+    ----------
+    definition : :obj:`dict`
+        An object definition, following the BIDS schema object rules.
+
+    Returns
+    -------
+    :obj:`str`
+        A sentence describing valid values for the object.
+    """
+    description = ""
+    if "anyOf" in definition.keys():
+        return description
+
+    if definition["type"] == "boolean":
+        description = 'Must be one of: `"true"`, `"false"`.'
+
+    elif definition["type"] == "string":
+        if "enum" in definition.keys():
+            # Allow enums to be "objects" (dicts) or strings
+            enum_values = [
+                list(v.keys())[0] if isinstance(v, dict) else v for v in definition["enum"]
+            ]
+            enum_values = [f'`"{v}"`' for v in enum_values]
+            description = f"Must be one of: {', '.join(enum_values)}."
+
+    elif definition["type"] in ("integer", "number"):
+        if "minimum" in definition.keys():
+            minstr = f"greater than or equal to {definition['minimum']}"
+        elif "exclusiveMinimum" in definition.keys():
+            minstr = f"greater than {definition['exclusiveMinimum']}"
+        else:
+            minstr = ""
+
+        if "maximum" in definition.keys():
+            maxstr = f"less than or equal to {definition['maximum']}"
+        elif "exclusiveMaximum" in definition.keys():
+            maxstr = f"less than {definition['exclusiveMaximum']}"
+        else:
+            maxstr = ""
+
+        if minstr and maxstr:
+            minmaxstr = f"{minstr} and {maxstr}"
+        elif minstr:
+            minmaxstr = minstr
+        elif maxstr:
+            minmaxstr = maxstr
+        else:
+            minmaxstr = ""
+
+        if minmaxstr:
+            description = f"Must be a number {minmaxstr}."
+        else:
+            description = ""
+
+    return description

From e53a367663bf4d53f538276155a706897df6e23f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 1 Feb 2022 19:20:39 +0100
Subject: [PATCH 178/347] fix typo (#991)

---
 .../01-magnetic-resonance-imaging-data.md                      | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 5422515ad8..41969de679 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -194,8 +194,7 @@ whenever possible. See also
 
 {{ MACROS___make_filename_template(datatypes=["anat"]) }}
 
-Anatomical (structural) data acquired for that participant. Currently supported
-non-parametric structural MR images include:
+Currently supported non-parametric structural MR images include:
 
 {{ MACROS___make_suffix_table(
       [

From a3cfa1a980bfb4f6cb7f53f3a672dd7120ddebfe Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 1 Feb 2022 13:25:41 -0500
Subject: [PATCH 179/347] ENH: Update B0Field metadata to accommodate
 single-blip fieldmaps (#968)

---
 src/schema/objects/metadata.yaml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 6fe9ecfc20..d54d144365 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -173,30 +173,33 @@ B0FieldIdentifier:
   description: |
     The presence of this key states that this particular 3D or 4D image MAY be
     used for fieldmap estimation purposes.
-    The `B0FieldIdentifier` MUST be a unique string within one participant's tree,
+    Each `B0FieldIdentifier` MUST be a unique string within one participant's tree,
     shared only by the images meant to be used as inputs for the estimation of a
     particular instance of the *B<sub>0</sub> field* estimation.
     It is RECOMMENDED to derive this identifier from DICOM Tags, for example,
     DICOM tag 0018, 1030 `Protocol Name`, or DICOM tag 0018, 0024 `Sequence Name`
     when the former is not defined (for example, in GE devices.)
-  type: string
-  format: participant_relative
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
 B0FieldSource:
   name: B0FieldSource
   description: |
-    At least one existing `B0FieldIdentifier` defined by other images in the
+    At least one existing `B0FieldIdentifier` defined by images in the
     participant's tree.
     This field states the *B<sub>0</sub> field* estimation designated by the
     `B0FieldIdentifier` that may be used to correct the dataset for distortions
     caused by B<sub>0</sub> inhomogeneities.
-    `B0FieldSource` and `B0FieldIdentifier` are mutually exclusive.
+    `B0FieldSource` and `B0FieldIdentifier` MAY both be present for images that
+    are used to estimate their own B<sub>0</sub> field, for example, in "pepolar"
+    acquisitions.
   anyOf:
   - type: string
-    format: participant_relative
   - type: array
     items:
       type: string
-      format: participant_relative
 BIDSVersion:
   name: BIDSVersion
   description: |

From a277b872b0b4c21159c95d27ba517795a9af14f2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 1 Feb 2022 19:29:39 +0100
Subject: [PATCH 180/347] [SCHEMA] add physio to schema or EEG, MEG, iEEG, PET,
 ASL, DWI (#894)

* add physio to schema

* update filename template macros

* move recording right before space in entity order

* lint yml

* fix markdown

* rm split entity for physio for MEG datatype

* try fix pdf build

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 .../02-magnetoencephalography.md                 |  5 ++++-
 .../03-electroencephalography.md                 |  5 ++++-
 .../04-intracranial-electroencephalography.md    |  5 ++++-
 .../09-positron-emission-tomography.md           |  5 ++++-
 src/schema/rules/datatypes/dwi.yaml              | 16 ++++++++++++++++
 src/schema/rules/datatypes/eeg.yaml              | 15 +++++++++++++++
 src/schema/rules/datatypes/ieeg.yaml             | 15 +++++++++++++++
 src/schema/rules/datatypes/meg.yaml              | 16 ++++++++++++++++
 src/schema/rules/datatypes/perf.yaml             | 16 ++++++++++++++++
 src/schema/rules/datatypes/pet.yaml              | 16 ++++++++++++++++
 src/schema/rules/entities.yaml                   |  2 +-
 11 files changed, 111 insertions(+), 5 deletions(-)

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 77169924e9..d6ea1790a5 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -16,7 +16,10 @@ the [BIDS examples repository](https://github.com/bids-standard/bids-examples).
 
 ## MEG recording data
 
-{{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["meg", "markers", "events"]) }}
+{{ MACROS___make_filename_template(
+   datatypes=["meg"],
+   suffixes=["meg", "markers", "events", "physio", "stim"])
+}}
 
 Unprocessed MEG data MUST be stored in the native file format of the MEG
 instrument with which the data was collected.
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index e6b7178491..c0b6232e8e 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -12,7 +12,10 @@ and can be used for practical guidance when curating a new dataset.
 
 ## EEG recording data
 
-{{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["eeg", "events"]) }}
+{{ MACROS___make_filename_template(
+   datatypes=["eeg"],
+   suffixes=["eeg", "events", "physio", "stim"])
+}}
 
 The EEG community uses a variety of formats for storing raw data, and there is
 no single standard that all researchers agree on. For BIDS, EEG data MUST be
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index 2c2983e8ba..7896b57037 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -12,7 +12,10 @@ and can be used for practical guidance when curating a new dataset.
 
 ## iEEG recording data
 
-{{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["ieeg", "events"]) }}
+{{ MACROS___make_filename_template(
+   datatypes=["ieeg"],
+   suffixes=["ieeg", "events", "physio", "stim"])
+}}
 
 The iEEG community uses a variety of formats for storing raw data, and there is
 no single standard that all researchers agree on. For BIDS, iEEG data MUST be
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 70e6d77f18..81d6babe01 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -60,7 +60,10 @@ In this example, tracer injection coincides with scan start.
 
 ## PET recording data
 
-{{ MACROS___make_filename_template(datatypes=["pet"], suffixes=["pet", "events"]) }}
+{{ MACROS___make_filename_template(
+   datatypes=["pet"],
+   suffixes=["pet", "events", "physio", "stim"])
+}}
 
 PET data MUST be stored in the `pet` directory.
 PET imaging data SHOULD be stored in 4D (or 3D, if only one volume was acquired)
diff --git a/src/schema/rules/datatypes/dwi.yaml b/src/schema/rules/datatypes/dwi.yaml
index b867d3dc6e..dfb178760b 100644
--- a/src/schema/rules/datatypes/dwi.yaml
+++ b/src/schema/rules/datatypes/dwi.yaml
@@ -30,3 +30,19 @@
     direction: optional
     run: optional
     part: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    acquisition: optional
+    direction: optional
+    run: optional
+    part: optional
+    recording: optional
diff --git a/src/schema/rules/datatypes/eeg.yaml b/src/schema/rules/datatypes/eeg.yaml
index 5951137af6..6b112e343d 100644
--- a/src/schema/rules/datatypes/eeg.yaml
+++ b/src/schema/rules/datatypes/eeg.yaml
@@ -70,3 +70,18 @@
     subject: required
     session: optional
     acquisition: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    task: required
+    acquisition: optional
+    run: optional
+    recording: optional
diff --git a/src/schema/rules/datatypes/ieeg.yaml b/src/schema/rules/datatypes/ieeg.yaml
index 2b393cda54..37c02963f5 100644
--- a/src/schema/rules/datatypes/ieeg.yaml
+++ b/src/schema/rules/datatypes/ieeg.yaml
@@ -71,3 +71,18 @@
     subject: required
     session: optional
     acquisition: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    task: required
+    acquisition: optional
+    run: optional
+    recording: optional
diff --git a/src/schema/rules/datatypes/meg.yaml b/src/schema/rules/datatypes/meg.yaml
index 2b77b6b209..104689b7f1 100644
--- a/src/schema/rules/datatypes/meg.yaml
+++ b/src/schema/rules/datatypes/meg.yaml
@@ -123,3 +123,19 @@
     subject: required
     session: optional
     acquisition: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    task: required
+    acquisition: optional
+    run: optional
+    processing: optional
+    recording: optional
diff --git a/src/schema/rules/datatypes/perf.yaml b/src/schema/rules/datatypes/perf.yaml
index 4db73d61ca..14b4ffe407 100644
--- a/src/schema/rules/datatypes/perf.yaml
+++ b/src/schema/rules/datatypes/perf.yaml
@@ -40,3 +40,19 @@
     acquisition: optional
     reconstruction: optional
     run: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    acquisition: optional
+    reconstruction: optional
+    direction: optional
+    run: optional
+    recording: optional
diff --git a/src/schema/rules/datatypes/pet.yaml b/src/schema/rules/datatypes/pet.yaml
index 1faed9482a..33f1a9f3e3 100644
--- a/src/schema/rules/datatypes/pet.yaml
+++ b/src/schema/rules/datatypes/pet.yaml
@@ -42,3 +42,19 @@
     tracer: optional
     reconstruction: optional
     run: optional
+
+# Timeseries
+- suffixes:
+  - physio
+  - stim
+  extensions:
+  - .tsv.gz
+  - .json
+  entities:
+    subject: required
+    session: optional
+    task: optional
+    tracer: optional
+    reconstruction: optional
+    run: optional
+    recording: optional
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 1e145edee6..3590bea80e 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -18,11 +18,11 @@
 - inversion
 - mtransfer
 - part
-- recording
 - processing
 - hemisphere
 - space
 - split
+- recording
 - chunk
 - resolution
 - density

From 8870e6f3578b429b4e5346d922b57e53dff77b0f Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Tue, 1 Feb 2022 18:35:18 +0000
Subject: [PATCH 181/347] [DOC] Auto-generate changelog entry for PR #993

---
 src/CHANGES.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index b72d0cf706..fb524db047 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,11 +2,14 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] Fix linkchecker [#982](https://github.com/bids-standard/bids-specification/pull/982) ([sappelhoff](https://github.com/sappelhoff))
 -   \[DOC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))
 -   customize footer on html spec [#975](https://github.com/bids-standard/bids-specification/pull/975) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Update HED appendix to comply with current HED version [#970](https://github.com/bids-standard/bids-specification/pull/970) ([VisLab](https://github.com/VisLab))
+-   ENH: Update B0Field metadata to accommodate single-blip fieldmaps [#968](https://github.com/bids-standard/bids-specification/pull/968) ([effigies](https://github.com/effigies))
 -   \[FIX] harmonize 'file name' into 'filename' [#962](https://github.com/bids-standard/bids-specification/pull/962) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Reword front page [#958](https://github.com/bids-standard/bids-specification/pull/958) ([arokem](https://github.com/arokem))
 -   \[MAINT] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies))
@@ -27,6 +30,7 @@
 -   \[INFRA] add (optional) pre-commit config file [#929](https://github.com/bids-standard/bids-specification/pull/929) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Clarify that EDF/BDF files MUST have lower case extensions in BIDS [#927](https://github.com/bids-standard/bids-specification/pull/927) ([adam2392](https://github.com/adam2392))
 -   \[ENH] Generate glossary page from schema [#923](https://github.com/bids-standard/bids-specification/pull/923) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Render valid value restrictions in tables based on object definitions in schema [#921](https://github.com/bids-standard/bids-specification/pull/921) ([tsalo](https://github.com/tsalo))
 -   \[ENH] add `hemi` entity to schema [#917](https://github.com/bids-standard/bids-specification/pull/917) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] PDF version of spec: fix handling of internal links [#915](https://github.com/bids-standard/bids-specification/pull/915) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] update and reformat table for template in coordinate system page [#903](https://github.com/bids-standard/bids-specification/pull/903) ([Remi-Gau](https://github.com/Remi-Gau))
@@ -36,6 +40,7 @@
 -   \[FIX] small typo in json example [#897](https://github.com/bids-standard/bids-specification/pull/897) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] tiny speedup of building PDF by moving `re.compile\(\)` outside of a loop [#896](https://github.com/bids-standard/bids-specification/pull/896) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[INFRA] Document \*.webm video files as binary [#895](https://github.com/bids-standard/bids-specification/pull/895) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[SCHEMA] add physio to schema or EEG, MEG, iEEG, PET, ASL, DWI [#894](https://github.com/bids-standard/bids-specification/pull/894) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[SCHEMA] Reorganize schema code into a package [#892](https://github.com/bids-standard/bids-specification/pull/892) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Clarify shifting dates RECOMMENDED, add example EDF [#891](https://github.com/bids-standard/bids-specification/pull/891) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix draft rendering css on mobile or when browser window is narrow [#889](https://github.com/bids-standard/bids-specification/pull/889) ([sappelhoff](https://github.com/sappelhoff))

From 8242d0af9698b5847507f1f689509bb33f91dc12 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 1 Feb 2022 15:09:39 -0500
Subject: [PATCH 182/347] [SCHEMA, FIX] Remove mentions of auxdatatypes (#996)

---
 src/99-appendices/04-entity-table.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 91bf0381a6..3056eb326d 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -20,7 +20,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Magnetic Resonance Imaging
 
-{{ MACROS___make_entity_table(datatypes=["anat", "dwi", "func", "fmap", "perf"], auxdatatypes=[]) }}
+{{ MACROS___make_entity_table(datatypes=["anat", "dwi", "func", "fmap", "perf"]) }}
 
 ## Biopotential Amplification (EEG and iEEG)
 
@@ -28,7 +28,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Magnetoencephalography (MEG)
 
-{{ MACROS___make_entity_table(datatypes=["meg"], auxdatatypes=["channels", "events", "photo"]) }}
+{{ MACROS___make_entity_table(datatypes=["meg"]) }}
 
 ## Positron Emission Tomography (PET)
 
@@ -36,8 +36,8 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Behavioral Data
 
-{{ MACROS___make_entity_table(datatypes=["beh"], auxdatatypes=[]) }}
+{{ MACROS___make_entity_table(datatypes=["beh"]) }}
 
 ## Microscopy
 
-{{ MACROS___make_entity_table(datatypes=["micr"], auxdatatypes=[]) }}
+{{ MACROS___make_entity_table(datatypes=["micr"]) }}

From 49b9f48632aba31f5770acb39d3d475b4bd7d3cf Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Wed, 2 Feb 2022 09:50:36 +0000
Subject: [PATCH 183/347] [DOC] Auto-generate changelog entry for PR #989

---
 src/CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index fb524db047..7100727fa2 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,8 +2,10 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[SCHEMA, FIX] Remove mentions of auxdatatypes [#996](https://github.com/bids-standard/bids-specification/pull/996) ([tsalo](https://github.com/tsalo))
 -   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] Optionally support echo entity for VFA suffix [#989](https://github.com/bids-standard/bids-specification/pull/989) ([TheChymera](https://github.com/TheChymera))
 -   \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] Fix linkchecker [#982](https://github.com/bids-standard/bids-specification/pull/982) ([sappelhoff](https://github.com/sappelhoff))
 -   \[DOC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))

From 439714ca7f7d0bf61262761df2fafc64fc3309b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 15:48:19 +0100
Subject: [PATCH 184/347] ENH: Add atlas to src/schema/rules/entities.yaml

---
 src/schema/rules/entities.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 3590bea80e..08209723e5 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -24,6 +24,7 @@
 - split
 - recording
 - chunk
+- atlas
 - resolution
 - density
 - label

From 08327b523bd7962b26d45ea47ee06485bac02c2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 16:11:11 +0100
Subject: [PATCH 185/347] ENH: Introduce the atlas entity and replace
 segmentation atlas metadata

---
 src/05-derivatives/03-imaging.md | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/05-derivatives/03-imaging.md b/src/05-derivatives/03-imaging.md
index 0cce5b1733..21db53dba0 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/05-derivatives/03-imaging.md
@@ -211,7 +211,6 @@ The following metadata fields apply to all segmentation files:
 {{ MACROS___make_metadata_table(
    {
       "Manual": "OPTIONAL",
-      "Atlas": "OPTIONAL",
       "Resolution": "REQUIRED if `res` is present",
       "Density": "REQUIRED if `den` is present",
    }
@@ -230,7 +229,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         anat|func|dwi/
-            <source_entities>[_space-<space>][_res-<label>][_den-<label>]_dseg.nii.gz
+            <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
 ```
 
 Example:
@@ -254,7 +253,7 @@ In this case, the mask suffix MUST be used,
 the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
-and the `Atlas` metadata SHOULD be defined.
+and the [`atlas` entity](../99-appendices/09-entities.md#atlas) SHOULD be defined.
 For example:
 
 {{ MACROS___make_filetree_example(
@@ -262,7 +261,7 @@ For example:
     "pipeline": {
         "sub-001": {
             "anat": {
-                "sub-001_space-orig_label-GM_mask.nii.gz": "",
+                "sub-001_space-orig_atlas-_label-GM_mask.nii.gz": "",
                 },
             },
         }
@@ -284,7 +283,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         func|anat|dwi/
-            <source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
+            <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
 ```
 
 Example:
@@ -350,7 +349,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         anat/
-            <source_entities>[_hemi-{L|R}][_space-<space>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
+            <source_entities>[_hemi-{L|R}][_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
 ```
 
 The [`hemi-<label>`](../99-appendices/09-entities.md#hemi) entity is REQUIRED for GIFTI files storing information about

From 33293583eaedec84f9c7f56222132edd51de59e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 16:12:06 +0100
Subject: [PATCH 186/347] ENH: Add atlas entity and description to
 schema/objects/entities.yaml

---
 src/schema/objects/entities.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index de278d3dc3..fcff5de50e 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -25,6 +25,15 @@ acquisition:
     remains at the discretion of the researcher.
   type: string
   format: label
+atlas:
+  name: Atlas
+  entity: atlas
+  description: |
+    The `atlas-<label>` key/value pair corresponds to a custom label the
+    user MAY use to distinguish a different atlas used for similar type of
+    derivatives data.
+  type: string
+  format: label
 ceagent:
   name: Contrast Enhancing Agent
   entity: ce

From d58dd29d5a2d17c500b545348035cdaa44f797b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 16:14:31 +0100
Subject: [PATCH 187/347] ENH: Modify description of atlas entity in
 schema/objects/entities.yaml

---
 src/schema/objects/entities.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index fcff5de50e..f9d260fca2 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -29,9 +29,10 @@ atlas:
   name: Atlas
   entity: atlas
   description: |
-    The `atlas-<label>` key/value pair corresponds to a custom label the
-    user MAY use to distinguish a different atlas used for similar type of
-    derivatives data.
+    The `atlas-<label>` key/value pair corresponds to a custom label the user
+    MAY use to distinguish a different atlas used for similar type of data.
+
+    This entity is only applicable to derivative data.
   type: string
   format: label
 ceagent:

From 711cc48b3a487d4b3d9e9dc3835dbdd9e59d915d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 17:23:16 +0100
Subject: [PATCH 188/347] ENH: Add sentence to introduce atlas entity and
 reintroduce Atlas metadata

---
 src/05-derivatives/03-imaging.md | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/05-derivatives/03-imaging.md b/src/05-derivatives/03-imaging.md
index 21db53dba0..e279301282 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/05-derivatives/03-imaging.md
@@ -202,6 +202,11 @@ structure may be concatenated in a single file.
 Segmentations may be defined in a volume (labeled voxels), a surface (labeled
 vertices) or a combined volume/surface space.
 
+If the segmentation can be derived from different atlases,
+the [`atlas` entity](../99-appendices/09-entities.md#atlas) MAY be used to
+distinguish the different segmentations.
+If so, the `Atlas` metadata SHOULD also be defined. 
+
 The following section describes discrete and probabilistic segmentations of
 volumes, followed by discrete segmentations of surface/combined spaces.
 Probabilistic segmentations of surfaces are currently [unspecified][].
@@ -211,6 +216,7 @@ The following metadata fields apply to all segmentation files:
 {{ MACROS___make_metadata_table(
    {
       "Manual": "OPTIONAL",
+      "Atlas": "REQUIRED if `atlas` is present",
       "Resolution": "REQUIRED if `res` is present",
       "Density": "REQUIRED if `den` is present",
    }
@@ -253,7 +259,9 @@ In this case, the mask suffix MUST be used,
 the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
-and the [`atlas` entity](../99-appendices/09-entities.md#atlas) SHOULD be defined.
+the [`atlas` entity](../99-appendices/09-entities.md#atlas) and the
+`Atlas` metadata SHOULD be defined,
+
 For example:
 
 {{ MACROS___make_filetree_example(
@@ -261,7 +269,8 @@ For example:
     "pipeline": {
         "sub-001": {
             "anat": {
-                "sub-001_space-orig_atlas-_label-GM_mask.nii.gz": "",
+                "sub-001_space-orig_atlas-Desikan_label-GM_mask.nii.gz": "",
+                "sub-001_space-orig_atlas-Desikan_label-GM_mask.json": "",
                 },
             },
         }

From 2ef9207c4bc995fc9c00b207f8a9b88a354114e6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Tourbier?= <sebastien.tourbier1@gmail.com>
Date: Wed, 2 Feb 2022 17:26:16 +0100
Subject: [PATCH 189/347] STY: Make markdown linter happy

---
 src/05-derivatives/03-imaging.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/05-derivatives/03-imaging.md b/src/05-derivatives/03-imaging.md
index e279301282..6814889c6c 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/05-derivatives/03-imaging.md
@@ -205,7 +205,7 @@ vertices) or a combined volume/surface space.
 If the segmentation can be derived from different atlases,
 the [`atlas` entity](../99-appendices/09-entities.md#atlas) MAY be used to
 distinguish the different segmentations.
-If so, the `Atlas` metadata SHOULD also be defined. 
+If so, the `Atlas` metadata SHOULD also be defined.
 
 The following section describes discrete and probabilistic segmentations of
 volumes, followed by discrete segmentations of surface/combined spaces.
@@ -260,7 +260,7 @@ the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
 the [`atlas` entity](../99-appendices/09-entities.md#atlas) and the
-`Atlas` metadata SHOULD be defined,
+`Atlas` metadata SHOULD be defined.
 
 For example:
 

From 03a5604afd9cb68db394ee07a97232991d051e93 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 3 Feb 2022 21:06:29 +0100
Subject: [PATCH 190/347] split acq time definition in 2 for session and scans
 TSV

---
 src/03-modality-agnostic-files.md |  4 ++--
 src/schema/objects/columns.yaml   | 15 +++++++++++++--
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index d1cac29292..0de4fddd52 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file.
 {{ MACROS___make_columns_table(
    {
       "filename": ("REQUIRED", "There MUST be exactly one row for each file."),
-      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical."),
+      "acq_time__scans": ("OPTIONAL"),
    }
 ) }}
 
@@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip
 {{ MACROS___make_columns_table(
    {
       "session_id": ("REQUIRED", "There MUST be exactly one row for each session."),
-      "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired."),
+      "acq_time__sessions": ("OPTIONAL"),
       "pathology": "RECOMMENDED",
    }
 ) }}
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 776a6334e6..316a2bd6af 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -10,9 +10,20 @@ abbreviation:
   description: |
     The unique label abbreviation
   type: string
-acq_time:
+acq_time__scans:
   name: acq_time
-  description: Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
+  description: |
+    Acquisition time refers to when the first data point in each run was acquired.
+    Furthermore, if this header is provided, the acquisition times of all files
+    from the same recording MUST be identical.
+    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
+  type: string
+  format: datetime
+acq_time__sessions:
+  name: acq_time
+  description: |
+    Acquisition time refers to when the first data point of the first run was acquired.
+    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
   type: string
   format: datetime
 age:

From 5b90d788efa5b4e6c44fa931b65961b6f9fc8528 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Fri, 4 Feb 2022 08:47:06 +0000
Subject: [PATCH 191/347] [DOC] Auto-generate changelog entry for PR #440

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 7100727fa2..2cc68c643b 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -103,6 +103,7 @@
 -   \[SCHEMA] Add suffix term files [#772](https://github.com/bids-standard/bids-specification/pull/772) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Allow encoding the fieldmapping intent of the protocol [#622](https://github.com/bids-standard/bids-specification/pull/622) ([oesteban](https://github.com/oesteban))
 -   \[FIX] Correct iEEG example that contained double suffixes [#463](https://github.com/bids-standard/bids-specification/pull/463) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] introduce GeneratedBy to "core" BIDS [#440](https://github.com/bids-standard/bids-specification/pull/440) ([yarikoptic](https://github.com/yarikoptic))
 
 ## [v1.6.0](https://github.com/bids-standard/bids-specification/tree/v1.6.0) (2021-04-22)
 

From 577cc82cbf845e5ed2c5ca7e0786fca3bbae1ad0 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Fri, 4 Feb 2022 08:50:56 +0000
Subject: [PATCH 192/347] [DOC] Auto-generate changelog entry for PR #986

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 2cc68c643b..3693c6cc51 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -6,6 +6,7 @@
 -   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] Optionally support echo entity for VFA suffix [#989](https://github.com/bids-standard/bids-specification/pull/989) ([TheChymera](https://github.com/TheChymera))
+-   \[FIX] update definition acq_time for sessions.tsv [#986](https://github.com/bids-standard/bids-specification/pull/986) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] Fix linkchecker [#982](https://github.com/bids-standard/bids-specification/pull/982) ([sappelhoff](https://github.com/sappelhoff))
 -   \[DOC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))

From e47283a268f20b98d5c05ad1bb8c63da3d2a1ceb Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 4 Feb 2022 10:08:51 +0100
Subject: [PATCH 193/347] [FIX] update highlighting of examples, JSON keys and
 values, and TSV headers or values in the schema (#998)

* remove extra double quotes from examples in columns.yml

* update example highlighting and add double quotes for JSON keys or values for entities.yml

* update example and JSON keys and values highlighting in metadata.yml

* Apply suggestions from code review

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Apply suggestions from code review

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/schema/objects/columns.yaml  |  24 ++---
 src/schema/objects/entities.yaml |  36 +++----
 src/schema/objects/metadata.yaml | 164 +++++++++++++++----------------
 3 files changed, 112 insertions(+), 112 deletions(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index c610509f1b..1c34c936bd 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -65,7 +65,7 @@ duration:
   name: duration
   description: |
     Duration of the event (measured from onset) in seconds.
-    Must always be either zero or positive (or `"n/a"` if unavailable).
+    Must always be either zero or positive (or `n/a` if unavailable).
     A "duration" value of zero implies that the delta function or event is so
     short as to be effectively modeled as an impulse.
   anyOf:
@@ -183,7 +183,7 @@ mapping:
 material:
   name: material
   description: |
-    Material of the electrode (for example, `"Tin"`, `"Ag/AgCl"`, `"Gold"`).
+    Material of the electrode (for example, `Tin`, `Ag/AgCl`, `Gold`).
   type: string
 metabolite_parent_fraction:
   name: metabolite_parent_fraction
@@ -264,7 +264,7 @@ participant_id:
 plasma_radioactivity:
   name: plasma_radioactivity
   description: |
-    Radioactivity in plasma, in unit of plasma radioactivity (for example, `"kBq/mL"`).
+    Radioactivity in plasma, in unit of plasma radioactivity (for example, `kBq/mL`).
   type: number
 # reference column for channels.tsv files for EEG data
 reference__eeg:
@@ -278,7 +278,7 @@ reference__eeg:
 reference__ieeg:
   name: reference
   description: |
-    Specification of the reference (for example, 'mastoid', 'ElectrodeName01', 'intracranial', 'CAR', 'other', 'n/a').
+    Specification of the reference (for example, `mastoid`, `ElectrodeName01`, `intracranial`, `CAR`, `other`, `n/a`).
     If the channel is not an electrode channel (for example, a microphone channel) use `n/a`.
   anyOf:
   - type: string
@@ -295,7 +295,7 @@ response_time:
   description: |
     Response time measured in seconds.
     A negative response time can be used to represent preemptive responses and
-    "n/a" denotes a missed response.
+    `n/a` denotes a missed response.
   anyOf:
   - type: number
     unit: s
@@ -382,7 +382,7 @@ software_filters:
   name: software_filters
   description: |
     List of temporal and/or spatial software filters applied
-    (for example, "SSS", `"SpatialCompensation"`).
+    (for example, `SSS`, `SpatialCompensation`).
     Note that parameters should be defined in the general MEG sidecar .json file.
     Indicate `n/a` in the absence of software filters applied.
   anyOf:
@@ -403,8 +403,8 @@ status:
   name: status
   description: |
     Data quality observed on the channel.
-    A channel is considered `"bad"` if its data quality is compromised by excessive noise.
-    If quality is unknown, then a value of `"n/a"` may be used.
+    A channel is considered `bad` if its data quality is compromised by excessive noise.
+    If quality is unknown, then a value of `n/a` may be used.
     Description of noise type SHOULD be provided in `[status_description]`.
   type: string
   enum:
@@ -427,7 +427,7 @@ stim_file:
     (under the root folder of the dataset; with optional subfolders).
     The values under the `stim_file` column correspond to a path relative to
     `/stimuli`.
-    For example `"images/cat03.jpg"` will be translated to `"/stimuli/images/cat03.jpg"`.
+    For example `images/cat03.jpg` will be translated to `/stimuli/images/cat03.jpg`.
   type: string
   format: stimuli_relative
 strain:
@@ -456,8 +456,8 @@ trial_type:
   description: |
     Primary categorisation of each trial to identify them as instances of the
     experimental conditions.
-    For example: for a response inhibition task, it could take on values "go" and
-    "no-go" to refer to response initiation and response inhibition experimental
+    For example: for a response inhibition task, it could take on values `go` and
+    `no-go` to refer to response initiation and response inhibition experimental
     conditions.
   type: string
 trigger:
@@ -539,7 +539,7 @@ whole_blood_radioactivity:
   name: whole_blood_radioactivity
   description: |
     Radioactivity in whole blood samples,
-    in unit of radioactivity measurements in whole blood samples (for example, `"kBq/mL"`).
+    in unit of radioactivity measurements in whole blood samples (for example, `kBq/mL`).
   type: number
 x:
   name: x
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index de278d3dc3..3df87f7eec 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -15,13 +15,13 @@ acquisition:
     resolution.
     In such case two files could have the following names:
     `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
-    the user is free to choose any other label than highres and lowres as long
+    the user is free to choose any other label than `highres` and `lowres` as long
     as they are consistent across subjects and sessions.
     In case different sequences are used to record the same modality
-    (for example, RARE and FLASH for T1w)
+    (for example, `RARE` and `FLASH` for T1w)
     this field can also be used to make that distinction.
     At what level of detail to make the distinction (for example,
-    just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
+    just between `RARE` and `FLASH`, or between `RARE`, `FLASH`, and `FLASHsubsampled`)
     remains at the discretion of the researcher.
   type: string
   format: label
@@ -32,7 +32,7 @@ ceagent:
     The `ce-<label>` key/value can be used to distinguish
     sequences using different contrast enhanced images.
     The label is the name of the contrast agent.
-    The key `ContrastBolusIngredient` MAY also be added in the JSON file,
+    The key `"ContrastBolusIngredient"` MAY also be added in the JSON file,
     with the same label.
   type: string
   format: label
@@ -82,9 +82,9 @@ echo:
     If files belonging to an entity-linked file collection are acquired at different
     echo times, the `_echo-<index>` key/value pair MUST be used to distinguish
     individual files.
-    This entity represents the `EchoTime` metadata field. Please note that the `<index>`
+    This entity represents the `"EchoTime"` metadata field. Please note that the `<index>`
     denotes the number/index (in the form of a nonnegative integer), not the
-    `EchoTime` value which needs to be stored in the field `EchoTime` of the separate
+    `"EchoTime"` value which needs to be stored in the field `"EchoTime"` of the separate
     JSON file.
   type: string
   format: index
@@ -95,9 +95,9 @@ flip:
     If files belonging to an entity-linked file collection are acquired at different
     flip angles, the `_flip-<index>` key/value pair MUST be used to distinguish
     individual files.
-    This entity represents the `FlipAngle` metadata field. Please note that the `<index>`
-    denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
-    value which needs to be stored in the field `FlipAngle` of the separate JSON file.
+    This entity represents the `"FlipAngle"` metadata field. Please note that the `<index>`
+    denotes the number/index (in the form of a nonnegative integer), not the `"FlipAngle"`
+    value which needs to be stored in the field `"FlipAngle"` of the separate JSON file.
   type: string
   format: index
 hemisphere:
@@ -119,9 +119,9 @@ inversion:
     If files belonging to an entity-linked file collection are acquired at different
     inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
     individual files.
-    This entity represents the `InversionTime` metadata field. Please note that the `<index>`
-    denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
-    value which needs to be stored in the field `InversionTime` of the separate JSON file.
+    This entity represents the `"InversionTime` metadata field. Please note that the `<index>`
+    denotes the number/index (in the form of a nonnegative integer), not the `"InversionTime"`
+    value which needs to be stored in the field `"InversionTime"` of the separate JSON file.
   type: string
   format: index
 label:
@@ -151,7 +151,7 @@ mtransfer:
     If files belonging to an entity-linked file collection are acquired at different
     magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
     distinguish individual files.
-    This entity represents the `MTState` metadata field. Allowed label values for this
+    This entity represents the `"MTState"` metadata field. Allowed label values for this
     entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
     respectively.
   type: string
@@ -172,7 +172,7 @@ part:
 
     Phase images MAY be in radians or in arbitrary units.
     The sidecar JSON file MUST include the units of the `phase` image.
-    The possible options are `rad` or `arbitrary`.
+    The possible options are `"rad"` or `"arbitrary"`.
 
     When there is only a magnitude image of a given type, the `part` key MAY be
     omitted.
@@ -190,7 +190,7 @@ processing:
     a file that was a result of particular processing performed on the device.
 
     This is useful for files produced in particular by Elekta's MaxFilter
-    (for example, sss, tsss, trans, quat or mc),
+    (for example, `sss`, `tsss`, `trans`, `quat` or `mc`),
     which some installations impose to be run on raw data because of active
     shielding software corrections before the MEG data can actually be
     exploited.
@@ -201,7 +201,7 @@ reconstruction:
   entity: rec
   description: |
     The `rec-<label>` key/value can be used to distinguish
-    different reconstruction algorithms (for example ones using motion
+    different reconstruction algorithms (for example `MoCo` for the ones using motion
     correction).
   type: string
   format: label
@@ -220,7 +220,7 @@ resolution:
   entity: res
   description: |
     Resolution of regularly sampled N-dimensional data.
-    MUST have a corresponding `Resolution` metadata field to provide
+    MUST have a corresponding `"Resolution"` metadata field to provide
     interpretation.
 
     This entity is only applicable to derivative data.
@@ -350,7 +350,7 @@ tracer:
   description: |
     The `trc-<label>` key/value can be used to distinguish
     sequences using different tracers.
-    The key `TracerName` MUST also be included in the associated JSON file,
+    The key `"TracerName"` MUST also be included in the associated JSON file,
     although the label may be different.
   type: string
   format: label
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index b8b867257e..8a010bb03e 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -13,7 +13,7 @@ AcquisitionDuration:
   description: |
     Duration (in seconds) of volume acquisition.
     Corresponds to DICOM Tag 0018, 9073 `Acquisition Duration`.
-    This field is mutually exclusive with RepetitionTime.
+    This field is mutually exclusive with `"RepetitionTime"`.
   type: number
   exclusiveMinimum: 0
   unit: s
@@ -46,7 +46,7 @@ Anaesthesia:
 AnalyticalApproach:
   name: AnalyticalApproach
   description: |
-    Methodology or methodologies used to analyse the `GeneticLevel`.
+    Methodology or methodologies used to analyse the `"GeneticLevel"`.
     Values MUST be taken from the
     [database of Genotypes and Phenotypes
     (dbGaP)](https://www.ncbi.nlm.nih.gov/gap/advanced)
@@ -64,7 +64,7 @@ AnatomicalLandmarkCoordinateSystem:
     See [Appendix VIII](/99-appendices/08-coordinate-systems.html)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
-    `AnatomicalLandmarkCoordinateSystemDescription`.
+    `"AnatomicalLandmarkCoordinateSystemDescription"`.
   anyOf:
   - $ref: _MEGCoordSys
   - $ref: _EEGCoordSys
@@ -80,7 +80,7 @@ AnatomicalLandmarkCoordinateSystemDescription:
 AnatomicalLandmarkCoordinateUnits:
   name: AnatomicalLandmarkCoordinateUnits
   description: |
-    Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`.
+    Units of the coordinates of `"AnatomicalLandmarkCoordinateSystem"`.
   type: string
   enum:
   - m
@@ -91,7 +91,7 @@ AnatomicalLandmarkCoordinates:
   name: AnatomicalLandmarkCoordinates
   description: |
     Key:value pairs of the labels and 3-D digitized locations of anatomical landmarks,
-    interpreted following the `AnatomicalLandmarkCoordinateSystem`
+    interpreted following the `"AnatomicalLandmarkCoordinateSystem"`
     (for example, `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6],
     "RPA": [20.2,11.3,9.1]}`.
     Each array MUST contain three numeric values corresponding to x, y, and z
@@ -173,7 +173,7 @@ B0FieldIdentifier:
   description: |
     The presence of this key states that this particular 3D or 4D image MAY be
     used for fieldmap estimation purposes.
-    Each `B0FieldIdentifier` MUST be a unique string within one participant's tree,
+    Each `"B0FieldIdentifier"` MUST be a unique string within one participant's tree,
     shared only by the images meant to be used as inputs for the estimation of a
     particular instance of the *B<sub>0</sub> field* estimation.
     It is RECOMMENDED to derive this identifier from DICOM Tags, for example,
@@ -187,12 +187,12 @@ B0FieldIdentifier:
 B0FieldSource:
   name: B0FieldSource
   description: |
-    At least one existing `B0FieldIdentifier` defined by images in the
+    At least one existing `"B0FieldIdentifier"` defined by images in the
     participant's tree.
     This field states the *B<sub>0</sub> field* estimation designated by the
-    `B0FieldIdentifier` that may be used to correct the dataset for distortions
+    `"B0FieldIdentifier"` that may be used to correct the dataset for distortions
     caused by B<sub>0</sub> inhomogeneities.
-    `B0FieldSource` and `B0FieldIdentifier` MAY both be present for images that
+    `"B0FieldSource"` and `"B0FieldIdentifier"` MAY both be present for images that
     are used to estimate their own B<sub>0</sub> field, for example, in "pepolar"
     acquisitions.
   anyOf:
@@ -301,7 +301,7 @@ BolusCutOffTechnique:
 BrainLocation:
   name: BrainLocation
   description: |
-    Refers to the location in space of the `TissueOrigin`.
+    Refers to the location in space of the `"TissueOrigin"`.
     Values may be an MNI coordinate,
     a label taken from the
     [Allen Brain Atlas](https://atlas.brain-map.org/atlas?atlas=265297125&plate=\
@@ -473,7 +473,7 @@ DelayAfterTrigger:
     Duration (in seconds) from trigger delivery to scan onset.
     This delay is commonly caused by adjustments and loading times.
     This specification is entirely independent of
-    `NumberOfVolumesDiscardedByScanner` or `NumberOfVolumesDiscardedByUser`,
+    `"NumberOfVolumesDiscardedByScanner"` or `"NumberOfVolumesDiscardedByUser"`,
     as the delay precedes the acquisition.
   type: number
   unit: s
@@ -484,10 +484,10 @@ DelayTime:
     following volume.
     If the field is not present it is assumed to be set to zero.
     Corresponds to Siemens CSA header field `lDelayTimeInTR`.
-    This field is REQUIRED for sparse sequences using the `RepetitionTime` field
-    that do not have the `SliceTiming` field set to allowed for accurate
+    This field is REQUIRED for sparse sequences using the `"RepetitionTime"` field
+    that do not have the `"SliceTiming"` field set to allowed for accurate
     calculation of "acquisition time".
-    This field is mutually exclusive with `VolumeTiming`.
+    This field is mutually exclusive with `"VolumeTiming"`.
   type: number
   unit: s
 Density:
@@ -541,7 +541,7 @@ DigitizedHeadPointsCoordinateSystem:
     [Appendix VIII](/99-appendices/08-coordinate-systems.html)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
-    `DigitizedHeadPointsCoordinateSystemDescription`.
+    `"DigitizedHeadPointsCoordinateSystemDescription"`.
   anyOf:
   - $ref: _MEGCoordSys
   - $ref: _EEGCoordSys
@@ -557,7 +557,7 @@ DigitizedHeadPointsCoordinateSystemDescription:
 DigitizedHeadPointsCoordinateUnits:
   name: DigitizedHeadPointsCoordinateUnits
   description: |
-    Units of the coordinates of `DigitizedHeadPointsCoordinateSystem`.
+    Units of the coordinates of `"DigitizedHeadPointsCoordinateSystem"`.
   type: string
   enum:
   - m
@@ -599,7 +599,7 @@ DwellTime:
     anatomicals in the HCP Pipelines.
     It also usefully provides a handle on the readout bandwidth,
     which isn't captured in the other metadata tags.
-    Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling
+    Not to be confused with `"EffectiveEchoSpacing"`, and the frequent mislabeling
     of echo spacing (which is spacing in the phase encoding direction) as
     "dwell time" (which is spacing in the readout direction).
   type: number
@@ -744,7 +744,7 @@ EffectiveEchoSpacing:
     between lines in the phase-encoding direction,
     defined based on the size of the reconstructed image in the phase direction.
     It is frequently, but incorrectly, referred to as "dwell time"
-    (see `DwellTime` parameter below for actual dwell time).
+    (see the `"DwellTime"` parameter for actual dwell time).
     It is required for unwarping distortions using field maps.
     Note that beyond just in-plane acceleration,
     a variety of other manipulations to the phase encoding need to be accounted
@@ -758,7 +758,7 @@ ElectricalStimulation:
   description: |
     Boolean field to specify if electrical stimulation was done during the
     recording (options are `true` or `false`). Parameters for event-like
-    stimulation should be specified in the events.tsv file.
+    stimulation should be specified in the `events.tsv` file.
   type: boolean
 ElectricalStimulationParameters:
   name: ElectricalStimulationParameters
@@ -793,7 +793,7 @@ EstimationAlgorithm:
   name: EstimationAlgorithm
   description: |
     Type of algorithm used to perform fitting
-    (for example, linear, non-linear, LM and such).
+    (for example, `"linear"`, `"non-linear"`, `"LM"` and such).
   type: string
 EstimationReference:
   name: EstimationReference
@@ -812,12 +812,12 @@ FiducialsCoordinateSystem:
   name: FiducialsCoordinateSystem
   description: |
     Defines the coordinate system for the fiducials.
-    Preferably the same as the `EEGCoordinateSystem`.
+    Preferably the same as the `"EEGCoordinateSystem"`.
     See
     [Appendix VIII](/99-appendices/08-coordinate-systems.html)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
-    `FiducialsCoordinateSystemDescription`.
+    `"FiducialsCoordinateSystemDescription"`.
   anyOf:
   - $ref: _MEGCoordSys
   - $ref: _EEGCoordSys
@@ -834,7 +834,7 @@ FiducialsCoordinateUnits:
   name: FiducialsCoordinateUnits
   description: |
     Units in which the coordinates that are  listed in the field
-    `FiducialsCoordinateSystem` are represented.
+    `"FiducialsCoordinateSystem"` are represented.
   type: string
   enum:
   - m
@@ -845,7 +845,7 @@ FiducialsCoordinates:
   name: FiducialsCoordinates
   description: |
     Key:value pairs of the labels and 3-D digitized position of anatomical
-    landmarks, interpreted following the `FiducialsCoordinateSystem`
+    landmarks, interpreted following the `"FiducialsCoordinateSystem"`
     (for example, `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6],
     "RPA": [20.2,11.3,9.1]}`).
     Each array MUST contain three numeric values corresponding to x, y, and z
@@ -863,7 +863,7 @@ FiducialsDescription:
     Free-form text description of how the fiducials such as vitamin-E capsules
     were placed relative to anatomical landmarks,
     and how the position of the fiducials were measured
-    (for example, both with Polhemus and with T1w MRI).
+    (for example, `"both with Polhemus and with T1w MRI"`).
   type: string
 FlipAngle:
   name: FlipAngle
@@ -905,7 +905,7 @@ FrameDuration:
 FrameTimesStart:
   name: FrameTimesStart
   description: |
-    Start times for all frames relative to `TimeZero` in default unit seconds.
+    Start times for all frames relative to `"TimeZero"` in default unit seconds.
   type: array
   items:
     type: number
@@ -1034,7 +1034,7 @@ HardcopyDeviceSoftwareVersion:
 HardwareFilters:
   name: HardwareFilters
   description: |
-    Object of temporal hardware filters applied, or "n/a" if the data is not
+    Object of temporal hardware filters applied, or `"n/a"` if the data is not
     available. Each key:value pair in the JSON object is a name of the filter and
     an object in which its parameters are defined as key:value pairs.
     For example, `{"Highpass RC filter": {"Half amplitude cutoff (Hz)":
@@ -1142,7 +1142,7 @@ ImageDecayCorrectionTime:
   name: ImageDecayCorrectionTime
   description: |
     Point in time from which the decay correction was applied with respect to
-    TimeZero in the default unit seconds.
+    `"TimeZero"` in the default unit seconds.
   type: number
   unit: s
 Immersion:
@@ -1156,8 +1156,8 @@ InfusionRadioactivity:
   description: |
     Amount of radioactivity infused into the patient.
     This value must be less than or equal to the total injected radioactivity
-    (`InjectedRadioactivity`).
-    Units should be the same as `InjectedRadioactivityUnits`.
+    (`"InjectedRadioactivity"`).
+    Units should be the same as `"InjectedRadioactivityUnits"`.
   type: number
 InfusionSpeed:
   name: InfusionSpeed
@@ -1173,16 +1173,16 @@ InfusionSpeedUnits:
 InfusionStart:
   name: InfusionStart
   description: |
-    Time of start of infusion with respect to `TimeZero` in the default unit
+    Time of start of infusion with respect to `"TimeZero"` in the default unit
     seconds.
   type: number
   unit: s
 InjectedMass:
   name: InjectedMass
   description: |
-    Total mass of radiolabeled compound injected into subject (for example, 10).
-    This can be derived as the ratio of the `InjectedRadioactivity` and
-    `MolarRadioactivity`.
+    Total mass of radiolabeled compound injected into subject (for example, `10`).
+    This can be derived as the ratio of the `"InjectedRadioactivity"` and
+    `"MolarRadioactivity"`.
     **For those tracers in which injected mass is not available (for example FDG)
     can be set to `"n/a"`)**.
   anyOf:
@@ -1218,7 +1218,7 @@ InjectedMassUnits:
 InjectedRadioactivity:
   name: InjectedRadioactivity
   description: |
-    Total amount of radioactivity injected into the patient (for example, 400).
+    Total amount of radioactivity injected into the patient (for example, `400`).
     For bolus-infusion experiments, this value should be the sum of all injected
     radioactivity originating from both bolus and infusion.
     Corresponds to DICOM Tag 0018, 1074 `Radionuclide Total Dose`.
@@ -1238,17 +1238,17 @@ InjectedVolume:
 InjectionEnd:
   name: InjectionEnd
   description: |
-    Time of end of injection with respect to `TimeZero` in the default unit
+    Time of end of injection with respect to `"TimeZero"` in the default unit
     seconds.
   type: number
   unit: s
 InjectionStart:
   name: InjectionStart
   description: |
-    Time of start of injection with respect to `TimeZero` in the default unit
+    Time of start of injection with respect to `"TimeZero"` in the default unit
     seconds.
     This corresponds to DICOM Tag 0018, 1042 `Contrast/Bolus Start Time`
-    converted to seconds relative to `TimeZero`.
+    converted to seconds relative to `"TimeZero"`.
   type: number
   unit: s
 InstitutionAddress:
@@ -1320,8 +1320,8 @@ LabelingDuration:
     In case all control-label volumes (or deltam or CBF) have the same
     `LabelingDuration`, a scalar must be specified.
     In case the control-label volumes (or deltam or cbf) have a different
-    `LabelingDuration`, an array of numbers must be specified,
-    for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+    `"LabelingDuration"`, an array of numbers must be specified,
+    for which any `m0scan` in the timeseries has a `"LabelingDuration"` of zero.
     In case an array of numbers is provided,
     its length should be equal to the number of volumes specified in
     `*_aslcontext.tsv`.
@@ -1367,7 +1367,7 @@ LabelingPulseAverageB1:
   name: LabelingPulseAverageB1
   description: |
     The average B1-field strength of the RF labeling pulses, in microteslas.
-    As an alternative, `LabelingPulseFlipAngle` can be provided.
+    As an alternative, `"LabelingPulseFlipAngle"` can be provided.
   type: number
   exclusiveMinimum: 0
   unit: uT
@@ -1389,7 +1389,7 @@ LabelingPulseFlipAngle:
   name: LabelingPulseFlipAngle
   description: |
     The flip angle of a single labeling pulse, in degrees,
-    which can be given as an alternative to `LabelingPulseAverageB1`.
+    which can be given as an alternative to `"LabelingPulseAverageB1"`.
   type: number
   exclusiveMinimum: 0
   maximum: 360
@@ -1471,7 +1471,7 @@ M0Type:
 MEGChannelCount:
   name: MEGChannelCount
   description: |
-    Number of MEG channels (for example, 275).
+    Number of MEG channels (for example, `275`).
   type: integer
   minimum: 0
 MEGCoordinateSystem:
@@ -1481,7 +1481,7 @@ MEGCoordinateSystem:
     See [Appendix VIII](/99-appendices/08-coordinate-systems.html)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
-    `MEGCoordinateSystemDescription`.
+    `"MEGCoordinateSystemDescription"`.
   anyOf:
   - $ref: _MEGCoordSys
   - $ref: _EEGCoordSys
@@ -1497,7 +1497,7 @@ MEGCoordinateSystemDescription:
 MEGCoordinateUnits:
   name: MEGCoordinateUnits
   description: |
-    Units of the coordinates of `MEGCoordinateSystem`.
+    Units of the coordinates of `"MEGCoordinateSystem"`.
   type: string
   enum:
   - m
@@ -1507,7 +1507,7 @@ MEGCoordinateUnits:
 MEGREFChannelCount:
   name: MEGREFChannelCount
   description: |
-    Number of MEG reference channels (for example, 23).
+    Number of MEG reference channels (for example, `23`).
     For systems without such channels (for example, Neuromag Vectorview),
     `MEGREFChannelCount` should be set to `0`.
   type: integer
@@ -1583,7 +1583,7 @@ Magnification:
   name: Magnification
   description: |
     Lens magnification (for example: `40`). If the file format is OME-TIFF,
-    the value MUST be consistent with the `NominalMagnification` OME metadata field.
+    the value MUST be consistent with the `"NominalMagnification"` OME metadata field.
   type: number
   exclusiveMinimum: 0
 Manual:
@@ -1615,7 +1615,7 @@ MaxMovement:
   name: MaxMovement
   description: |
     Maximum head movement (in mm) detected during the recording,
-    as measured by the head localisation coils (for example, 4.8).
+    as measured by the head localisation coils (for example, `4.8`).
   type: number
   unit: mm
 MeasurementToolMetadata:
@@ -1733,11 +1733,11 @@ NumberOfVolumesDiscardedByScanner:
     before saving the imaging file.
     For example, a sequence that automatically discards the first 4 volumes
     before saving would have this field as 4.
-    A sequence that doesn't discard dummy scans would have this set to 0.
+    A sequence that does not discard dummy scans would have this set to 0.
     Please note that the onsets recorded in the `events.tsv` file should always
     refer to the beginning of the acquisition of the first volume in the
     corresponding imaging file - independent of the value of
-    `NumberOfVolumesDiscardedByScanner` field.
+    `"NumberOfVolumesDiscardedByScanner"` field.
   type: integer
   minimum: 0
 NumberOfVolumesDiscardedByUser:
@@ -1749,7 +1749,7 @@ NumberOfVolumesDiscardedByUser:
     Please note that the onsets recorded in the `events.tsv` file should always
     refer to the beginning of the acquisition of the first volume in the
     corresponding imaging file - independent of the value of
-    `NumberOfVolumesDiscardedByUser` field.
+    `"NumberOfVolumesDiscardedByUser"` field.
   type: integer
   minimum: 0
 NumberShots:
@@ -1762,7 +1762,7 @@ NumberShots:
     The data type array is applicable for specifying this parameter before and
     after the k-space center is sampled.
     Please see
-    [`NumberShots` metadata field]\
+    [`"NumberShots"` metadata field]\
     (/99-appendices/11-qmri.html#numbershots-metadata-field)
     in the qMRI appendix for corresponding calculations.
   anyOf:
@@ -1797,7 +1797,7 @@ PASLType:
 PCASLType:
   name: PCASLType
   description: |
-    The type of gradient pulses used in the `"control"` condition.
+    The type of gradient pulses used in the `control` condition.
   type: string
   enum:
   - balanced
@@ -1851,7 +1851,7 @@ PharmaceuticalDoseTime:
     For an infusion, this should be a vector with two elements specifying the
     start and end of the infusion period. For more complex dose regimens,
     the regimen description should be complete enough to enable unambiguous
-    interpretation of `PharmaceuticalDoseTime`.
+    interpretation of `"PharmaceuticalDoseTime"`.
     Unit format of the specified pharmaceutical dose time MUST be seconds.
   anyOf:
   - type: number
@@ -1912,7 +1912,7 @@ PixelSize:
 PixelSizeUnits:
   name: PixelSizeUnits
   description: |
-    Unit format of the specified `PixelSize`. MUST be one of: `"mm"` (millimeter), `"um"`
+    Unit format of the specified `"PixelSize"`. MUST be one of: `"mm"` (millimeter), `"um"`
     (micrometer) or `"nm"` (nanometer).
   type: string
   enum:
@@ -2007,7 +2007,7 @@ Purity:
 RandomRate:
   name: RandomRate
   description: |
-    Random rate for each frame (same units as `Units`, for example, `"Bq/mL"`).
+    Random rate for each frame (same units as `"Units"`, for example, `"Bq/mL"`).
   type: array
   items:
     type: number
@@ -2024,7 +2024,7 @@ ReceiveCoilActiveElements:
   name: ReceiveCoilActiveElements
   description: |
     Information describing the active/selected elements of the receiver coil.
-    This doesn't correspond to a tag in the DICOM ontology.
+    This does not correspond to a tag in the DICOM ontology.
     The vendor-defined terminology for active coil elements can go in this field.
   type: string
 ReceiveCoilName:
@@ -2142,12 +2142,12 @@ RepetitionTimeExcitation:
     The interval, in seconds, between two successive excitations.
     [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)
     best refers to this parameter.
-    This field may be used together with the `RepetitionTimePreparation` for
+    This field may be used together with the `"RepetitionTimePreparation"` for
     certain use cases, such as
     [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002).
     Use `RepetitionTimeExcitation` (in combination with
-    `RepetitionTimePreparation` if needed) for anatomy imaging data rather than
-    `RepetitionTime` as it is already defined as the amount of time that it takes
+    `"RepetitionTimePreparation"` if needed) for anatomy imaging data rather than
+    `"RepetitionTime"` as it is already defined as the amount of time that it takes
     to acquire a single volume in the
     [task imaging data](/04-modality-specific-files/01-magnetic-resonance-\
     imaging-data.html#task-including-resting-state-imaging-data)
@@ -2372,15 +2372,15 @@ SliceEncodingDirection:
   name: SliceEncodingDirection
   description: |
     The axis of the NIfTI data along which slices were acquired,
-    and the direction in which `SliceTiming` is defined with respect to.
+    and the direction in which `"SliceTiming"` is defined with respect to.
     `i`, `j`, `k` identifiers correspond to the first, second and third axis of
     the data in the NIfTI file.
-    A `-` sign indicates that the contents of `SliceTiming` are defined in
+    A `-` sign indicates that the contents of `"SliceTiming"` are defined in
     reverse order - that is, the first entry corresponds to the slice with the
     largest index, and the final entry corresponds to slice index zero.
-    When present, the axis defined by `SliceEncodingDirection` needs to be
+    When present, the axis defined by `"SliceEncodingDirection"` needs to be
     consistent with the `slice_dim` field in the NIfTI header.
-    When absent, the entries in `SliceTiming` must be in the order of increasing
+    When absent, the entries in `"SliceTiming"` must be in the order of increasing
     slice index as defined by the NIfTI header.
   type: string
   enum:
@@ -2407,11 +2407,11 @@ SliceTiming:
     of volume acquisition.
     The list goes through the slices along the slice axis in the slice encoding
     dimension (see below).
-    Note that to ensure the proper interpretation of the `SliceTiming` field,
+    Note that to ensure the proper interpretation of the `"SliceTiming"` field,
     it is important to check if the OPTIONAL `SliceEncodingDirection` exists.
-    In particular, if `SliceEncodingDirection` is negative,
-    the entries in `SliceTiming` are defined in reverse order with respect to the
-    slice axis, such that the final entry in the `SliceTiming` list is the time
+    In particular, if `"SliceEncodingDirection"` is negative,
+    the entries in `"SliceTiming"` are defined in reverse order with respect to the
+    slice axis, such that the final entry in the `"SliceTiming"` list is the time
     of acquisition of slice 0. Without this parameter slice time correction will
     not be possible.
   type: array
@@ -2465,9 +2465,9 @@ SourceDatasets:
   name: SourceDatasets
   description: |
     Used to specify the locations and relevant attributes of all source datasets.
-    Valid keys in each object include `URL`, `DOI` (see
+    Valid keys in each object include `"URL"`, `"DOI"` (see
     [URI](/02-common-principles.html#uniform-resource-indicator)), and
-    `Version` with
+    `"Version"` with
     [string](https://www.w3schools.com/js/js_json_datatypes.asp)
     values.
   type: array
@@ -2488,9 +2488,9 @@ Sources:
     these files were directly used in the creation of this derivative data file.
     For example, if a derivative A is used in the creation of another
     derivative B, which is in turn used to generate C in a chain of A->B->C,
-    C should only list B in `Sources`, and B should only list A in `Sources`.
+    C should only list B in `"Sources"`, and B should only list A in `"Sources"`.
     However, in case both X and Y are directly used in the creation of Z,
-    then Z should list X and Y in `Sources`,
+    then Z should list X and Y in `"Sources"`,
     regardless of whether X was used to generate Y.
   type: array
   items:
@@ -2605,8 +2605,8 @@ StimulusPresentation:
   description: |
     Object containing key value pairs related to the software used to present
     the stimuli during the experiment, specifically:
-    `OperatingSystem`, `SoftwareName`, `SoftwareRRID`, `SoftwareVersion` and
-    `Code`.
+    `"OperatingSystem"`, `"SoftwareName"`, `"SoftwareRRID"`, `"SoftwareVersion"` and
+    `"Code"`.
     See table below for more information.
   type: object
   properties:
@@ -2638,9 +2638,9 @@ TaskName:
   description: |
     Name of the task.
     No two tasks should have the same name.
-    The task label included in the file name is derived from this TaskName field
+    The task label included in the file name is derived from this `"TaskName"` field
     by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters.
-    For example `TaskName` `"faces n-back"` will correspond to task label
+    For example `"TaskName"` `"faces n-back"` will correspond to task label
     `facesnback`.
   type: string
 TermURL:
@@ -2654,7 +2654,7 @@ TimeZero:
   description: |
     Time zero to which all scan and/or blood measurements have been adjusted to,
     in the unit "hh:mm:ss".
-    This should be equal to `InjectionStart` or `ScanStart`.
+    This should be equal to `"InjectionStart"` or `"ScanStart"`.
   type: string
   pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
 TissueDeformationScaling:
@@ -2668,7 +2668,7 @@ TissueDeformationScaling:
 TissueOrigin:
   name: TissueOrigin
   description: |
-    Describes the type of tissue analyzed for `SampleOrigin` `brain`.
+    Describes the type of tissue analyzed for `"SampleOrigin"` `brain`.
   type: string
   enum:
   - gray matter
@@ -2691,7 +2691,7 @@ TotalReadoutTime:
     defined as the readout duration, specified in seconds,
     that would have generated data with the given level of distortion.
     It is NOT the actual, physical duration of the readout train.
-    If `EffectiveEchoSpacing` has been properly computed,
+    If `"EffectiveEchoSpacing"` has been properly computed,
     it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.
   type: number
   unit: s
@@ -2796,9 +2796,9 @@ VolumeTiming:
     in the BOLD series.
     The list must have the same length as the BOLD series,
     and the values must be non-negative and monotonically increasing.
-    This field is mutually exclusive with `RepetitionTime` and `DelayTime`.
+    This field is mutually exclusive with `"RepetitionTime"` and `"DelayTime"`.
     If defined, this requires acquisition time (TA) be defined via either
-    `SliceTiming` or `AcquisitionDuration` be defined.
+    `"SliceTiming"` or `"AcquisitionDuration"` be defined.
   type: array
   minItems: 1
   items:
@@ -2990,5 +2990,5 @@ iEEGReference:
     `"upside down electrode"`).
     If different channels have a different reference,
     this field should have a general description and the channel specific
-    reference should be defined in the channels.tsv file.
+    reference should be defined in the `channels.tsv` file.
   type: string

From 43c1308fdf4678b8171737f8ab32960c83e02e80 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 10 Feb 2022 09:57:13 -0500
Subject: [PATCH 194/347] BF: Use wikipedia for TIFF URL, adobe's page is
 404ing now

Attn was brought up in https://github.com/bids-standard/bids-specification/pull/1006#issuecomment-1034936048
by @TheChymera
---
 src/04-modality-specific-files/10-microscopy.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index efb1542c52..4c03988744 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -41,7 +41,7 @@ Microscopy raw data MUST be stored in one of the following formats:
 
 -   [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
 
--   [Tag Image File Format](https://www.adobe.io/open/standards/TIFF.html) (`.tif`)
+-   [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) (`.tif`)
 
 -   [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
     (`.ome.tif` for standard TIFF files or `.ome.btf` for

From 5e2c32a90dc5130e19c546bfee5a1abe1324137e Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Thu, 10 Feb 2022 15:26:29 +0000
Subject: [PATCH 195/347] [DOC] Auto-generate changelog entry for PR #1007

---
 src/CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 3693c6cc51..4472843cf0 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,8 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   BF: Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[SCHEMA, FIX] Remove mentions of auxdatatypes [#996](https://github.com/bids-standard/bids-specification/pull/996) ([tsalo](https://github.com/tsalo))
 -   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau))

From d25831a5068b1d7cf92d228d231096489be6f019 Mon Sep 17 00:00:00 2001
From: Franklin <franklin.feingold@gmail.com>
Date: Tue, 8 Feb 2022 22:25:54 -0800
Subject: [PATCH 196/347] REL: v1.7.0

---
 mkdocs.yml                           |   2 +-
 src/99-appendices/01-contributors.md | 105 ++++++++++++++++++++++++++-
 src/CHANGES.md                       |  33 +++------
 3 files changed, 112 insertions(+), 28 deletions(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index d7867faea3..5979e5219a 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Brain Imaging Data Structure v1.6.1-dev
+site_name: Brain Imaging Data Structure v1.7.0
 site_url: https://bids-specification.readthedocs.io/en/stable/
 theme:
     name: material
diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index 61c144a1fc..0e22113de1 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -38,55 +38,91 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 
 -   Eric Achten 📖🔣📓
 -   Azeez Adebimpe 📖
+-   Rémi Adon 📖
 -   Fidel Alfaro Almagro 💬📖💡🔌
 -   David Alsop 📖
 -   Stefan Appelhoff 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝🚧🔣
+-   Yoni Ashar 📖
+-   Tal Pal Attia 📖
 -   Tibor Auer 💬📖💡🔧📢🐛🤔
 -   Sylvain Baillet 📖🔍
+-   Shashank Bansal 📖
 -   Arshitha Basavaraj 📖🚇💻
+-   Leandro Beltrachini 📖
+-   Chris Benjamin 📖
+-   Timo Berg 📖
+-   Étienne Bergeron 🔣💻
+-   Suyash Bhogawar 📖💡⚠️🔧💬
 -   Stephan Bickel 📖
+-   Ulrike Bingel 📖
+-   Ethan Blackwood 👀📖
+-   David Boas 📖
 -   Elizabeth Bock 📖💡
+-   Hugo Boniface 📖
 -   Kristofer Bouchard 📖
 -   Mathieu Boudreau 💬🤔📢
+-   Marie-Hélène Bourget 📖🔣💻🤔
 -   Eric Bridgeford 📖🔧
 -   Teon L. Brooks 📖💻⚠️💬👀🤔🔧🐛📢
--   Suyash Bhogawar 📖💡⚠️🔧💬
+-   Christian Büchel 📖
 -   Vince D. Calhoun 📖
+-   Giulio Castegnaro 📖
 -   Marco Castellaro 💬🐛💻📖💡⚠️📢🚇
+-   Filippo Maria Castelli 📖🔣
 -   Michael Chappell 📖🔣📆
+-   Gang Chen 📖
+-   William Clarke 📖
 -   Patricia Clement 💬🐛💻📖🔣💡📋🤔📆⚠️📢
+-   Helena Cockx 📖
 -   Alexander L. Cohen 🐛💻📖💬
+-   Julien Cohen-Adad 📖🔣🤔
 -   R. Cameron Craddock 📖📢
 -   Martin Craig 🔣
 -   Sasha D'Ambrosio 📖
 -   Samir Das 📖
 -   Olivier David 📖
 -   Orrin Devinsky 📖
+-   Gilles de Hollander 📖
 -   Alejandro de la Vega 🐛💻⚠️
 -   Arnaud Delorme 📖💡
+-   John Detre 📖
 -   Benjamin Dichter 📖
 -   Erin W. Dickie 📖🤔👀📢💬
+-   Timo Dickscheid 📖
+-   Dejan Draschkow 📖
 -   Eugene P. Duff 📖
 -   Elizabeth DuPre 📖💡🔍🤔💬
+-   Joke Durnez 📖🔧💻
 -   Eric Earl 📖💬🐛🚧🔧🤔
 -   Anders Eklund 📖📢💻
+-   Sara Elgayar 📖
 -   Oscar Esteban 📖🔧🤔💬💻
 -   Franklin W. Feingold 📋📝✅💬🤔🎨📢👀🚇🖋📆
 -   Guillaume Flandin 📖💻
 -   Adeen Flinker 📖
+-   Alexandru Foias 📖🔣
 -   Brett L. Foster 📖
 -   Ana Fouto 📓
+-   Benjamin Gagl 📖
+-   Chris Gahnström 📖
+-   Anthony Galassi 📖
+-   Giuseppe Gallitto 📖
 -   Melanie Ganz-Benjaminsen 📖🔣💻🤔📆🔍📢
+-   Samuel Garcia 🤔👀📖
 -   Remi Gau 📖💻💬📢🐛💻🚇👀🔧🤔
+-   James Gholam 📖
 -   Satrajit S. Ghosh 📖💻
 -   Ashley G. Gillman 📖
+-   Greydon Gilmore 📖
 -   Tristan Glatard 📖💻
 -   Mathias Goncalves 💻🔧📢
 -   Krzysztof J. Gorgolewski 📖💻💬🤔🔍📢📝💡🔌
 -   Alexandre Gramfort 📖💡
+-   Klara Gregorova 📖
 -   Jeffrey S. Grethe 💬🐛✅📢
 -   Iris Groen 📖
 -   David Groppe 📖
+-   Sören Grothkopp 📖
 -   Aysegul Gunduz 📖
 -   Matthias Günther 📖
 -   Yaroslav O. Halchenko 📖📢🔧💬🐛
@@ -95,25 +131,38 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 -   Daniel A. Handwerker 📖
 -   Michael Hanke 📖🤔🔧🐛📢
 -   Michael P. Harms 📖⚠️🔧
+-   Soichi Hayashi 📖🔧🐛
 -   Richard N. Henson 📖
 -   Peer Herholz 💬📖👀🔧✅📢
 -   Dora Hermes 📖💻✅🔍🤔
 -   Luis Hernandez-Garcia 📖📓
 -   Katja Heuer 🔧
+-   Dorien Huijser 📖
+-   Alexandre Hutton 📖
 -   Richard Höchenberger 📖
 -   Chris Holdgraf 📖🤔
 -   Christopher J. Honey 📖
+-   Andrew Hoopes 📖
+-   Christian Horea 📖
 -   Jean-Christophe Houde 📖
+-   Maria de la Iglesia 📖
+-   Ilkay Isik 📖
+-   Hamish Innes-Brown 📖
 -   International Neuroinformatics Coordinating Facility 💵📋
 -   Andrew Jahn 📓
 -   Andrew Janke 📖💻
 -   Mainak Jas 📖💻
+-   Sein Jeung 📖
 -   Alexander Jones 💻🐛
 -   Tamás Józsa 📓
+-   Jakub Kaczmarzyk 📖🔧🚇
+-   Lee Kamentsky 📖
 -   Agah Karakuzu 💬📖🔣🤔
 -   David Keator 📖
 -   James Kent 💬💻
+-   Ali Khan 📖
 -   Gregory Kiar 📖💻🎨🔧
+-   Balint Kincses 📖
 -   Thomas Kirk 📖
 -   Robert Knight 📖
 -   Joost Kuijer 📖
@@ -123,42 +172,62 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 -   Kevin Larcher 💬
 -   Jonathan C. Lau 📖
 -   Laura and John Arnold Foundation 💵
+-   Alexander von Lautz 📖
+-   Alberto Lazari 📖
+-   Kangjoo Lee 📖
 -   Christopher Lee-Messer 📖
 -   Jon Haitz Legarreta 💻📖
 -   Dan Levitas 📖
 -   Adam Li 📖💻
 -   Xiangrui Li 📖💻
+-   Ilona Lipp 📖
 -   Vladimir Litvak 📖
+-   Hanzhang Lu 📖
+-   Robert Luke 📖
 -   Brian N. Lundstrom 📖
 -   Dan Lurie 🤔📖🔧🔌💻💬
 -   Camille Maumet 📖
 -   Christopher J. Markiewicz 💬🐛💻📖🎨💡🤔🔌👀🔧📢🔣📋🚧
+-   Giacomo Mazzamuto 📖🔣
+-   David McAlpine 📖
+-   Manuel Mercier 📖🤔
+-   Mark Mikkelsen 📖
 -   Kai J. Miller 📖
+-   Markus Morawski 📖
+-   Clara Moreau 📖
 -   Jeremy Moreau 📖💡
 -   Zachary Michael 📖
 -   Ezequiel Mikulan 📖💻
 -   Michael P. Milham 💡🔍
+-   Jeanette Mumford 📖
+-   Athanasia Monika Mowinckel 📖
 -   Henk Mutsaerts 💬🐛💻📖💡📋🤔📆📢📓
+-   Manjari Narayan 📖
 -   National Institute of Mental Health 💵
 -   Mikael Naveau 🐛
 -   B. Nolan Nichols 📖
 -   Thomas E. Nichols 📖📢🔧👀🚧
 -   Dylan Nielson 📖💻🔧
+-   Aki Nikolaidis 📖
+-   Gustav Nilsonne 📖
 -   Guiomar Niso 🤔🎨🔍👀📋📝🔧🐛💻🔣✅💬📖💡📢
 -   Martin Noergaard 📖🔣💻🤔📢
 -   Michael P. Notter 💬📝✅📢📖
 -   Jeffrey G. Ojemann 📖
 -   Thomas Okell 📖
 -   Aaron Oliver-Taylor 📖
+-   Hernando Ombao 📖
 -   Robert Oostenveld 📖🔧📢💡✅⚠️🤔💬🐛📝💻🖋🔣🎨📋🚇👀📓📹
 -   Dimitri Papadopoulos Orfanos 📖💡🤔💬
+-   Felipe Orihuela-Espina 📖
 -   Eduard Ort 📖
 -   Patrick Park 📖💡💬
 -   Maurice Pasternak 📓
+-   Chloé Pasturel 📖
 -   Dianne Patterson 📖
 -   John Pellman 📖
 -   Cyril Pernet 💬📝📖🎨💡📋🤔📢
--   Franco Pestilli 📖💻🎨💡🤔👀🔧
+-   Franco Pestilli 📖💻🎨💡🤔👀🔧📋🔍🚇
 -   Jan Petr 💬🐛💻📖🔣💡📋🤔📆⚠️📢
 -   Natalia Petridou 📖
 -   Dmitry Petrov 📖💻
@@ -167,39 +236,67 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 -   Andrea Pigorini 📖
 -   Russell A. Poldrack 📖🔍📢
 -   Jean-Baptiste Poline 📖📢🤔🎨
+-   Luca Pollonini 📖
 -   Wouter V. Potters 📖
 -   Nader Pouratian 📖
 -   Pradeep Reddy Raamana 💻🔧
 -   Vasudev Raguram 💻🎨📖🔧
 -   Nick F. Ramsey 📖
+-   Travis Riddle 📖🔧🐛
+-   Pierre Rioux 📖
+-   Petra Ritter 📖
 -   Kay Robbins 💻📖🐛
 -   Alex Rockhill 📖🔧
 -   Ariel Rokem 📖
 -   Chris Rorden 📖💻
+-   Jose Manuel Saborit 📖
 -   Taylor Salo 💬📖🔌
 -   Matt Sanderson 📖💻
 -   Gunnar Schaefer 📖
+-   Michael Schirner 📖
 -   Jan-Mathijs Schoffelen 📖
+-   Graham Searle 📖
+-   Parul Sethi 📖🔧⚠️💻
+-   Maureen J Shader 📖
 -   Robert E. Smith 💻📖
 -   Vanessa Sochat 📖
+-   Tamas Spisak 📖
+-   Julia Sprenger 📖
+-   Isla Staden 📖
 -   Arjen Stolk 📖
 -   Nicole C. Swann 📖
+-   Filip Szczepankiewicz 📖
+-   Martin Szinte 📖
 -   François Tadel 📖🔌💡
+-   Sylvain Takerkart 📖
+-   Bertrand Thirion 📖
 -   David Thomas 📖🔣
 -   Roberto Toro 🔧
 -   Sébastien Tourbier 🤔👀📢🐛💻📖
+-   Paule-Joanne Toussaint 📖
+-   Nicholas Traut 📖🔧💻
 -   William Triplett 📖
 -   Jessica A. Turner 📖
 -   Pieter Vandemaele 📖💻
 -   Max A. van den Boom 💻👀📖
 -   Wietske van der Zwaag 🔣💬
 -   Matthias Van Osch 📖
+-   Gaël Varoquaux 📖
+-   Jaap von der Aar 📖
+-   Sjoerd Vos 📖
 -   Bradley Voytek 📖
--   Brian A. Wandell 📖
+-   Tor Wager 📖
 -   Adina S. Wagner 🎨
+-   Lennart Walger 📖
+-   Brian A. Wandell 📖
+-   Hao Ting Wang 📖🐛
+-   Yuan Wang 💻
+-   Julius Welzel 📖
 -   Joseph Wexler 📖💡
 -   Kirstie Whitaker 📖💡🔍🤔📢💬
+-   Martin Wilson 📖
 -   Jonathan Winawer 📖
--   Gaël Varoquaux 📖
+-   Lennart Wittkuhn 📖
+-   Joseph Woods 📖
 -   Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨
 -   Lyuba Zehl 📖
diff --git a/src/CHANGES.md b/src/CHANGES.md
index 4472843cf0..e4421cbff4 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
+## [v1.7.0](https://bids-specification.readthedocs.io/en/v1.7.0/) (2021-02-15)
 
 -   BF: Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau))
@@ -108,10 +108,9 @@
 -   \[FIX] Correct iEEG example that contained double suffixes [#463](https://github.com/bids-standard/bids-specification/pull/463) ([yarikoptic](https://github.com/yarikoptic))
 -   \[ENH] introduce GeneratedBy to "core" BIDS [#440](https://github.com/bids-standard/bids-specification/pull/440) ([yarikoptic](https://github.com/yarikoptic))
 
-## [v1.6.0](https://github.com/bids-standard/bids-specification/tree/v1.6.0) (2021-04-22)
+## [v1.6.0](https://bids-specification.readthedocs.io/en/v1.6.0) (2021-04-22)
 
 -   \[FIX] Typos discovered by codespell [#784](https://github.com/bids-standard/bids-specification/pull/784) ([yarikoptic](https://github.com/yarikoptic))
--   REL: v1.6.0 [#776](https://github.com/bids-standard/bids-specification/pull/776) ([effigies](https://github.com/effigies))
 -   \[FIX] Rename "Unit" metadata to "Units" for consistency with existing fields [#773](https://github.com/bids-standard/bids-specification/pull/773) ([effigies](https://github.com/effigies))
 -   \[FIX] typo in pet: institution -> institutional [#771](https://github.com/bids-standard/bids-specification/pull/771) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] install git in linkchecker job [#767](https://github.com/bids-standard/bids-specification/pull/767) ([sappelhoff](https://github.com/sappelhoff))
@@ -128,10 +127,9 @@
 -   \[MISC] refactor stimuli mentioning sections in the events page [#697](https://github.com/bids-standard/bids-specification/pull/697) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] Bep 009: Positron Emission Tomography [#633](https://github.com/bids-standard/bids-specification/pull/633) ([melanieganz](https://github.com/melanieganz))
 
-## [v1.5.0](https://github.com/bids-standard/bids-specification/tree/v1.5.0) (2021-02-23)
+## [v1.5.0](https://bids-specification.readthedocs.io/en/v1.5.0) (2021-02-23)
 
 -   \[MISC] Updated TotalAcquiredVolumes into TotalAcquiredPairs [#742](https://github.com/bids-standard/bids-specification/pull/742) ([effigies](https://github.com/effigies))
--   REL: v1.5.0 [#736](https://github.com/bids-standard/bids-specification/pull/736) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[SCHEMA] Update qMRI fieldmap schema [#728](https://github.com/bids-standard/bids-specification/pull/728) ([effigies](https://github.com/effigies))
 -   \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Correct schema irregularities for func datatype [#724](https://github.com/bids-standard/bids-specification/pull/724) ([tsalo](https://github.com/tsalo))
@@ -167,11 +165,10 @@
 -   \[SCHEMA] Render schema elements in text [#610](https://github.com/bids-standard/bids-specification/pull/610) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Add part entity for complex-valued data [#424](https://github.com/bids-standard/bids-specification/pull/424) ([tsalo](https://github.com/tsalo))
 
-## [v1.4.1](https://github.com/bids-standard/bids-specification/tree/v1.4.1) (2020-10-13)
+## [v1.4.1](https://bids-specification.readthedocs.io/en/v1.4.1) (2020-10-13)
 
 -   \[INFRA] minor robustness enhancements to pdf build shell script  [#642](https://github.com/bids-standard/bids-specification/pull/642) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] consistent CoordinateSystem fields for ephys [#641](https://github.com/bids-standard/bids-specification/pull/641) ([sappelhoff](https://github.com/sappelhoff))
--   REL: v1.4.1 [#640](https://github.com/bids-standard/bids-specification/pull/640) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] set up github action to detect latin phrases [#636](https://github.com/bids-standard/bids-specification/pull/636) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] Add a definition for "deprecation" [#634](https://github.com/bids-standard/bids-specification/pull/634) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] consolidate BIDS citations in introduction [#630](https://github.com/bids-standard/bids-specification/pull/630) ([sappelhoff](https://github.com/sappelhoff))
@@ -228,9 +225,8 @@
 -   \[INFRA] Convert entity table to yaml [#475](https://github.com/bids-standard/bids-specification/pull/475) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Recommend SI units formatting to adhere to CMIXF-12 [#411](https://github.com/bids-standard/bids-specification/pull/411) ([sappelhoff](https://github.com/sappelhoff))
 
-## [v1.4.0](https://github.com/bids-standard/bids-specification/tree/v1.4.0) (2020-06-11)
+## [v1.4.0](https://bids-specification.readthedocs.io/en/v1.4.0) (2020-06-11)
 
--   REL: v1.4.0 [#496](https://github.com/bids-standard/bids-specification/pull/496) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] Clarify language on unsetting a key/value pair [#495](https://github.com/bids-standard/bids-specification/pull/495) ([nicholst](https://github.com/nicholst))
 -   \[ENH] optionally allow LICENSE file [#483](https://github.com/bids-standard/bids-specification/pull/483) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] linkchecker - ignore github pull and tree URLs [#477](https://github.com/bids-standard/bids-specification/pull/477) ([yarikoptic](https://github.com/yarikoptic))
@@ -244,20 +240,18 @@
 -   \[FIX] Add reference to PDF on front page of specification [#452](https://github.com/bids-standard/bids-specification/pull/452) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] Add conditional for link-checking releases [#451](https://github.com/bids-standard/bids-specification/pull/451) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] unordered list formatting in BEP018 [#449](https://github.com/bids-standard/bids-specification/pull/449) ([sappelhoff](https://github.com/sappelhoff))
--   REL: 1.3.1-dev [#448](https://github.com/bids-standard/bids-specification/pull/448) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] fix inconsistencies for task label between sections [#446](https://github.com/bids-standard/bids-specification/pull/446) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] update DECISION-MAKING.md document with new governance [#441](https://github.com/bids-standard/bids-specification/pull/441) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] BEP 003: Common Derivatives [#265](https://github.com/bids-standard/bids-specification/pull/265) ([effigies](https://github.com/effigies))
 -   \[ENH] Add Glossary of terms/abbreviations used in the specification [#152](https://github.com/bids-standard/bids-specification/pull/152) ([yarikoptic](https://github.com/yarikoptic))
 
-## [v1.3.0](https://github.com/bids-standard/bids-specification/tree/v1.3.0) (2020-04-14)
+## [v1.3.0](https://bids-specification.readthedocs.io/en/v1.3.0) (2020-04-14)
 
 -   \[INFRA] add zenodo badge to README [#447](https://github.com/bids-standard/bids-specification/pull/447) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Added contributors from VisLab [#444](https://github.com/bids-standard/bids-specification/pull/444) ([VisLab](https://github.com/VisLab))
 -   \[FIX] Clarify  snake_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Eliminate web/online-specific language [#437](https://github.com/bids-standard/bids-specification/pull/437) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] ensure build_docs_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff))
--   REL: v1.3.0 [#435](https://github.com/bids-standard/bids-specification/pull/435) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Add issue templates for GitHub [#434](https://github.com/bids-standard/bids-specification/pull/434) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Get latest PDF build from CircleCI artifacts [#433](https://github.com/bids-standard/bids-specification/pull/433) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Update release protocol [#432](https://github.com/bids-standard/bids-specification/pull/432) ([franklin-feingold](https://github.com/franklin-feingold))
@@ -267,15 +261,13 @@
 -   \[FIX] Unify section titles and table-of-contents entries [#422](https://github.com/bids-standard/bids-specification/pull/422) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] add # before heading in CHANGES [#419](https://github.com/bids-standard/bids-specification/pull/419) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix heading of auto changelog to be a markdown header [#417](https://github.com/bids-standard/bids-specification/pull/417) ([sappelhoff](https://github.com/sappelhoff))
--   REL: 1.3.0-dev [#413](https://github.com/bids-standard/bids-specification/pull/413) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Add OPTIONAL EthicsApprovals field to dataset description [#412](https://github.com/bids-standard/bids-specification/pull/412) ([effigies](https://github.com/effigies))
 -   \[ENH] BEP 018 - Genetic Information [#395](https://github.com/bids-standard/bids-specification/pull/395) ([effigies](https://github.com/effigies))
 
-## [v1.2.2](https://github.com/bids-standard/bids-specification/tree/v1.2.2) (2020-02-12)
+## [v1.2.2](https://bids-specification.readthedocs.io/en/v1.2.2) (2020-02-12)
 
 -   \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] update contributions by CPernet [#409](https://github.com/bids-standard/bids-specification/pull/409) ([CPernet](https://github.com/CPernet))
--   REL: v1.2.2 [#405](https://github.com/bids-standard/bids-specification/pull/405) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Add Sébastien Tourbier to contributors [#394](https://github.com/bids-standard/bids-specification/pull/394) ([sebastientourbier](https://github.com/sebastientourbier))
 -   \[FIX] consistent units description between EEG/MEG/iEEG. Clarify (derived) SI units + prefixes [#391](https://github.com/bids-standard/bids-specification/pull/391) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] moved list of extension proposals to the main BIDS website [#389](https://github.com/bids-standard/bids-specification/pull/389) ([robertoostenveld](https://github.com/robertoostenveld))
@@ -306,17 +298,15 @@
 -   \[FIX] Add CBV and phase to Entity table [#312](https://github.com/bids-standard/bids-specification/pull/312) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold))
--   REL: 1.3.0-dev [#303](https://github.com/bids-standard/bids-specification/pull/303) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Adding contributor appendix sentence to PR template  [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Added discontinuous datatype for EEG and iEEG [#286](https://github.com/bids-standard/bids-specification/pull/286) ([wouterpotters](https://github.com/wouterpotters))
 -   \[FIX] Clarify paragraph about custom data types [#264](https://github.com/bids-standard/bids-specification/pull/264) ([effigies](https://github.com/effigies))
 
-## [v1.2.1](https://github.com/bids-standard/bids-specification/tree/v1.2.1) (2019-08-14)
+## [v1.2.1](https://bids-specification.readthedocs.io/en/v1.2.1) (2019-08-14)
 
 -   \[FIX] repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA+FIX] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic))
--   REL: v1.2.1 [#291](https://github.com/bids-standard/bids-specification/pull/291) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Adding Contributors and updating contributions [#284](https://github.com/bids-standard/bids-specification/pull/284) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] update Code of Conduct contact [#281](https://github.com/bids-standard/bids-specification/pull/281) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Update contributing guide and README to make discussion forums easy to find [#279](https://github.com/bids-standard/bids-specification/pull/279) ([emdupre](https://github.com/emdupre))
@@ -337,7 +327,6 @@
 -   \[MISC] Document BEPs that are not active anymore, but have not been merged [#240](https://github.com/bids-standard/bids-specification/pull/240) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] remove ManufacturersAmplifierModelName (again) [#236](https://github.com/bids-standard/bids-specification/pull/236) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[INFRA] Update release protocol [#235](https://github.com/bids-standard/bids-specification/pull/235) ([effigies](https://github.com/effigies))
--   REL: 1.3.0-dev [#234](https://github.com/bids-standard/bids-specification/pull/234) ([effigies](https://github.com/effigies))
 -   \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies))
 -   \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Trivial column header fix  [#220](https://github.com/bids-standard/bids-specification/pull/220) ([nicholst](https://github.com/nicholst))
@@ -367,9 +356,8 @@
 -   \[FIX] Specify marker filenames for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
-## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
+## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0) (2019-03-04)
 
--   REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
@@ -385,9 +373,8 @@
 -   \[MISC] Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[FIX] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
-## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
+## [v1.1.2](https://bids-specification.readthedocs.io/en/v1.1.2) (2019-01-10)
 
--   REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore))

From 3b7b9b0e415eeab3199bc14f31f730877a549bea Mon Sep 17 00:00:00 2001
From: Franklin Feingold <35307458+franklin-feingold@users.noreply.github.com>
Date: Tue, 15 Feb 2022 10:41:59 -0800
Subject: [PATCH 197/347] fix release date

---
 src/CHANGES.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index e4421cbff4..727a72046a 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## [v1.7.0](https://bids-specification.readthedocs.io/en/v1.7.0/) (2021-02-15)
+## [v1.7.0](https://bids-specification.readthedocs.io/en/v1.7.0/) (2022-02-15)
 
 -   BF: Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau))

From 3c483ac3cff1b6b57e93d5012196693c7b833c97 Mon Sep 17 00:00:00 2001
From: Franklin Feingold <35307458+franklin-feingold@users.noreply.github.com>
Date: Tue, 15 Feb 2022 11:07:30 -0800
Subject: [PATCH 198/347] REL: v1.7.1-dev

---
 mkdocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index 5979e5219a..01eb96dd5c 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Brain Imaging Data Structure v1.7.0
+site_name: Brain Imaging Data Structure v1.7.1-dev
 site_url: https://bids-specification.readthedocs.io/en/stable/
 theme:
     name: material

From a4b4584f350b44cb6002f3537634041976374b74 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Thu, 10 Feb 2022 08:10:31 -0500
Subject: [PATCH 199/347] [ENH] Tabular metadata rules for both top and
 second-level tabular files

* Representation of second-level files added.
* Homogenization of modality and non-modality file representation.
* Documenting file identifiers such as README and _sessions as
  suffixes..

Closes: https://github.com/bids-standard/bids-specification/issues/978
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 src/schema/objects/suffixes.yaml       | 27 ++++++++++++++++++++++++++
 src/schema/rules/tabular_metadata.yaml | 20 +++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 src/schema/rules/tabular_metadata.yaml

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index e809e375ea..10efeaedb0 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -617,6 +617,33 @@ sbref:
   name: Single-band reference image
   description: |
     Single-band reference for one or more multi-band `dwi` images.
+scans:
+  name: Scans file
+  description: |
+    The purpose of this file is to describe timing and other properties of each imaging acquisition
+    sequence (each run file) within one session.
+    Each neural recording file SHOULD be described by exactly one row. Some recordings consist of
+    multiple parts, that span several files, for example through echo-, part-, or split- entities.
+    Such recordings MUST be documented with one row per file.
+    Relative paths to files should be used under a compulsory filename header.
+    If acquisition time is included it should be listed under the acq_time header.
+    Acquisition time refers to when the first data point in each run was acquired.
+    Furthermore, if this header is provided, the acquisition times of all files that belong to a
+    recording MUST be identical.
+    Datetime should be expressed as described in Units.
+    Additional fields can include external behavioral measures relevant to the scan.
+    For example vigilance questionnaire score administered after a resting state scan.
+    All such included additional fields SHOULD be documented in an accompanying _scans.json file
+    that describes these fields in detail (see Tabular files).
+sessions:
+  name: Sessions file
+  description: |
+    In case of multiple sessions there is an option of adding additional sessions.tsv files
+    describing variables changing between sessions.
+    In such case one file per participant SHOULD be added.
+    These files MUST include a session_id column and describe each session by one and only one row.
+    Column names in sessions.tsv files MUST be different from group level participant key column
+    names in the participants.tsv file.
 stim:
   name: Continuous recording
   description: |
diff --git a/src/schema/rules/tabular_metadata.yaml b/src/schema/rules/tabular_metadata.yaml
new file mode 100644
index 0000000000..e04d10c1f6
--- /dev/null
+++ b/src/schema/rules/tabular_metadata.yaml
@@ -0,0 +1,20 @@
+---
+# scans.tsv
+- suffixes:
+  - scans
+  extensions:
+  - .tsv
+  - .json
+  entities:
+    subject: required
+    # session is required if session is present in the dataset.
+    session: optional
+# sessions.tsv
+# This file may only exist if session is present in the dataset.
+- suffixes:
+  - sessions
+  extensions:
+  - .tsv
+  - .json
+  entities:
+    subject: required

From ddc491c591668566443648f824a44c436af1a11e Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Fri, 18 Feb 2022 01:16:19 +0000
Subject: [PATCH 200/347] [DOC] Auto-generate changelog entry for PR #1006

---
 src/CHANGES.md | 40 +++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 727a72046a..ceb8262641 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -1,8 +1,13 @@
 # Changelog
 
-## [v1.7.0](https://bids-specification.readthedocs.io/en/v1.7.0/) (2022-02-15)
+## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
--   BF: Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
+-   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
+
+## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
+
+-   \[FIX] Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
+-   REL: v1.7.0 [#1004](https://github.com/bids-standard/bids-specification/pull/1004) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[SCHEMA, FIX] Remove mentions of auxdatatypes [#996](https://github.com/bids-standard/bids-specification/pull/996) ([tsalo](https://github.com/tsalo))
 -   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
@@ -108,9 +113,10 @@
 -   \[FIX] Correct iEEG example that contained double suffixes [#463](https://github.com/bids-standard/bids-specification/pull/463) ([yarikoptic](https://github.com/yarikoptic))
 -   \[ENH] introduce GeneratedBy to "core" BIDS [#440](https://github.com/bids-standard/bids-specification/pull/440) ([yarikoptic](https://github.com/yarikoptic))
 
-## [v1.6.0](https://bids-specification.readthedocs.io/en/v1.6.0) (2021-04-22)
+## [v1.6.0](https://github.com/bids-standard/bids-specification/tree/v1.6.0) (2021-04-22)
 
 -   \[FIX] Typos discovered by codespell [#784](https://github.com/bids-standard/bids-specification/pull/784) ([yarikoptic](https://github.com/yarikoptic))
+-   REL: v1.6.0 [#776](https://github.com/bids-standard/bids-specification/pull/776) ([effigies](https://github.com/effigies))
 -   \[FIX] Rename "Unit" metadata to "Units" for consistency with existing fields [#773](https://github.com/bids-standard/bids-specification/pull/773) ([effigies](https://github.com/effigies))
 -   \[FIX] typo in pet: institution -> institutional [#771](https://github.com/bids-standard/bids-specification/pull/771) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] install git in linkchecker job [#767](https://github.com/bids-standard/bids-specification/pull/767) ([sappelhoff](https://github.com/sappelhoff))
@@ -127,9 +133,10 @@
 -   \[MISC] refactor stimuli mentioning sections in the events page [#697](https://github.com/bids-standard/bids-specification/pull/697) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] Bep 009: Positron Emission Tomography [#633](https://github.com/bids-standard/bids-specification/pull/633) ([melanieganz](https://github.com/melanieganz))
 
-## [v1.5.0](https://bids-specification.readthedocs.io/en/v1.5.0) (2021-02-23)
+## [v1.5.0](https://github.com/bids-standard/bids-specification/tree/v1.5.0) (2021-02-23)
 
 -   \[MISC] Updated TotalAcquiredVolumes into TotalAcquiredPairs [#742](https://github.com/bids-standard/bids-specification/pull/742) ([effigies](https://github.com/effigies))
+-   REL: v1.5.0 [#736](https://github.com/bids-standard/bids-specification/pull/736) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[SCHEMA] Update qMRI fieldmap schema [#728](https://github.com/bids-standard/bids-specification/pull/728) ([effigies](https://github.com/effigies))
 -   \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Correct schema irregularities for func datatype [#724](https://github.com/bids-standard/bids-specification/pull/724) ([tsalo](https://github.com/tsalo))
@@ -165,10 +172,11 @@
 -   \[SCHEMA] Render schema elements in text [#610](https://github.com/bids-standard/bids-specification/pull/610) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Add part entity for complex-valued data [#424](https://github.com/bids-standard/bids-specification/pull/424) ([tsalo](https://github.com/tsalo))
 
-## [v1.4.1](https://bids-specification.readthedocs.io/en/v1.4.1) (2020-10-13)
+## [v1.4.1](https://github.com/bids-standard/bids-specification/tree/v1.4.1) (2020-10-13)
 
 -   \[INFRA] minor robustness enhancements to pdf build shell script  [#642](https://github.com/bids-standard/bids-specification/pull/642) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] consistent CoordinateSystem fields for ephys [#641](https://github.com/bids-standard/bids-specification/pull/641) ([sappelhoff](https://github.com/sappelhoff))
+-   REL: v1.4.1 [#640](https://github.com/bids-standard/bids-specification/pull/640) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] set up github action to detect latin phrases [#636](https://github.com/bids-standard/bids-specification/pull/636) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] Add a definition for "deprecation" [#634](https://github.com/bids-standard/bids-specification/pull/634) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] consolidate BIDS citations in introduction [#630](https://github.com/bids-standard/bids-specification/pull/630) ([sappelhoff](https://github.com/sappelhoff))
@@ -225,8 +233,9 @@
 -   \[INFRA] Convert entity table to yaml [#475](https://github.com/bids-standard/bids-specification/pull/475) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Recommend SI units formatting to adhere to CMIXF-12 [#411](https://github.com/bids-standard/bids-specification/pull/411) ([sappelhoff](https://github.com/sappelhoff))
 
-## [v1.4.0](https://bids-specification.readthedocs.io/en/v1.4.0) (2020-06-11)
+## [v1.4.0](https://github.com/bids-standard/bids-specification/tree/v1.4.0) (2020-06-11)
 
+-   REL: v1.4.0 [#496](https://github.com/bids-standard/bids-specification/pull/496) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] Clarify language on unsetting a key/value pair [#495](https://github.com/bids-standard/bids-specification/pull/495) ([nicholst](https://github.com/nicholst))
 -   \[ENH] optionally allow LICENSE file [#483](https://github.com/bids-standard/bids-specification/pull/483) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] linkchecker - ignore github pull and tree URLs [#477](https://github.com/bids-standard/bids-specification/pull/477) ([yarikoptic](https://github.com/yarikoptic))
@@ -240,18 +249,20 @@
 -   \[FIX] Add reference to PDF on front page of specification [#452](https://github.com/bids-standard/bids-specification/pull/452) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] Add conditional for link-checking releases [#451](https://github.com/bids-standard/bids-specification/pull/451) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] unordered list formatting in BEP018 [#449](https://github.com/bids-standard/bids-specification/pull/449) ([sappelhoff](https://github.com/sappelhoff))
+-   REL: 1.3.1-dev [#448](https://github.com/bids-standard/bids-specification/pull/448) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] fix inconsistencies for task label between sections [#446](https://github.com/bids-standard/bids-specification/pull/446) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] update DECISION-MAKING.md document with new governance [#441](https://github.com/bids-standard/bids-specification/pull/441) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] BEP 003: Common Derivatives [#265](https://github.com/bids-standard/bids-specification/pull/265) ([effigies](https://github.com/effigies))
 -   \[ENH] Add Glossary of terms/abbreviations used in the specification [#152](https://github.com/bids-standard/bids-specification/pull/152) ([yarikoptic](https://github.com/yarikoptic))
 
-## [v1.3.0](https://bids-specification.readthedocs.io/en/v1.3.0) (2020-04-14)
+## [v1.3.0](https://github.com/bids-standard/bids-specification/tree/v1.3.0) (2020-04-14)
 
 -   \[INFRA] add zenodo badge to README [#447](https://github.com/bids-standard/bids-specification/pull/447) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Added contributors from VisLab [#444](https://github.com/bids-standard/bids-specification/pull/444) ([VisLab](https://github.com/VisLab))
 -   \[FIX] Clarify  snake_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Eliminate web/online-specific language [#437](https://github.com/bids-standard/bids-specification/pull/437) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] ensure build_docs_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff))
+-   REL: v1.3.0 [#435](https://github.com/bids-standard/bids-specification/pull/435) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Add issue templates for GitHub [#434](https://github.com/bids-standard/bids-specification/pull/434) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Get latest PDF build from CircleCI artifacts [#433](https://github.com/bids-standard/bids-specification/pull/433) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Update release protocol [#432](https://github.com/bids-standard/bids-specification/pull/432) ([franklin-feingold](https://github.com/franklin-feingold))
@@ -261,13 +272,15 @@
 -   \[FIX] Unify section titles and table-of-contents entries [#422](https://github.com/bids-standard/bids-specification/pull/422) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] add # before heading in CHANGES [#419](https://github.com/bids-standard/bids-specification/pull/419) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix heading of auto changelog to be a markdown header [#417](https://github.com/bids-standard/bids-specification/pull/417) ([sappelhoff](https://github.com/sappelhoff))
+-   REL: 1.3.0-dev [#413](https://github.com/bids-standard/bids-specification/pull/413) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Add OPTIONAL EthicsApprovals field to dataset description [#412](https://github.com/bids-standard/bids-specification/pull/412) ([effigies](https://github.com/effigies))
 -   \[ENH] BEP 018 - Genetic Information [#395](https://github.com/bids-standard/bids-specification/pull/395) ([effigies](https://github.com/effigies))
 
-## [v1.2.2](https://bids-specification.readthedocs.io/en/v1.2.2) (2020-02-12)
+## [v1.2.2](https://github.com/bids-standard/bids-specification/tree/v1.2.2) (2020-02-12)
 
 -   \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] update contributions by CPernet [#409](https://github.com/bids-standard/bids-specification/pull/409) ([CPernet](https://github.com/CPernet))
+-   REL: v1.2.2 [#405](https://github.com/bids-standard/bids-specification/pull/405) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Add Sébastien Tourbier to contributors [#394](https://github.com/bids-standard/bids-specification/pull/394) ([sebastientourbier](https://github.com/sebastientourbier))
 -   \[FIX] consistent units description between EEG/MEG/iEEG. Clarify (derived) SI units + prefixes [#391](https://github.com/bids-standard/bids-specification/pull/391) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] moved list of extension proposals to the main BIDS website [#389](https://github.com/bids-standard/bids-specification/pull/389) ([robertoostenveld](https://github.com/robertoostenveld))
@@ -298,15 +311,17 @@
 -   \[FIX] Add CBV and phase to Entity table [#312](https://github.com/bids-standard/bids-specification/pull/312) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold))
+-   REL: 1.3.0-dev [#303](https://github.com/bids-standard/bids-specification/pull/303) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Adding contributor appendix sentence to PR template  [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Added discontinuous datatype for EEG and iEEG [#286](https://github.com/bids-standard/bids-specification/pull/286) ([wouterpotters](https://github.com/wouterpotters))
 -   \[FIX] Clarify paragraph about custom data types [#264](https://github.com/bids-standard/bids-specification/pull/264) ([effigies](https://github.com/effigies))
 
-## [v1.2.1](https://bids-specification.readthedocs.io/en/v1.2.1) (2019-08-14)
+## [v1.2.1](https://github.com/bids-standard/bids-specification/tree/v1.2.1) (2019-08-14)
 
 -   \[FIX] repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA+FIX] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic))
+-   REL: v1.2.1 [#291](https://github.com/bids-standard/bids-specification/pull/291) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Adding Contributors and updating contributions [#284](https://github.com/bids-standard/bids-specification/pull/284) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] update Code of Conduct contact [#281](https://github.com/bids-standard/bids-specification/pull/281) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Update contributing guide and README to make discussion forums easy to find [#279](https://github.com/bids-standard/bids-specification/pull/279) ([emdupre](https://github.com/emdupre))
@@ -327,6 +342,7 @@
 -   \[MISC] Document BEPs that are not active anymore, but have not been merged [#240](https://github.com/bids-standard/bids-specification/pull/240) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] remove ManufacturersAmplifierModelName (again) [#236](https://github.com/bids-standard/bids-specification/pull/236) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[INFRA] Update release protocol [#235](https://github.com/bids-standard/bids-specification/pull/235) ([effigies](https://github.com/effigies))
+-   REL: 1.3.0-dev [#234](https://github.com/bids-standard/bids-specification/pull/234) ([effigies](https://github.com/effigies))
 -   \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies))
 -   \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Trivial column header fix  [#220](https://github.com/bids-standard/bids-specification/pull/220) ([nicholst](https://github.com/nicholst))
@@ -356,8 +372,9 @@
 -   \[FIX] Specify marker filenames for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
-## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0) (2019-03-04)
+## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
 
+-   REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
@@ -373,8 +390,9 @@
 -   \[MISC] Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[FIX] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
-## [v1.1.2](https://bids-specification.readthedocs.io/en/v1.1.2) (2019-01-10)
+## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
 
+-   REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore))

From 9201b203ffaa72d83b2fa30d1c61f46f089f77de Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Sat, 19 Feb 2022 01:46:22 +0000
Subject: [PATCH 201/347] [DOC] Auto-generate changelog entry for PR #997

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index ceb8262641..607ebec60b 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -3,6 +3,7 @@
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
 -   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
+-   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
 
 ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
 

From c5f89c60abe4049b595810f52e187ac8d551c4a9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Feb 2022 15:10:02 -0500
Subject: [PATCH 202/347] SCHEMA: Encode first two MR metadata tables as
 "sidecars.yml" (#1016)

Co-authored-by: Christopher J. Markiewicz <markiewicz@stanford.edu>
---
 src/schema/rules/sidecars.yml | 103 ++++++++++++++++++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 src/schema/rules/sidecars.yml

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
new file mode 100644
index 0000000000..5acd81d19f
--- /dev/null
+++ b/src/schema/rules/sidecars.yml
@@ -0,0 +1,103 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+MRIScannerHardware:
+    selectors:
+        - modality == "MRI"
+    fields:
+        Manufacturer:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
+        ManufacturersModelName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
+        DeviceSerialNumber:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`.
+        StationName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 1010 `Station Name`.
+        SoftwareVersions:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`.
+        HardcopyDeviceSoftwareVersion: DEPRECATED
+        MagneticFieldStrength:
+            level: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
+        ReceiveCoilName: RECOMMENDED
+        ReceiveCoilActiveElements: RECOMMENDED
+        GradientSetType: RECOMMENDED
+        MRTransmitCoilSequence: RECOMMENDED
+        MatrixCoilMode: RECOMMENDED
+        CoilCombinationMethod: RECOMMENDED
+
+MRISequenceSpecifics:
+    selectors:
+        - modality == "MRI"
+    fields:
+        PulseSequenceType: RECOMMENDED
+        ScanningSequence: RECOMMENDED
+        SequenceVariant: RECOMMENDED
+        ScanOptions: RECOMMENDED
+        SequenceName: RECOMMENDED
+        PulseSequenceDetails: RECOMMENDED
+        NonlinearGradientCorrection: RECOMMENDED, but REQUIRED if [PET](./09-positron-emission-tomography.md) data are present
+        MRAcquisitionType: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
+        MTState: RECOMMENDED
+        MTOffsetFrequency: OPTIONAL
+        MTPulseBandwidth: OPTIONAL
+        MTNumberOfPulses: OPTIONAL
+        MTPulseShape: OPTIONAL
+        MTPulseDuration: OPTIONAL
+        SpoilingState: RECOMMENDED
+        SpoilingType: OPTIONAL
+        SpoilingRFPhaseIncrement: OPTIONAL
+        SpoilingGradientMoment: OPTIONAL
+        SpoilingGradientDuration: OPTIONAL
+
+PETMRISequenceSpecifics:
+    selectors:
+        - modality == "MRI"
+        - "PET" in dataset.modalities
+    fields:
+        NonLinearGradientCorrection: REQUIRED
+
+ASLMRISequenceSpecifics:
+    selectors:
+        - modality == "MRI"
+        - datatype == "perf"
+    fields:
+        MRAcquisitionType: REQUIRED
+
+MTParameters:
+    selectors:
+        - sidecar.MTState == True
+    fields:
+        MTOffsetFrequency: RECOMMENDED
+        MTPulseBandwidth: RECOMMENDED
+        MTNumberOfPulses: RECOMMENDED
+        MTPulseShape: RECOMMENDED
+        MTPulseDuration: RECOMMENDED
+
+SpoilingType:
+    selectors:
+        - sidecar.SpoilingState == True
+    fields:
+        SpoilingType: RECOMMENDED
+
+SpoilingRF:
+    selectors:
+        - sidecar.SpoilingType in ["RF", "COMBINED"]
+    fields:
+        SpoilingRFPhaseIncrement: RECOMMENDED
+
+SpoilingGradient:
+    selectors:
+        - sidecar.SpoilingType in ["GRADIENT", "COMBINED"]
+    fields:
+        SpoilingGradientMoment: RECOMMENDED
+        SpoilingGradientDuration: RECOMMENDED

From 3af5b98c6df8361e0a1a60da0cc021b16fab524b Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Feb 2022 15:57:05 -0500
Subject: [PATCH 203/347] Add rules for the rest of MRI common fields.

---
 src/schema/rules/sidecars.yml | 116 ++++++++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index 5acd81d19f..ad967917a7 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -6,6 +6,7 @@
 
 
 ---
+# MRI Common metadata fields
 MRIScannerHardware:
     selectors:
         - modality == "MRI"
@@ -101,3 +102,118 @@ SpoilingGradient:
     fields:
         SpoilingGradientMoment: RECOMMENDED
         SpoilingGradientDuration: RECOMMENDED
+
+MRISpatialEncoding:
+    selectors:
+        - modality == "MRI"
+    fields:
+        NumberShots: RECOMMENDED
+        ParallelReductionFactorInPlane: RECOMMENDED
+        ParallelAcquisitionTechnique: RECOMMENDED
+        PartialFourier: RECOMMENDED
+        PartialFourierDirection: RECOMMENDED
+        PhaseEncodingDirection:
+            level: RECOMMENDED
+            level_addendum: |
+                This parameter is REQUIRED if corresponding fieldmap data is present
+                or when using multiple runs with different phase encoding directions
+                (which can be later used for field inhomogeneity correction).
+        EffectiveEchoSpacing:
+            level: RECOMMENDED
+            level_addendum: |
+                <sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data
+                is present.
+        TotalReadoutTime:
+            level: RECOMMENDED
+            level_addendum: |
+                <sup>3</sup> This parameter is REQUIRED if corresponding 'field/distortion' maps
+                acquired with opposing phase encoding directions are present
+                (see [Case 4: Multiple phase encoded
+                directions](#case-4-multiple-phase-encoded-directions-pepolar)).
+        MixingTime: RECOMMENDED
+
+MRITimingParameters:
+    selectors:
+        - modality == "MRI"
+    fields:
+        EchoTime:
+            level: RECOMMENDED
+            level_addendum: |
+                REQUIRED if corresponding fieldmap data is present,
+                or the data comes from a multi-echo sequence or Arterial Spin Labeling.
+        InversionTime: RECOMMENDED
+        SliceTiming:
+            level: RECOMMENDED
+            level_addendum: |
+                REQUIRED for sparse sequences that do not have the `DelayTime` field set,
+                and Arterial Spin Labeling with `MRAcquisitionType` set on `2D`.
+        SliceEncodingDirection: RECOMMENDED
+        DwellTime: RECOMMENDED
+
+SliceTimingASL:
+    selectors:
+        - modality == "MRI"
+        - datatype == "perf"
+        - suffix in ["asl", "m0scan"]
+        - sidecar.MRAcquisitionType == "2D"
+    fields:
+        SliceTiming: REQUIRED
+
+# This is technically for sparse sequences only, but I don't know how to encode that.
+SliceTimingSparse:
+    selectors:
+        - modality == "MRI"
+        # NOTE: This is my idea for "field is defined", but I don't know if it's the best approach.
+        - sidecar.DelayTime != "n/a"
+    fields:
+        SliceTiming: REQUIRED
+
+MRIRFandContrast:
+    selectors:
+        - modality == "MRI"
+    fields:
+        FlipAngle:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if LookLocker is set to `true`.
+        NegativeContrast: OPTIONAL
+
+MRIFlipAngleLookLocker:
+    selectors:
+        - modality == "MRI"
+        - sidecar.LookLocker == "true"
+    fields:
+        FlipAngle: REQUIRED
+
+MRISliceAcceleration:
+    selectors:
+        - modality == "MRI"
+    fields:
+        MultibandAccelerationFactor: RECOMMENDED
+
+MRIAnatomicalLandmarks:
+    selectors:
+        - modality == "MRI"
+    fields:
+        AnatomicalLandmarkCoordinates__mri: RECOMMENDED
+
+MRIEchoPlanarImagingAndB0Mapping:
+    selectors:
+        - modality == "MRI"
+    fields:
+        B0FieldIdentifier: RECOMMENDED
+        B0FieldSource: RECOMMENDED
+
+MRIInstitutionInformation:
+    selectors:
+        - modality == "MRI"
+    fields:
+        InstitutionName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
+        InstitutionAddress:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
+        InstitutionalDepartmentName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
+

From 0422a16e52f4e1d84988bde96972a6d8821ebf2d Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Feb 2022 15:57:16 -0500
Subject: [PATCH 204/347] Add anatomical MRI rules.

---
 src/schema/rules/sidecars.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index ad967917a7..acce7d18ee 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -217,3 +217,13 @@ MRIInstitutionInformation:
             level: RECOMMENDED
             addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
 
+# Anatomy imaging data
+
+MRIAnatomyCommonMetadataFields:
+    selectors:
+        - modality == "MRI"
+        - datatype == "anat"
+    fields:
+        ContrastBolusIngredient: OPTIONAL
+        RepetitionTimeExcitation: OPTIONAL
+        RepetitionTimePreparation: OPTIONAL

From f2d9b8d9416c56c87430fde2cafd6aee53dd7ec7 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Feb 2022 16:13:03 -0500
Subject: [PATCH 205/347] Draft entity-metadata rules too.

---
 src/schema/rules/sidecars.yml | 71 +++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index acce7d18ee..454110d262 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -227,3 +227,74 @@ MRIAnatomyCommonMetadataFields:
         ContrastBolusIngredient: OPTIONAL
         RepetitionTimeExcitation: OPTIONAL
         RepetitionTimePreparation: OPTIONAL
+
+# Entities
+
+EntitiesTaskMetadata:
+    selectors:
+        - entities.task != "n/a"
+    fields:
+        TaskName: RECOMMENDED
+
+EntitiesCeMetadata:
+    selectors:
+        - entities.ce != "n/a"
+    fields:
+        ContrastBolusIngredient: OPTIONAL
+
+EntitiesTrcMetadata:
+    selectors:
+        - entities.trc != "n/a"
+    fields:
+        TracerName: REQUIRED
+
+EntitiesStainMetadata:
+    selectors:
+        - entities.stain != "n/a"
+    fields:
+        SampleStaining: RECOMMENDED
+        SamplePrimaryAntibodies: RECOMMENDED
+        SampleSecondaryAntibodies: RECOMMENDED
+
+EntitiesEchoMetadata:
+    selectors:
+        - entities.echo != "n/a"
+    fields:
+        EchoTime: REQUIRED
+
+EntitiesFlipMetadata:
+    selectors:
+        - entities.flip != "n/a"
+    fields:
+        FlipAngle: REQUIRED
+
+EntitiesInvMetadata:
+    selectors:
+        - entities.inv != "n/a"
+    fields:
+        InversionTime: REQUIRED
+
+EntitiesMTMetadata:
+    selectors:
+        - entities.mt != "n/a"
+    fields:
+        MTState: REQUIRED
+
+EntitiesPartMetadata:
+    selectors:
+        - entities.part == "phase"
+    fields:
+        # Can we require Units to be either "rad" or "arbitrary" here?
+        Units: REQUIRED
+
+EntitiesResMetadata:
+    selectors:
+        - entities.res != "n/a"
+    fields:
+        Resolution: REQUIRED
+
+EntitiesDenMetadata:
+    selectors:
+        - entities.den != "n/a"
+    fields:
+        Density: REQUIRED

From 1bf3866a108a023289a4c47248c357ca24a9b917 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Feb 2022 17:34:59 -0500
Subject: [PATCH 206/347] Fix formatting.

---
 src/schema/rules/sidecars.yml | 81 ++++++++++++++++++-----------------
 1 file changed, 41 insertions(+), 40 deletions(-)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index 454110d262..3998a26c0b 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -9,7 +9,7 @@
 # MRI Common metadata fields
 MRIScannerHardware:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         Manufacturer:
             level: RECOMMENDED
@@ -38,7 +38,7 @@ MRIScannerHardware:
 
 MRISequenceSpecifics:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         PulseSequenceType: RECOMMENDED
         ScanningSequence: RECOMMENDED
@@ -46,7 +46,8 @@ MRISequenceSpecifics:
         ScanOptions: RECOMMENDED
         SequenceName: RECOMMENDED
         PulseSequenceDetails: RECOMMENDED
-        NonlinearGradientCorrection: RECOMMENDED, but REQUIRED if [PET](./09-positron-emission-tomography.md) data are present
+        NonlinearGradientCorrection: |
+            RECOMMENDED, but REQUIRED if [PET](./09-positron-emission-tomography.md) data are present
         MRAcquisitionType: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
         MTState: RECOMMENDED
         MTOffsetFrequency: OPTIONAL
@@ -62,21 +63,21 @@ MRISequenceSpecifics:
 
 PETMRISequenceSpecifics:
     selectors:
-        - modality == "MRI"
-        - "PET" in dataset.modalities
+    - modality == "MRI"
+    - PET in dataset.modalities
     fields:
         NonLinearGradientCorrection: REQUIRED
 
 ASLMRISequenceSpecifics:
     selectors:
-        - modality == "MRI"
-        - datatype == "perf"
+    - modality == "MRI"
+    - datatype == "perf"
     fields:
         MRAcquisitionType: REQUIRED
 
 MTParameters:
     selectors:
-        - sidecar.MTState == True
+    - sidecar.MTState == True
     fields:
         MTOffsetFrequency: RECOMMENDED
         MTPulseBandwidth: RECOMMENDED
@@ -86,26 +87,26 @@ MTParameters:
 
 SpoilingType:
     selectors:
-        - sidecar.SpoilingState == True
+    - sidecar.SpoilingState == True
     fields:
         SpoilingType: RECOMMENDED
 
 SpoilingRF:
     selectors:
-        - sidecar.SpoilingType in ["RF", "COMBINED"]
+    - sidecar.SpoilingType in ["RF", "COMBINED"]
     fields:
         SpoilingRFPhaseIncrement: RECOMMENDED
 
 SpoilingGradient:
     selectors:
-        - sidecar.SpoilingType in ["GRADIENT", "COMBINED"]
+    - sidecar.SpoilingType in ["GRADIENT", "COMBINED"]
     fields:
         SpoilingGradientMoment: RECOMMENDED
         SpoilingGradientDuration: RECOMMENDED
 
 MRISpatialEncoding:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         NumberShots: RECOMMENDED
         ParallelReductionFactorInPlane: RECOMMENDED
@@ -134,7 +135,7 @@ MRISpatialEncoding:
 
 MRITimingParameters:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         EchoTime:
             level: RECOMMENDED
@@ -152,25 +153,25 @@ MRITimingParameters:
 
 SliceTimingASL:
     selectors:
-        - modality == "MRI"
-        - datatype == "perf"
-        - suffix in ["asl", "m0scan"]
-        - sidecar.MRAcquisitionType == "2D"
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix in ["asl", "m0scan"]
+    - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming: REQUIRED
 
 # This is technically for sparse sequences only, but I don't know how to encode that.
 SliceTimingSparse:
     selectors:
-        - modality == "MRI"
-        # NOTE: This is my idea for "field is defined", but I don't know if it's the best approach.
-        - sidecar.DelayTime != "n/a"
+    - modality == "MRI"
+    # NOTE: This is my idea for "field is defined", but I don't know if it's the best approach.
+    - sidecar.DelayTime != "n/a"
     fields:
         SliceTiming: REQUIRED
 
 MRIRFandContrast:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         FlipAngle:
             level: RECOMMENDED
@@ -179,33 +180,33 @@ MRIRFandContrast:
 
 MRIFlipAngleLookLocker:
     selectors:
-        - modality == "MRI"
-        - sidecar.LookLocker == "true"
+    - modality == "MRI"
+    - sidecar.LookLocker == "true"
     fields:
         FlipAngle: REQUIRED
 
 MRISliceAcceleration:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         MultibandAccelerationFactor: RECOMMENDED
 
 MRIAnatomicalLandmarks:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         AnatomicalLandmarkCoordinates__mri: RECOMMENDED
 
 MRIEchoPlanarImagingAndB0Mapping:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         B0FieldIdentifier: RECOMMENDED
         B0FieldSource: RECOMMENDED
 
 MRIInstitutionInformation:
     selectors:
-        - modality == "MRI"
+    - modality == "MRI"
     fields:
         InstitutionName:
             level: RECOMMENDED
@@ -221,8 +222,8 @@ MRIInstitutionInformation:
 
 MRIAnatomyCommonMetadataFields:
     selectors:
-        - modality == "MRI"
-        - datatype == "anat"
+    - modality == "MRI"
+    - datatype == "anat"
     fields:
         ContrastBolusIngredient: OPTIONAL
         RepetitionTimeExcitation: OPTIONAL
@@ -232,25 +233,25 @@ MRIAnatomyCommonMetadataFields:
 
 EntitiesTaskMetadata:
     selectors:
-        - entities.task != "n/a"
+    - entities.task != "n/a"
     fields:
         TaskName: RECOMMENDED
 
 EntitiesCeMetadata:
     selectors:
-        - entities.ce != "n/a"
+    - entities.ce != "n/a"
     fields:
         ContrastBolusIngredient: OPTIONAL
 
 EntitiesTrcMetadata:
     selectors:
-        - entities.trc != "n/a"
+    - entities.trc != "n/a"
     fields:
         TracerName: REQUIRED
 
 EntitiesStainMetadata:
     selectors:
-        - entities.stain != "n/a"
+    - entities.stain != "n/a"
     fields:
         SampleStaining: RECOMMENDED
         SamplePrimaryAntibodies: RECOMMENDED
@@ -258,43 +259,43 @@ EntitiesStainMetadata:
 
 EntitiesEchoMetadata:
     selectors:
-        - entities.echo != "n/a"
+    - entities.echo != "n/a"
     fields:
         EchoTime: REQUIRED
 
 EntitiesFlipMetadata:
     selectors:
-        - entities.flip != "n/a"
+    - entities.flip != "n/a"
     fields:
         FlipAngle: REQUIRED
 
 EntitiesInvMetadata:
     selectors:
-        - entities.inv != "n/a"
+    - entities.inv != "n/a"
     fields:
         InversionTime: REQUIRED
 
 EntitiesMTMetadata:
     selectors:
-        - entities.mt != "n/a"
+    - entities.mt != "n/a"
     fields:
         MTState: REQUIRED
 
 EntitiesPartMetadata:
     selectors:
-        - entities.part == "phase"
+    - entities.part == "phase"
     fields:
         # Can we require Units to be either "rad" or "arbitrary" here?
         Units: REQUIRED
 
 EntitiesResMetadata:
     selectors:
-        - entities.res != "n/a"
+    - entities.res != "n/a"
     fields:
         Resolution: REQUIRED
 
 EntitiesDenMetadata:
     selectors:
-        - entities.den != "n/a"
+    - entities.den != "n/a"
     fields:
         Density: REQUIRED

From 7ced46612c39dde2d8797f841fb7120e63eab3b2 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Mon, 28 Feb 2022 04:20:12 -0500
Subject: [PATCH 207/347] [SCHEMA] Tests for render listings

---
 .../schemacode/tests/test_render.py           | 73 +++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 tools/schemacode/schemacode/tests/test_render.py

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
new file mode 100644
index 0000000000..5c02c443cd
--- /dev/null
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -0,0 +1,73 @@
+"""Tests for the schemacode package."""
+import pytest
+import os
+
+from schemacode import render
+
+def test_make_entity_definitions(schema_obj):
+    schema_text = render.make_entity_definitions(schema_obj)
+    assert "Format: `sub-<label>`" in schema_text
+    assert "Format: `ses-<label>`" in schema_text
+    assert "Format: `sample-<label>`" in schema_text
+    assert "Format: `task-<label>`" in schema_text
+    assert "Format: `acq-<label>`" in schema_text
+    assert "Format: `ce-<label>`" in schema_text
+
+def test_make_glossary(schema_obj, schema_dir):
+    # Test consistency
+    object_files = []
+    for root, dirs, files in os.walk(schema_dir, topdown=False):
+       if "objects" in root:
+           for object_file in files:
+               object_base, _ = os.path.splitext(object_file)
+               object_files.append(object_base)
+    rule_files = []
+    for root, dirs, files in os.walk(schema_dir, topdown=False):
+       if "rules" in root:
+           for rule_file in files:
+               rule_base, _ = os.path.splitext(rule_file)
+               rule_files.append(rule_base)
+    objects_only = list(filter(lambda a: a not in rule_files, object_files))
+    rules_only = list(filter(lambda a: a not in object_files, rule_files))
+
+    glossary = render.make_glossary(schema_obj)
+    for line in glossary.split('\n'):
+        if line.startswith('<a name="objects.'):
+            # Are all objects objects?
+            assert any([line.startswith(f'<a name="objects.{i}') for i in object_files])
+            assert not any([line.startswith(f'<a name="objects.{i}') for i in rules_only])
+
+def test_make_filename_template(schema_obj, schema_dir):
+    filename_template = render.make_filename_template(schema_obj)
+
+    # Test predefined substrings
+    expected_template_part = """
+sub-<label>/
+    [ses-<label>/]
+        anat/
+    """
+    assert expected_template_part in filename_template
+
+    # Test consistency
+    datatype_bases = []
+    for root, dirs, files in os.walk(schema_dir, topdown=False):
+       if "datatype" in root:
+           for datatype_file in files:
+               datatype_base, _ = os.path.splitext(datatype_file)
+               datatype_bases.append(datatype_base)
+
+    datatype_count = len(datatype_bases)
+    datatype_bases = [f'        {i}/' for i in datatype_bases]
+    datatype_level = False
+    datatype_file_start = '            sub-<label>'
+    datatype_bases_found = 0
+    for line in filename_template.split('\n'):
+        if datatype_level:
+            # Is there at least one file pattern per datatype?
+            assert line.startswith(datatype_file_start)
+            datatype_level = False
+        if line in datatype_bases:
+            datatype_level = True
+            datatype_bases_found+=1
+    # Are all datatypes listed?
+    assert datatype_bases_found == datatype_count

From 4750ec05ccef938507339f45b1b6a086593dd968 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Tue, 1 Mar 2022 21:37:20 +0100
Subject: [PATCH 208/347] [MISC] clarify copyright for logo

---
 BIDS_logo/README.md | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/BIDS_logo/README.md b/BIDS_logo/README.md
index 4605ec1542..a6f19ed9cc 100644
--- a/BIDS_logo/README.md
+++ b/BIDS_logo/README.md
@@ -1,11 +1,21 @@
-The BIDS logo originates from a [design competition](https://en.99designs.de/logo-design/contests/design-brain-imaging-data-standard-logo-916110).
+# BIDS logo
+
+The BIDS logo originates from a
+[design competition](https://en.99designs.de/logo-design/contests/design-brain-imaging-data-standard-logo-916110).
 
 See the related discussion here: https://github.com/bids-standard/bids-specification/issues/216
 
-The sources of the animated version of the logo can be found at
+All static versions of the logo are shared under a CC BY 4.0 license, see
+[LICENSE](../LICENSE)
+in the root of the repository.
+
+The animated version of the logo is shared under a CC BY-SA 4.0 license,
+copyright Adina Wagner,
+please see the source:
 [github.com/adswa/animated-bids-logo](https://github.com/adswa/animated-bids-logo).
 
 # Files
+
 - Standard formats
     - `BIDS_logo.jpg`
     - Transparent background

From 74b65be391bfb79ec330624d4b02d39e91234884 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Tue, 1 Mar 2022 21:45:53 +0100
Subject: [PATCH 209/347] replace online wiley link with DOI link

---
 src/schema/objects/suffixes.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 10efeaedb0..25ed8a5b8c 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -15,7 +15,7 @@ Chimap:
     In parts per million (ppm).
     QSM allows for determining the underlying magnetic susceptibility of tissue
     (Chi)
-    ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)).
+    ([Wang & Liu, 2014](https://doi.org/10.1002/mrm.25358)).
     Chi maps are REQUIRED to use this suffix regardless of the method used to
     generate them.
   unit: ppm

From b7868fa5de06e851b161fdd9a10f76437625106f Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Thu, 3 Mar 2022 04:06:31 -0500
Subject: [PATCH 210/347] Black and isort fixes

---
 .../schemacode/tests/test_render.py           | 40 ++++++++++---------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index 5c02c443cd..01f78a1d4e 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -1,9 +1,11 @@
 """Tests for the schemacode package."""
-import pytest
 import os
 
+import pytest
+
 from schemacode import render
 
+
 def test_make_entity_definitions(schema_obj):
     schema_text = render.make_entity_definitions(schema_obj)
     assert "Format: `sub-<label>`" in schema_text
@@ -13,30 +15,32 @@ def test_make_entity_definitions(schema_obj):
     assert "Format: `acq-<label>`" in schema_text
     assert "Format: `ce-<label>`" in schema_text
 
+
 def test_make_glossary(schema_obj, schema_dir):
     # Test consistency
     object_files = []
     for root, dirs, files in os.walk(schema_dir, topdown=False):
-       if "objects" in root:
-           for object_file in files:
-               object_base, _ = os.path.splitext(object_file)
-               object_files.append(object_base)
+        if "objects" in root:
+            for object_file in files:
+                object_base, _ = os.path.splitext(object_file)
+                object_files.append(object_base)
     rule_files = []
     for root, dirs, files in os.walk(schema_dir, topdown=False):
-       if "rules" in root:
-           for rule_file in files:
-               rule_base, _ = os.path.splitext(rule_file)
-               rule_files.append(rule_base)
+        if "rules" in root:
+            for rule_file in files:
+                rule_base, _ = os.path.splitext(rule_file)
+                rule_files.append(rule_base)
     objects_only = list(filter(lambda a: a not in rule_files, object_files))
     rules_only = list(filter(lambda a: a not in object_files, rule_files))
 
     glossary = render.make_glossary(schema_obj)
-    for line in glossary.split('\n'):
+    for line in glossary.split("\n"):
         if line.startswith('<a name="objects.'):
             # Are all objects objects?
             assert any([line.startswith(f'<a name="objects.{i}') for i in object_files])
             assert not any([line.startswith(f'<a name="objects.{i}') for i in rules_only])
 
+
 def test_make_filename_template(schema_obj, schema_dir):
     filename_template = render.make_filename_template(schema_obj)
 
@@ -51,23 +55,23 @@ def test_make_filename_template(schema_obj, schema_dir):
     # Test consistency
     datatype_bases = []
     for root, dirs, files in os.walk(schema_dir, topdown=False):
-       if "datatype" in root:
-           for datatype_file in files:
-               datatype_base, _ = os.path.splitext(datatype_file)
-               datatype_bases.append(datatype_base)
+        if "datatype" in root:
+            for datatype_file in files:
+                datatype_base, _ = os.path.splitext(datatype_file)
+                datatype_bases.append(datatype_base)
 
     datatype_count = len(datatype_bases)
-    datatype_bases = [f'        {i}/' for i in datatype_bases]
+    datatype_bases = [f"        {i}/" for i in datatype_bases]
     datatype_level = False
-    datatype_file_start = '            sub-<label>'
+    datatype_file_start = "            sub-<label>"
     datatype_bases_found = 0
-    for line in filename_template.split('\n'):
+    for line in filename_template.split("\n"):
         if datatype_level:
             # Is there at least one file pattern per datatype?
             assert line.startswith(datatype_file_start)
             datatype_level = False
         if line in datatype_bases:
             datatype_level = True
-            datatype_bases_found+=1
+            datatype_bases_found += 1
     # Are all datatypes listed?
     assert datatype_bases_found == datatype_count

From 2ef6f1a07ae4c4491df512d82124d0fc1063130d Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 3 Mar 2022 16:24:54 -0500
Subject: [PATCH 211/347] Update based on discussion today.

---
 src/schema/rules/sidecars.yml | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index 3998a26c0b..459e992d14 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -164,8 +164,7 @@ SliceTimingASL:
 SliceTimingSparse:
     selectors:
     - modality == "MRI"
-    # NOTE: This is my idea for "field is defined", but I don't know if it's the best approach.
-    - sidecar.DelayTime != "n/a"
+    - sidecar.DelayTime isDefined
     fields:
         SliceTiming: REQUIRED
 
@@ -181,7 +180,7 @@ MRIRFandContrast:
 MRIFlipAngleLookLocker:
     selectors:
     - modality == "MRI"
-    - sidecar.LookLocker == "true"
+    - sidecar.LookLocker == True
     fields:
         FlipAngle: REQUIRED
 
@@ -233,25 +232,25 @@ MRIAnatomyCommonMetadataFields:
 
 EntitiesTaskMetadata:
     selectors:
-    - entities.task != "n/a"
+    - entities.task isDefined
     fields:
         TaskName: RECOMMENDED
 
 EntitiesCeMetadata:
     selectors:
-    - entities.ce != "n/a"
+    - entities.ce isDefined
     fields:
         ContrastBolusIngredient: OPTIONAL
 
 EntitiesTrcMetadata:
     selectors:
-    - entities.trc != "n/a"
+    - entities.trc isDefined
     fields:
         TracerName: REQUIRED
 
 EntitiesStainMetadata:
     selectors:
-    - entities.stain != "n/a"
+    - entities.stain isDefined
     fields:
         SampleStaining: RECOMMENDED
         SamplePrimaryAntibodies: RECOMMENDED
@@ -259,25 +258,25 @@ EntitiesStainMetadata:
 
 EntitiesEchoMetadata:
     selectors:
-    - entities.echo != "n/a"
+    - entities.echo isDefined
     fields:
         EchoTime: REQUIRED
 
 EntitiesFlipMetadata:
     selectors:
-    - entities.flip != "n/a"
+    - entities.flip isDefined
     fields:
         FlipAngle: REQUIRED
 
 EntitiesInvMetadata:
     selectors:
-    - entities.inv != "n/a"
+    - entities.inv isDefined
     fields:
         InversionTime: REQUIRED
 
 EntitiesMTMetadata:
     selectors:
-    - entities.mt != "n/a"
+    - entities.mt isDefined
     fields:
         MTState: REQUIRED
 
@@ -285,17 +284,19 @@ EntitiesPartMetadata:
     selectors:
     - entities.part == "phase"
     fields:
-        # Can we require Units to be either "rad" or "arbitrary" here?
-        Units: REQUIRED
+        Units:
+            level: REQUIRED
+            rules:
+            - value in ["rad", "arbitrary"]
 
 EntitiesResMetadata:
     selectors:
-    - entities.res != "n/a"
+    - entities.res isDefined
     fields:
         Resolution: REQUIRED
 
 EntitiesDenMetadata:
     selectors:
-    - entities.den != "n/a"
+    - entities.den isDefined
     fields:
         Density: REQUIRED

From 629a33f618615e617a8c06bb0421657315599c9a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 6 Mar 2022 14:10:47 +0100
Subject: [PATCH 212/347] add example and autolint

---
 BIDS_logo/favicon_package_v0.16.zip | Bin 0 -> 56397 bytes
 macros_doc.md                       |  30 +++++++++++++++-------------
 2 files changed, 16 insertions(+), 14 deletions(-)
 create mode 100644 BIDS_logo/favicon_package_v0.16.zip

diff --git a/BIDS_logo/favicon_package_v0.16.zip b/BIDS_logo/favicon_package_v0.16.zip
new file mode 100644
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GIT binary patch
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zE>LTpS9WeLPBuLJq5?i>{G+l88-R6{a%So2Ljb_Iw~qw?{P)*C^S?mzhZMv_=~Dp!
zy=ajAjUS3WqLaG^6kW8%FU;qI#$UWQ|9{>;y3Gd;i@Y!afDdSp{*4!31n}3O&kyq9
z2mM9+XVCvQa^v-k0$&gS02b&-Q2rlU40Iq$LWjfv0C!7>r5lvzHPqSJ#+t{&(u&vJ
z%T`|x9f^OV_)jEqC!E^!i2#5DdH{gnZ;GuI|5D70o~!;-!esj1>uR*NO0+<dziCD4
zp|wIiY<RtGteh;Jp%5E)kN<@APhjOj{i_5_0e~Ph{@x)@_5VkQ5at)~LF2Co|C<i+
zKg;(1xx@L@qxt{WB0hA0|4rNdVgCEd<{!-eXuFRSfd6fs^PkcFeL?Zhf|DozYPWx0
YUi>Rsv>7;h!$*I7(N{~yk3awZ3)hq!O8@`>

literal 0
HcmV?d00001

diff --git a/macros_doc.md b/macros_doc.md
index 08892cc4b7..b130b961cd 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -6,8 +6,10 @@ Macros make it easy to achieve a consistent style throughout the specification,
 and changing a given macro will automatically change all appropriate paragraphs
 in the specification.
 
-Below you will find answers to frequently asked questions regarding using macros in the BIDS specification.
+Below you will find answers to frequently asked questions regarding using macros
+in the BIDS specification.
 
+- [Using MkDocs macros in the BIDS specification](#using-mkdocs-macros-in-the-bids-specification)
    - [What are macros and why use them?](#what-are-macros-and-why-use-them)
    - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros)
    - [What macros are available?](#what-macros-are-available)
@@ -78,16 +80,16 @@ consistency.
 All the macros we use are in listed in this
 [python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
 
-| Name                    | Purpose                                                                                | Uses schema | Example |
-| ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ------- |
-| make_columns_table      | Generate a markdown table of TSV column information.                                   | Yes         |         |
-| make_entity_table       | Generate an entity table from the schema, based on specific filters.                   | Yes         |         |
-| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes         |         |
-| make_filename_template  | Generate a filename template from the schema, based on specific filters.               | Yes         |         |
-| make_filetree_example   | Generate a filetree snippet from example content.                                      | No          |         |
-| make_glossary           |                                                                                        | Yes         |         |
-| make_metadata_table     | Generate a markdown table of metadata field information.                               | Yes         |         |
-| make_suffix_table       | Generate a markdown table of suffix information.                                       | Yes         |         |
+| Name                    | Purpose                                                                                | Uses schema | Example                                                                                                                                                                                     |
+| ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| make_columns_table      | Generate a markdown table of TSV column information.                                   | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/03-modality-agnostic-files.md?plain=1#L202)                                    |
+| make_entity_table       | Generate an entity table from the schema, based on specific filters.                   | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/04-entity-table.md?plain=1#L23)                                  |
+| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/09-entities.md?plain=1#L16)                                      |
+| make_filename_template  | Generate a filename template from the schema, based on specific filters.               | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/04-modality-specific-files/10-microscopy.md?plain=1#L21)                       |
+| make_filetree_example   | Generate a filetree snippet from example content.                                      | No          | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L268)                                          |
+| make_glossary           |                                                                                        | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/14-glossary.md?plain=1#L9)                                       |
+| make_metadata_table     | Generate a markdown table of metadata field information.                               | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L462)                                          |
+| make_suffix_table       | Generate a markdown table of suffix information.                                       | Yes         | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md?plain=1#L199) |
 
 ## When should I use a macro?
 
@@ -329,9 +331,9 @@ is wrong.
 
 #### Should I create a macro if I need a new kind of table?
 
-As a rule of thumb, no, unless it is clear that this kind of table will reappear many times in the
-future in the specification. But this is usually hard to predict so better start
-with a table in Markdown.
+As a rule of thumb, no, unless it is clear that this kind of table will reappear
+many times in the future in the specification. But this is usually hard to
+predict so better start with a table in Markdown.
 
 If later we see that the same type of table keeps reoccuring the specification
 we could create a macro to generate them.

From ba11771e76978264445cfc35d52eda14d1ca30fc Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Fri, 11 Mar 2022 15:04:00 +0000
Subject: [PATCH 213/347] [DOC] Auto-generate changelog entry for PR #1019

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 607ebec60b..6c091b94c4 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MISC] clarify copyright for logo [#1019](https://github.com/bids-standard/bids-specification/pull/1019) ([sappelhoff](https://github.com/sappelhoff))
 -   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
 -   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
 

From 576e93184637c69bcb9c433944bd06a092a8c490 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 17 Mar 2022 15:28:34 -0400
Subject: [PATCH 214/347] Address review.

---
 src/schema/rules/sidecars.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars.yml
index 459e992d14..e321c6a9f8 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars.yml
@@ -64,7 +64,7 @@ MRISequenceSpecifics:
 PETMRISequenceSpecifics:
     selectors:
     - modality == "MRI"
-    - PET in dataset.modalities
+    - dataset.modalities contains "PET"
     fields:
         NonLinearGradientCorrection: REQUIRED
 
@@ -164,7 +164,7 @@ SliceTimingASL:
 SliceTimingSparse:
     selectors:
     - modality == "MRI"
-    - sidecar.DelayTime isDefined
+    - sidecar contains "DelayTime"
     fields:
         SliceTiming: REQUIRED
 
@@ -232,25 +232,25 @@ MRIAnatomyCommonMetadataFields:
 
 EntitiesTaskMetadata:
     selectors:
-    - entities.task isDefined
+    - entities contains "task"
     fields:
         TaskName: RECOMMENDED
 
 EntitiesCeMetadata:
     selectors:
-    - entities.ce isDefined
+    - entities contains "ce"
     fields:
         ContrastBolusIngredient: OPTIONAL
 
 EntitiesTrcMetadata:
     selectors:
-    - entities.trc isDefined
+    - entities contains "trc"
     fields:
         TracerName: REQUIRED
 
 EntitiesStainMetadata:
     selectors:
-    - entities.stain isDefined
+    - entities contains "stain"
     fields:
         SampleStaining: RECOMMENDED
         SamplePrimaryAntibodies: RECOMMENDED
@@ -258,25 +258,25 @@ EntitiesStainMetadata:
 
 EntitiesEchoMetadata:
     selectors:
-    - entities.echo isDefined
+    - entities contains "echo"
     fields:
         EchoTime: REQUIRED
 
 EntitiesFlipMetadata:
     selectors:
-    - entities.flip isDefined
+    - entities contains "flip"
     fields:
         FlipAngle: REQUIRED
 
 EntitiesInvMetadata:
     selectors:
-    - entities.inv isDefined
+    - entities contains "inv"
     fields:
         InversionTime: REQUIRED
 
 EntitiesMTMetadata:
     selectors:
-    - entities.mt isDefined
+    - entities contains "mt"
     fields:
         MTState: REQUIRED
 
@@ -291,12 +291,12 @@ EntitiesPartMetadata:
 
 EntitiesResMetadata:
     selectors:
-    - entities.res isDefined
+    - entities contains "res"
     fields:
         Resolution: REQUIRED
 
 EntitiesDenMetadata:
     selectors:
-    - entities.den isDefined
+    - entities contains "den"
     fields:
         Density: REQUIRED

From b6e7312dff40756d20576f4597d2262b7ebb5b6f Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Thu, 17 Mar 2022 15:51:02 -0400
Subject: [PATCH 215/347] Added more tests

---
 .../schemacode/tests/test_render.py           | 108 +++++++++++++++++-
 1 file changed, 102 insertions(+), 6 deletions(-)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index 01f78a1d4e..73e798b995 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -1,5 +1,6 @@
 """Tests for the schemacode package."""
 import os
+import re
 
 import pytest
 
@@ -8,12 +9,26 @@
 
 def test_make_entity_definitions(schema_obj):
     schema_text = render.make_entity_definitions(schema_obj)
-    assert "Format: `sub-<label>`" in schema_text
-    assert "Format: `ses-<label>`" in schema_text
-    assert "Format: `sample-<label>`" in schema_text
-    assert "Format: `task-<label>`" in schema_text
-    assert "Format: `acq-<label>`" in schema_text
-    assert "Format: `ce-<label>`" in schema_text
+    expected_formats = [
+        "Format: `sub-<label>`",
+        "Format: `ses-<label>`",
+        "Format: `sample-<label>`",
+        "Format: `task-<label>`",
+        "Format: `acq-<label>`",
+        "Format: `ce-<label>`",
+        "Format: `trc-<label>`",
+        "Format: `stain-<label>`",
+        "Format: `rec-<label>`",
+        "Format: `dir-<label>`",
+        "Format: `run-<index>`",
+        "Format: `mod-<label>`",
+        "Format: `echo-<index>`",
+        "Format: `flip-<index>`",
+        "Format: `inv-<index>`",
+        "Format: `mt-<label>`",
+        ]
+    for expected_format in expected_formats:
+        assert expected_format in schema_text
 
 
 def test_make_glossary(schema_obj, schema_dir):
@@ -38,6 +53,7 @@ def test_make_glossary(schema_obj, schema_dir):
         if line.startswith('<a name="objects.'):
             # Are all objects objects?
             assert any([line.startswith(f'<a name="objects.{i}') for i in object_files])
+            # Are rules loaded incorrectly?
             assert not any([line.startswith(f'<a name="objects.{i}') for i in rules_only])
 
 
@@ -75,3 +91,83 @@ def test_make_filename_template(schema_obj, schema_dir):
             datatype_bases_found += 1
     # Are all datatypes listed?
     assert datatype_bases_found == datatype_count
+
+def test_make_entity_table(schema_obj):
+    entity_table = render.make_entity_table(schema_obj)
+
+    # Non-exhaustive list covering both value and index formats
+    expected_entities = [
+            "[`acq-<label>`](09-entities.md#acq)",
+            "[`ses-<label>`](09-entities.md#ses)",
+            "[`sample-<label>`](09-entities.md#sample)",
+            "[`task-<label>`](09-entities.md#task)",
+            "[`acq-<label>`](09-entities.md#acq)",
+            "[`ce-<label>`](09-entities.md#ce)",
+            "[`trc-<label>`](09-entities.md#trc)",
+            "[`stain-<label>`](09-entities.md#stain)",
+            "[`rec-<label>`](09-entities.md#rec)",
+            "[`dir-<label>`](09-entities.md#dir)",
+            "[`run-<index>`](09-entities.md#run)",
+            ]
+
+    for expected_entity in expected_entities:
+        assert expected_entity in entity_table
+
+def test_make_suffix_table(schema_obj):
+    target_suffixes = [
+            "beh",
+            "cbv",
+            "dwi",
+            ]
+    suffix_table = render.make_suffix_table(schema_obj, target_suffixes)
+
+    expected_names = [
+            "Behavioral recording",
+            "Cerebral blood volume image",
+            "Diffusion-weighted image",
+            ]
+
+    for expected_name in expected_names:
+        assert expected_name in suffix_table
+
+def test_make_metadata_table(schema_obj):
+    target_metadata = {
+            "Authors":"required",
+            "BIDSVersion":"required",
+            "DatasetDOI":"optional",
+            }
+    metadata_table = render.make_metadata_table(schema_obj, target_metadata).split("\n")
+
+    metadata_tracking = list(target_metadata.keys())
+
+    for line in metadata_table:
+        for i in metadata_tracking:
+            if i in line:
+                # Is the requirement level displayed correctly?
+                assert target_metadata[i] in line
+                # Mark found
+                metadata_tracking.remove(i)
+
+    # Have we found all fields?
+    assert len(metadata_tracking) == 0
+
+def test_make_columns_table(schema_obj):
+    target_columns = {
+            "time":"required",
+            "trial_type":"required",
+            "units":"optional",
+            }
+    columns_table = render.make_columns_table(schema_obj, target_columns).split("\n")
+
+    columns_tracking = list(target_columns.keys())
+
+    for line in columns_table:
+        for i in columns_tracking:
+            if i in line:
+                # Is the requirement level displayed correctly?
+                assert target_columns[i] in line
+                # Mark found
+                columns_tracking.remove(i)
+
+    # Have we found all fields?
+    assert len(columns_tracking) == 0

From ce191223ea2e7e13eafe0ab6c45e22b5e8f54e99 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Thu, 17 Mar 2022 15:51:15 -0400
Subject: [PATCH 216/347] Black compliance

---
 .../schemacode/tests/test_render.py           | 62 ++++++++++---------
 1 file changed, 33 insertions(+), 29 deletions(-)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index 73e798b995..b5a4484a26 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -26,7 +26,7 @@ def test_make_entity_definitions(schema_obj):
         "Format: `flip-<index>`",
         "Format: `inv-<index>`",
         "Format: `mt-<label>`",
-        ]
+    ]
     for expected_format in expected_formats:
         assert expected_format in schema_text
 
@@ -92,50 +92,53 @@ def test_make_filename_template(schema_obj, schema_dir):
     # Are all datatypes listed?
     assert datatype_bases_found == datatype_count
 
+
 def test_make_entity_table(schema_obj):
     entity_table = render.make_entity_table(schema_obj)
 
     # Non-exhaustive list covering both value and index formats
     expected_entities = [
-            "[`acq-<label>`](09-entities.md#acq)",
-            "[`ses-<label>`](09-entities.md#ses)",
-            "[`sample-<label>`](09-entities.md#sample)",
-            "[`task-<label>`](09-entities.md#task)",
-            "[`acq-<label>`](09-entities.md#acq)",
-            "[`ce-<label>`](09-entities.md#ce)",
-            "[`trc-<label>`](09-entities.md#trc)",
-            "[`stain-<label>`](09-entities.md#stain)",
-            "[`rec-<label>`](09-entities.md#rec)",
-            "[`dir-<label>`](09-entities.md#dir)",
-            "[`run-<index>`](09-entities.md#run)",
-            ]
+        "[`acq-<label>`](09-entities.md#acq)",
+        "[`ses-<label>`](09-entities.md#ses)",
+        "[`sample-<label>`](09-entities.md#sample)",
+        "[`task-<label>`](09-entities.md#task)",
+        "[`acq-<label>`](09-entities.md#acq)",
+        "[`ce-<label>`](09-entities.md#ce)",
+        "[`trc-<label>`](09-entities.md#trc)",
+        "[`stain-<label>`](09-entities.md#stain)",
+        "[`rec-<label>`](09-entities.md#rec)",
+        "[`dir-<label>`](09-entities.md#dir)",
+        "[`run-<index>`](09-entities.md#run)",
+    ]
 
     for expected_entity in expected_entities:
         assert expected_entity in entity_table
 
+
 def test_make_suffix_table(schema_obj):
     target_suffixes = [
-            "beh",
-            "cbv",
-            "dwi",
-            ]
+        "beh",
+        "cbv",
+        "dwi",
+    ]
     suffix_table = render.make_suffix_table(schema_obj, target_suffixes)
 
     expected_names = [
-            "Behavioral recording",
-            "Cerebral blood volume image",
-            "Diffusion-weighted image",
-            ]
+        "Behavioral recording",
+        "Cerebral blood volume image",
+        "Diffusion-weighted image",
+    ]
 
     for expected_name in expected_names:
         assert expected_name in suffix_table
 
+
 def test_make_metadata_table(schema_obj):
     target_metadata = {
-            "Authors":"required",
-            "BIDSVersion":"required",
-            "DatasetDOI":"optional",
-            }
+        "Authors": "required",
+        "BIDSVersion": "required",
+        "DatasetDOI": "optional",
+    }
     metadata_table = render.make_metadata_table(schema_obj, target_metadata).split("\n")
 
     metadata_tracking = list(target_metadata.keys())
@@ -151,12 +154,13 @@ def test_make_metadata_table(schema_obj):
     # Have we found all fields?
     assert len(metadata_tracking) == 0
 
+
 def test_make_columns_table(schema_obj):
     target_columns = {
-            "time":"required",
-            "trial_type":"required",
-            "units":"optional",
-            }
+        "time": "required",
+        "trial_type": "required",
+        "units": "optional",
+    }
     columns_table = render.make_columns_table(schema_obj, target_columns).split("\n")
 
     columns_tracking = list(target_columns.keys())

From 43cd22d14343d9ac20bb12345220f4dc4e08c4ef Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Thu, 17 Mar 2022 15:53:23 -0400
Subject: [PATCH 217/347] Lint fixes

---
 tools/schemacode/schemacode/tests/test_render.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index b5a4484a26..009a1df050 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -1,8 +1,5 @@
 """Tests for the schemacode package."""
 import os
-import re
-
-import pytest
 
 from schemacode import render
 
@@ -45,7 +42,6 @@ def test_make_glossary(schema_obj, schema_dir):
             for rule_file in files:
                 rule_base, _ = os.path.splitext(rule_file)
                 rule_files.append(rule_base)
-    objects_only = list(filter(lambda a: a not in rule_files, object_files))
     rules_only = list(filter(lambda a: a not in object_files, rule_files))
 
     glossary = render.make_glossary(schema_obj)

From a7592c19218be741d855a3905c0332717969da67 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Mon, 21 Mar 2022 23:34:38 -0400
Subject: [PATCH 218/347] Added docstrings

---
 .../schemacode/tests/test_render.py           | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index 009a1df050..1a05e5b188 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -5,6 +5,10 @@
 
 
 def test_make_entity_definitions(schema_obj):
+    """
+    Test whether expected format strings are present.
+    This should be stable with respect to schema format.
+    """
     schema_text = render.make_entity_definitions(schema_obj)
     expected_formats = [
         "Format: `sub-<label>`",
@@ -29,6 +33,11 @@ def test_make_entity_definitions(schema_obj):
 
 
 def test_make_glossary(schema_obj, schema_dir):
+    """
+    Test whether files under the schema objects subdirectory correspond to entries, and
+    that rules are not mis-loaded as objects.
+    This may need to be updated for schema hierarchy changes.
+    """
     # Test consistency
     object_files = []
     for root, dirs, files in os.walk(schema_dir, topdown=False):
@@ -54,6 +63,15 @@ def test_make_glossary(schema_obj, schema_dir):
 
 
 def test_make_filename_template(schema_obj, schema_dir):
+    """
+    Test whether:
+        * the base hierarchy structure of mandatory subject and optional session is
+        returned. This should be robust with respect to schema format.
+        * each directory contains at least one possible pattern.
+        This should be robust with respect to schema format.
+        * all files under the datatype rules subdirectory have corresponding entries.
+        This may need to be updated for schema hierarchy changes.
+    """
     filename_template = render.make_filename_template(schema_obj)
 
     # Test predefined substrings
@@ -90,6 +108,10 @@ def test_make_filename_template(schema_obj, schema_dir):
 
 
 def test_make_entity_table(schema_obj):
+    """
+    Test whether expected entities are present and listed correctly.
+    This should be robust with respect to schema format.
+    """
     entity_table = render.make_entity_table(schema_obj)
 
     # Non-exhaustive list covering both value and index formats
@@ -112,6 +134,11 @@ def test_make_entity_table(schema_obj):
 
 
 def test_make_suffix_table(schema_obj):
+    """
+    Test whether expected suffixes are present and listed with correct names.
+    Values are hard-coded from the present YAML, but should nevertheless be robust
+    with respect to schema format, other than case changes for the names.
+    """
     target_suffixes = [
         "beh",
         "cbv",
@@ -130,6 +157,11 @@ def test_make_suffix_table(schema_obj):
 
 
 def test_make_metadata_table(schema_obj):
+    """
+    Test whether expected metadata fields are present and the requirement level is
+    applied correctly.
+    This should be robust with respect to schema format.
+    """
     target_metadata = {
         "Authors": "required",
         "BIDSVersion": "required",
@@ -152,6 +184,11 @@ def test_make_metadata_table(schema_obj):
 
 
 def test_make_columns_table(schema_obj):
+    """
+    Test whether expected columns are present and the requirement level is applied
+    correctly.
+    This should be robust with respect to schema format.
+    """
     target_columns = {
         "time": "required",
         "trial_type": "required",

From 88a9730d566b5a82ee6ab89546220914e3f303a0 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Tue, 22 Mar 2022 17:34:34 +0000
Subject: [PATCH 219/347] [DOC] Auto-generate changelog entry for PR #963

---
 src/CHANGES.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 6c091b94c4..321b6c8ba5 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -5,6 +5,7 @@
 -   \[MISC] clarify copyright for logo [#1019](https://github.com/bids-standard/bids-specification/pull/1019) ([sappelhoff](https://github.com/sappelhoff))
 -   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
 -   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
+-   \[DOC] add documentation for macros [#963](https://github.com/bids-standard/bids-specification/pull/963) ([Remi-Gau](https://github.com/Remi-Gau))
 
 ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
 
@@ -423,7 +424,7 @@
 -   \[FIX] update HED appendix [#74](https://github.com/bids-standard/bids-specification/pull/74) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] unicode: replace greek mu and omega by micro and ohm signs [#73](https://github.com/bids-standard/bids-specification/pull/73) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Update 01-contributors.md [#72](https://github.com/bids-standard/bids-specification/pull/72) ([francopestilli](https://github.com/francopestilli))
--   \[ENH] add ce-\<label> for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge))
+-   \[ENH] add `ce-\<label\>` for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge))
 -   \[INFRA] pin pip version [#68](https://github.com/bids-standard/bids-specification/pull/68) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Fix link in index [#46](https://github.com/bids-standard/bids-specification/pull/46) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([Park-Patrick](https://github.com/Park-Patrick))

From 9dbab0e067c1778698e7709b9d782a522dff856e Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 24 Mar 2022 15:46:10 -0400
Subject: [PATCH 220/347] [SCHEMA] Add patterns for format validation (#885)

* Draft formats file.

* Limit time zones to between 3 and 4 characters.

* Add stimuli_relative format.

* Don't allow absolute paths or problematic start folders.

* Use URI regex.

From https://datatracker.ietf.org/doc/html/rfc3986#appendix-B.

* Fix(?) BIDS URI regex.

* Update formats.yaml

* Don't allow just zeros in index regex.

* pattern --> format.

* Document the rules for the different formats.

* Remove fancy n/a handling.

I was so proud of it too :sob:

* Move formats file into rules folder.

* Actually, the individual formats are really objects.

* Add patterns for rrid and time.

* Be more specific with RRIDs.

* Remove anchors around patterns and add quotes.

* Replace double-quotes with single-quotes.

* Draft a test for formats.

* Add names for tests. They probably won't ever be used.

* Add more valid pattern tests.

* Fix mistake in date/datetime patterns.

* Make time part of datetimes more restrictive.

* Make datetimes more robust.

* Add more bad-pattern checks.

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Test the new pattern changes.

* Apply suggestions from code review

Thanks for the suggestions @yarikoptic. They're great!

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Reorder formats alphabetically within each section.

* Run black on test and improve check.

* Comment out failing pattern, but add a note about it.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/schema/objects/formats.yaml               | 115 ++++++++++++++++++
 src/schema/objects/metadata.yaml              |   8 +-
 .../schemacode/tests/test_schema.py           | 108 ++++++++++++++++
 3 files changed, 227 insertions(+), 4 deletions(-)
 create mode 100644 src/schema/objects/formats.yaml

diff --git a/src/schema/objects/formats.yaml b/src/schema/objects/formats.yaml
new file mode 100644
index 0000000000..dab370d2c7
--- /dev/null
+++ b/src/schema/objects/formats.yaml
@@ -0,0 +1,115 @@
+---
+# This file defines valid patterns for different formats
+# Entity patterns
+index:
+  name: Index
+  description: |
+    Non-negative, non-zero integers, optionally prefixed with leading zeros for sortability.
+    An index may not be all zeros.
+  pattern: '[0-9]*[1-9]+[0-9]*'
+label:
+  name: Label
+  description: |
+    Freeform labels without special characters.
+  pattern: '[0-9a-zA-Z]+'
+# Metadata types
+boolean:
+  name: Boolean
+  description: |
+    A boolean.
+    Must be either "true" or "false".
+  pattern: '(true|false)'
+integer:
+  name: Integer
+  description: |
+    An integer which may be positive or negative.
+  pattern: '[+-]?\d+'
+number:
+  name: Number
+  description: |
+    A number which may be an integer or float, positive or negative.
+  pattern: '[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)([eE][+-]?[0-9]+)?'
+string:
+  name: String
+  description: |
+    The basic string type (not a specific format).
+    This should allow any free-form string.
+  pattern: '.*'
+# String formats
+bids_uri:
+  name: BIDS uniform resource indicator
+  description: |
+    A BIDS uniform resource indicator.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid URI,
+    starting with "bids:".
+  pattern: 'bids:[0-9a-zA-Z/#:\?\_\-\.]+'
+dataset_relative:
+  name: Path relative to the BIDS dataset folder
+  description: |
+    A path to a file, relative to the dataset folder.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path).
+  pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
+date:
+  name: Date
+  description: |
+    A date in the form `"YYYY-MM-DD[Z]"`,
+    where [Z] is an optional, valid timezone code.
+  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}([A-Z]{2,4})?'
+datetime:
+  name: Datetime
+  description: |
+    A datetime in the form `"YYYY-MM-DDThh:mm:ss[.000000][Z]"`,
+    where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
+    and [Z] is an optional, valid timezone code.
+  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?'
+participant_relative:
+  name: Path relative to the participant folder
+  description: |
+    A path to a file, relative to the participant's folder in the dataset.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path) or "sub/"
+    (a relative path starting with the participant folder, rather than relative to that folder).
+  pattern: '(?!/)(?!sub-)[0-9a-zA-Z/\_\-\.]+'
+rrid:
+  name: Research resource identifier
+  description: |
+    A [research resource identifier](https://scicrunch.org/resources).
+  pattern: 'RRID:.+_.+'
+stimuli_relative:
+  name: Path relative to the stimuli folder
+  description: |
+    A path to a stimulus file, relative to a `/stimuli` folder somewhere.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path) or "stimuli/"
+    (a relative path starting with the stimuli folder, rather than relative to that folder).
+  pattern: '(?!/)(?!stimuli/)[0-9a-zA-Z/\_\-\.]+'
+time:
+  name: Time
+  description: |
+    A time in the form `"hh:mm:ss"`.
+  pattern: '(?:2[0-3]|[01]?[0-9]):[0-5][0-9]:[0-5][0-9]'
+unit:
+  name: A standardized unit
+  description: |
+    A unit.
+    SI units in CMIXF formatting are RECOMMENDED
+    (see [Units](/02-common-principles.html#units)).
+
+    Currently this matches any string.
+
+    TODO: Somehow reference the actual unit options in the Units appendix.
+  pattern: '.*'
+uri:
+  name: Uniform resource indicator
+  description: |
+    A uniform resource indicator.
+  pattern: '(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?'
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 8a010bb03e..aca8e8ad0a 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -1686,7 +1686,7 @@ MolarActivityMeasTime:
     Time to which molar radioactivity measurement above applies in the default
     unit `"hh:mm:ss"`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 MolarActivityUnits:
   name: MolarActivityUnits
   description: |
@@ -2449,7 +2449,7 @@ SoftwareRRID:
     Examples: The RRID for Psychtoolbox is 'SCR_002881',
     and that of PsychoPy is 'SCR_006571'.
   type: string
-  pattern: .+_.+
+  format: rrid
 SoftwareVersion:
   name: SoftwareVersion
   description: |
@@ -2537,7 +2537,7 @@ SpecificRadioactivityMeasTime:
     Time to which specific radioactivity measurement above applies in the default
     unit `"hh:mm:ss"`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 SpecificRadioactivityUnits:
   name: SpecificRadioactivityUnits
   description: |
@@ -2656,7 +2656,7 @@ TimeZero:
     in the unit "hh:mm:ss".
     This should be equal to `"InjectionStart"` or `"ScanStart"`.
   type: string
-  pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+  format: time
 TissueDeformationScaling:
   name: TissueDeformationScaling
   description: |
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
index 5d1400a778..9e169d0f1c 100644
--- a/tools/schemacode/schemacode/tests/test_schema.py
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -27,3 +27,111 @@ def test_object_definitions(schema_obj):
 
             assert "name" in obj_def.keys(), obj_key
             assert "description" in obj_def.keys(), obj_key
+
+
+def test_formats(schema_obj):
+    """Test valid string patterns allowed by the specification."""
+    import re
+
+    # Check that valid strings match the search pattern.
+    GOOD_PATTERNS = {
+        "label": ["01", "test", "test01", "Test01"],
+        "index": ["01", "1", "10000", "00001"],
+        "string": ["any string is valid."],
+        "integer": ["5", "10", "-5", "-10"],
+        "number": [
+            "5",  # integers are allowed
+            "3.14",  # floats too
+            "-5",  # they can be negative
+            "-3.14",
+            "1e3",  # scientific notation is allowed
+            "-2.1E+5",
+        ],
+        "boolean": ["true", "false"],
+        "date": ["2022-01-05", "2022-01-05UTC", "2022-50-50"],
+        "datetime": [
+            "2022-01-05T13:16:30",
+            "2022-01-05T13:16:30.5",  # subsecond resolution is allowed
+            "2022-01-05T13:16:30.000005",  # up to 6 decimal points
+            "2022-01-05T13:16:30UTC",  # timezones are allowed
+            "2022-01-05T13:16:30.05UTC",
+        ],
+        "time": [
+            "13:16:30",
+            "09:00:00",
+            "9:00:00",  # leading zeros are not required for hours
+        ],
+        "unit": ["any string is valid."],
+        "stimuli_relative": ["any/arbitrary/path/file.txt"],
+        "dataset_relative": ["any/arbitrary/path/file.txt"],
+        "participant_relative": ["any/arbitrary/path/file.txt"],
+        "rrid": ["RRID:SCR_017398"],
+        "uri": ["foo://example.com:8042/over/there?name=ferret#nose"],
+        "bids_uri": [
+            "bids::sub-01/fmap/sub-01_dir-AP_epi.nii.gz",
+            "bids:ds000001:sub-02/anat/sub-02_T1w.nii.gz",
+            "bids:myderivatives:sub-03/func/sub-03_task-rest_space-MNI152_bold.nii.gz",
+        ],
+    }
+    for pattern, test_list in GOOD_PATTERNS.items():
+        pattern_format = schema_obj["objects"]["formats"][pattern]["pattern"]
+        search_pattern = "^" + pattern_format + "$"
+        search = re.compile(search_pattern)
+        for test_string in test_list:
+            assert bool(
+                search.fullmatch(test_string)
+            ), f"'{test_string}' is not a valid match for the pattern '{search.pattern}'"
+
+    # Check that invalid strings do not match the search pattern.
+    BAD_PATTERNS = {
+        "label": ["test_01", "!", "010101-", "01-01", "-01"],
+        "index": ["test", "0.1", "0-1", "0_1"],
+        "string": [],
+        "integer": ["3.14", "-3.14", "1.", "-1.", "string", "s1", "1%", "one"],
+        "number": ["string", "1%"],
+        "boolean": ["True", "False", "T", "F"],
+        "date": [
+            "05-01-2022",  # MM-DD-YYYY or DD-MM-YYYY
+            "05/01/2022",  # MM/DD/YYYY or DD/MM/YYYY
+        ],
+        "datetime": [
+            "2022-01-05T13:16:30.1000005",  # too many decimal points
+            "2022-01-05T13:16:30U",  # time zone too short
+            "2022-01-05T13:16:30UTCUTC",  # time zone too long
+            "2022-01-05T34:10:10",  # invalid time
+        ],
+        "time": [
+            "34:10:10",  # invalid time
+            "24:00:00",  # should be 00:00:00
+            "00:60:00",  # should be 01:00:00
+            "00:00:60",  # should be 00:01:00
+            "01:23",  # lacks either hours or seconds
+        ],
+        "unit": [],
+        "stimuli_relative": [
+            "/path/with/starting/slash/file.txt",
+            "stimuli/path/file.txt",
+        ],
+        "dataset_relative": [
+            "/path/with/starting/slash/file.txt",
+        ],
+        "participant_relative": [
+            "/path/with/starting/slash/file.txt",
+            "sub-01/path/file.txt",
+        ],
+        "rrid": [
+            "RRID:",  # empty one
+        ],
+        "uri": [
+            # "ftp://",  # lacks anything but protocol. This should fail, but doesn't ATM.
+        ],
+        "bids_uri": [],
+    }
+    for pattern, test_list in BAD_PATTERNS.items():
+        pattern_format = schema_obj["objects"]["formats"][pattern]["pattern"]
+        search_pattern = f"^{pattern_format}$"
+        search = re.compile(search_pattern)
+        for test_string in test_list:
+            assert not bool(
+                search.fullmatch(test_string)
+            ), f"'{test_string}' should not be a valid match for the pattern '{search.pattern}'"

From 658fa4d964502be41521601e259e0ae78b02549f Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Thu, 24 Mar 2022 20:20:44 +0000
Subject: [PATCH 221/347] [DOC] Auto-generate changelog entry for PR #1018

---
 src/CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 321b6c8ba5..2988478002 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -3,9 +3,11 @@
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
 -   \[MISC] clarify copyright for logo [#1019](https://github.com/bids-standard/bids-specification/pull/1019) ([sappelhoff](https://github.com/sappelhoff))
+-   \[SCHEMA] Tests for render listings [#1018](https://github.com/bids-standard/bids-specification/pull/1018) ([TheChymera](https://github.com/TheChymera))
 -   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
 -   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
 -   \[DOC] add documentation for macros [#963](https://github.com/bids-standard/bids-specification/pull/963) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[SCHEMA] Add patterns for format validation [#885](https://github.com/bids-standard/bids-specification/pull/885) ([tsalo](https://github.com/tsalo))
 
 ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
 

From edcbfabcbafc2cb888ae9278c584ef3888ae4487 Mon Sep 17 00:00:00 2001
From: Erdal Karaca <erdal.karaca.de@gmail.com>
Date: Tue, 29 Mar 2022 10:59:40 +0200
Subject: [PATCH 222/347] Update CODEOWNERS (#1040)

interested in schema related changes
---
 CODEOWNERS | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CODEOWNERS b/CODEOWNERS
index 24cc697363..6fd6504405 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -20,5 +20,5 @@
 /src/99-appendices/06-meg-file-formats.md @monkeyman192
 
 # The schema
-/src/schema/ @tsalo
-/tools/schemacode/ @tsalo
+/src/schema/ @tsalo @erdalkaraca
+/tools/schemacode/ @tsalo @erdalkaraca

From 67c3d90dcb0bd49a81b84b1da05d82f28ed2912c Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Tue, 29 Mar 2022 11:04:20 +0200
Subject: [PATCH 223/347] [MISC] Rewrite and update html build instructions
 (#1032)

* revamp build instructions

* add a note

* Apply suggestions from code review

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* streamline

* Update CONTRIBUTING.md

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* add remis comment on gitignore

* Update CONTRIBUTING.md

Co-authored-by: Mateusz Pawlik <mateusz.pawlik@plus.ac.at>

* add Geohackweek resource on conda

* add info on editable install

* CI: migrate from legacy convenience images

* try pin jinja <3.1

* use venv in new circleci images

* remove jinja pin, this has been fixed upstream

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: Mateusz Pawlik <mateusz.pawlik@plus.ac.at>
---
 .circleci/config.yml | 21 ++++++++----
 CONTRIBUTING.md      | 76 ++++++++++++++++++++++++++++++--------------
 2 files changed, 66 insertions(+), 31 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index db88083e9a..2ac96d2fcb 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,19 +2,23 @@ version: 2
 jobs:
   build_docs:
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.8
     steps:
       # checkout code to default ~/project
       - checkout
       - run:
           name: install dependencies
           command: |
+            python -m venv env
+            source env/bin/activate
             python -m pip install --upgrade pip
             pip install -r requirements.txt
-            pip install ~/project/tools/schemacode/
+            pip install -e ~/project/tools/schemacode/
       - run:
           name: generate docs
-          command: mkdocs build --clean --strict --verbose
+          command: |
+            source env/bin/activate
+            mkdocs build --clean --strict --verbose
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
@@ -25,7 +29,7 @@ jobs:
 
   linkchecker:
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.8
     steps:
       # checkout code to default ~/project
       - checkout
@@ -35,11 +39,14 @@ jobs:
       - run:
           name: install linkchecker
           command: |
-            python -m ensurepip
+            python -m venv env
+            source env/bin/activate
+            python -m pip install --upgrade pip
             python -m pip install linkchecker
       - run:
           name: check links
           command: |
+            source env/bin/activate
             git status
             if (! git log -1 --pretty=oneline | grep REL:) ; then
               chmod a+rX -R ~
@@ -123,7 +130,7 @@ jobs:
   # Run remark on the auto generated changes.md file
   remark:
     docker:
-      - image: node:latest
+      - image: cimg/node:lts
     steps:
       # checkout code to default ~/project
       - checkout
@@ -156,7 +163,7 @@ jobs:
   # Push built changelog to repo
   Changelog-bot:
     docker:
-      - image: circleci/openjdk:8-jdk
+      - image: cimg/base:stable
     steps:
       - setup_remote_docker:
           version: 17.11.0-ce
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index bd49034b93..807f7f345a 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -235,7 +235,34 @@ We have dedicated documentation for [this](./macro_doc.md).
 We are using mkdocs to render our specification.
 Please follow these instructions if you would like to build the specification locally.
 
-#### 1. Install mkdocs, the material theme and the required extensions
+#### 1. Download the BIDS specification [repository](https://github.com/bids-standard/bids-specification/tree/master) onto your computer
+
+This can be done by clicking the green button on the right titled "Clone or
+download"
+or using [this link](https://github.com/bids-standard/bids-specification/archive/master.zip).
+
+Or you can use the following `git` command in a terminal:
+
+```bash
+git clone https://github.com/bids-standard/bids-specification.git
+```
+
+#### 2. In the terminal (command line) navigate to your local version of the specification
+
+This location will have the same files you see on our
+[main specification page](https://github.com/bids-standard/bids-specification).
+Note that a file browser window may not show the hidden files
+(those that start with a period, like `.remarkrc`).
+
+If you cloned the repository using the `git` command above, you can then just do:
+
+```bash
+cd bids-specification
+```
+
+Enter all commands below from the command line prompt located at the root of the local version of the specification.
+
+#### 3. Install mkdocs, the material theme and the required extensions
 
 In the following links, you can find more information about
 
@@ -247,40 +274,41 @@ You will also need several other mkdocs plugins, like `branchcustomization` and
 To install all of this make sure you have a recent version of Python on your computer.
 The [DataLad Handbook](http://handbook.datalad.org/en/latest/intro/installation.html#python-3-all-operating-systems) provides helpful instructions for setting up Python.
 
-An easy way to install the correct version of mkdocs and all the other required extensions
-is to use the `requirements.txt` file contained in this repository,
-by using the following command:
+In general, we strongly recommend that you install all dependencies in an isolated Python environment.
+For example using `conda`, as described in this [Geohackweek tutorial](https://geohackweek.github.io/Introductory/01-conda-tutorial/).
 
 ```bash
-pip install -r requirements.txt
+conda create --name bids-spec
+conda activate bids-spec
 ```
 
-However this will also install some other packages you might not want to have (like `numpy`).
-So if you only want to install what you need to build the specification,
-use the following command:
+Or alternatively using `venv`, as described in this [Real Python tutorial](https://realpython.com/python-virtual-environments-a-primer/).
+
+A short version of the commands needed to create and activate your `venv` virtual environment would look like:
 
 ```bash
-pip install \
- mkdocs \
- mkdocs-material \
- pymdown-extensions \
- mkdocs-branchcustomization-plugin \
- mkdocs-macros-plugin \
- tabulate
+python -m venv env
+source env/bin/activate
 ```
 
-#### 2. Download the BIDS specification [repository](https://github.com/bids-standard/bids-specification/tree/master) onto your computer
+Note that this will create a local directory called `env` within the bids-specification directory
+but that its content will not be tracked by `git` because it is listed in the `.gitignore` file.
 
-This can be done by clicking the green button on the right titled "Clone or
-download"
-or using [this link](https://github.com/bids-standard/bids-specification/archive/master.zip).
+Once you have activated your isolated Python environment,
+an easy way to install the correct version of mkdocs and all the other required extensions
+is to use the `requirements.txt` file contained in this repository as follows:
 
-#### 3. In the terminal (command line) navigate to your local version of the specification
+```bash
+pip install -U pip
+pip install -r requirements.txt
+pip install -e tools/schemacode/
+```
 
-This location will have the same files you see on our
-[main specification page](https://github.com/bids-standard/bids-specification).
-Note: A finder window may not show the hidden files (those that start with a
-period, like `.remarkrc`)
+The first command ensures you are using an up to date version of `pip`,
+and the second command installs all dependencies.
+The third command ensures to install the BIDS schema code as an "editable" install,
+so that if you make changes to the schema files,
+these are automatically reflected in the sourcecode.
 
 #### 4. Ready to build!
 

From edd6b0e3cc5bd0ac2747a74a8533323edca63bf9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 30 Mar 2022 12:41:49 -0400
Subject: [PATCH 224/347] [SCHEMA] Add extensions to schema (#1036)

* Add extensions.

No meaningful names or definitions yet.

* Some more work.

* Update extensions.yaml

* Add more info.

* Missed one.

TBH I have probably missed a lot more than one.

* That's all the ones in the schema.

* Fix.

* Add the last missing one I found in the specification text.

* Fix headshape extension.

* Fix "any extension" definition.

* Add .trg, .chn. and .pos to schema rules.

* Update extensions.yaml

* Improve JSON description.

* Update src/schema/objects/extensions.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Add NIfTI definition.

* Update src/schema/objects/extensions.yaml

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 .gitignore                          |   1 +
 src/schema/objects/extensions.yaml  | 251 ++++++++++++++++++++++++++++
 src/schema/rules/datatypes/meg.yaml |   5 +-
 3 files changed, 256 insertions(+), 1 deletion(-)
 create mode 100644 src/schema/objects/extensions.yaml

diff --git a/.gitignore b/.gitignore
index 6e97a859ac..50f8037199 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@ site/
 .DS_Store
 .idea
 venvs
+.vscode/
 
 pdf_build_src/bids-spec.pdf
 pdf_build_src/bids-spec_pandoc_log.json
diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml
new file mode 100644
index 0000000000..f3d4d0dcf8
--- /dev/null
+++ b/src/schema/objects/extensions.yaml
@@ -0,0 +1,251 @@
+---
+# This file describes valid file extensions in the specification.
+.*:
+  name: Any Extension
+  description: |
+    Any extension is allowed.
+.ave:
+  name: AVE  # not sure what ave stands for
+  description: |
+    File containing data averaged by segments of interest.
+
+    Used by KIT, Yokogawa, and Ricoh MEG systems.
+.bdf:
+  name: Biosemi Data Format
+  description: |
+    A [Biosemi](https://www.biosemi.com/) Data Format file.
+
+    Each recording consists of a single `.bdf` file.
+    [`bdf+`](https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html) files are permitted.
+    The capital `.BDF` extension MUST NOT be used.
+.bval:
+  name: FSL-Format Gradient Amplitudes
+  description: |
+    A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.
+
+    The `bval` file contains the *b*-values (in s/mm<sup>2</sup>) corresponding to the
+    volumes in the relevant NIfTI file, with 0 designating *b*=0 volumes.
+.bvec:
+  name: FSL-Format Gradient Directions
+  description: |
+    A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.
+
+    This file contains 3 rows with *N* space-delimited floating-point numbers,
+    corresponding to the *N* volumes in the corresponding NIfTI file.
+
+    The first row contains the *x* elements, the second row contains the *y* elements and
+    the third row contains the *z* elements of a unit vector in the direction of the applied
+    diffusion gradient, where the *i*-th elements in each row correspond together to
+    the *i*-th volume, with `[0,0,0]` for *non-diffusion-weighted* (also called *b*=0 or *low-b*)
+    volumes.
+
+    Following the FSL format for the `bvec` specification, the coordinate system of
+    the *b* vectors MUST be defined with respect to the coordinate system defined by
+    the header of the corresponding `_dwi` NIfTI file and not the scanner's device
+    coordinate system (see [Coordinate systems](../99-appendices/08-coordinate-systems.md)).
+    The most relevant limitation imposed by this choice is that the gradient information cannot
+    be directly stored in this format if the scanner generates *b*-vectors in *scanner coordinates*.
+.chn:
+  name: KRISS CHN
+  description: |
+    A file generated by KRISS MEG systems containing the position of the center of the MEG coils.
+
+    Each experimental run on the KRISS system produces a file with extension `.kdf`.
+    Additional files that may be available in the same folder include
+    the digitized positions of the head points (`\_digitizer.txt`),
+    the position of the center of the MEG coils (`.chn`),
+    and the event markers (`.trg`).
+.con:
+  name: KIT/Yokogawa/Ricoh Continuous Data
+  description: |
+    Raw continuous data from a KIT/Yokogawa/Ricoh MEG system.
+
+    Successor to the `.sqd` extension for raw continuous data.
+.dat:
+  name: MEG Fine-Calibration Format
+  description: |
+    A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.
+.ds/:
+  name: CTF MEG Dataset Folder
+  description: |
+    A folder for MEG data, typically containing a `.meg4` file for the data and a `.res4` file for the resources.
+.edf:
+  name: European Data Format
+  description: |
+    A [European data format](https://www.edfplus.info/) file.
+
+    Each recording consists of a single `.edf`` file.
+    [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted.
+    The capital `.EDF` extension MUST NOT be used.
+.eeg:
+  name: BrainVision Binary Data
+  description: |
+    A binary data file in the
+    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
+    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
+.fdt:
+  name: EEGLAB FDT
+  description: |
+    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
+
+    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
+    Each recording consists of a `.set` file with an optional `.fdt` file.
+.fif:
+  name: Functional Imaging File Format
+  description: |
+    An MEG file format used by Neuromag, Elekta, and MEGIN.
+.jpg:
+  name: Joint Photographic Experts Group Format
+  description: |
+    A JPEG image file.
+.json:
+  name: JavaScript Object Notation
+  description: |
+    A JSON file.
+
+    In the BIDS specification, JSON files are primarily used as "sidecar" files, in which metadata describing "data"
+    files are encoded.
+    These sidecar files follow the inheritance principle.
+
+    There are also a few special cases of JSON files being first-order data files, such as `genetic_info.json`.
+.kdf:
+  name: KRISS KDF
+  description: |
+    A KRISS (file with extension `.kdf`) file.
+
+    Each experimental run on the KRISS system produces a file with extension `.kdf`.
+    Additional files that may be available in the same folder include
+    the digitized positions of the head points (`\_digitizer.txt`),
+    the position of the center of the MEG coils (`.chn`),
+    and the event markers (`.trg`).
+.md:
+  name: Markdown
+  description: |
+    A Markdown file.
+.mefd/:
+  name: Multiscale Electrophysiology File Format Version 3.0
+  description: |
+    A folder in the [MEF3](https://osf.io/e3sf9/) format.
+
+    Each recording consists of a `.mefd` directory.
+.mhd:
+  name: ITAB Binary Header
+  description: |
+    Produced by ITAB-ARGOS153 systems. This file a binary header file, and is generated along with a
+    raw data file with the `.raw` extension.
+.mrk:
+  name: MRK
+  description: |
+    A file containing MEG sensor coil positions.
+
+    Used by KIT, Yokogawa, and Ricoh MEG systems.
+    Successor to the `.sqd` extension for marker files.
+.nii:
+  name: NIfTI
+  description: |
+    A Neuroimaging Informatics Technology Initiative (NIfTI) data file.
+.nii.gz:
+  name: Compressed NIfTI
+  description: |
+    A compressed Neuroimaging Informatics Technology Initiative (NIfTI) data file.
+.nwb:
+  name: Neurodata Without Borders Format
+  description: |
+    A [Neurodata Without Borders](https://nwb-schema.readthedocs.io) file.
+
+    Each recording consists of a single `.nwb` file.
+.ome.btf:
+  name: Open Microscopy Environment BigTIFF
+  description: |
+    A [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) image file, for very large images.
+.ome.tif:
+  name: Open Microscopy Environment Tag Image File Format
+  description: |
+    An [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#) image file.
+.png:
+  name: Portable Network Graphics
+  description: |
+    A [Portable Network Graphics](http://www.libpng.org/pub/png/) file.
+.pos:
+  name: Head Point Position
+  description: |
+    File containing digitized positions of the head points.
+
+    This may be produced by a 4D neuroimaging/BTi MEG system or a CTF MEG system.
+.raw:
+  name: RAW
+  description: |
+    When produced by a KIT / Yokogawa / Ricoh MEG system, this file contains trial-based evoked fields.
+
+    When produced by an ITAB-ARGOS153 system, this file contains raw data and is generated along with
+    an associated binary header file  with the `.mhd` extension.
+.rst:
+  name: reStructuredText
+  description: |
+    A [reStructuredText](https://docutils.sourceforge.io/rst.html) file.
+.set:
+  name: EEGLAB SET
+  description: |
+    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
+
+    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
+    Each recording consists of a `.set` file with an optional `.fdt` file.
+.sqd:
+  name: SQD
+  description: |
+    A file containing either raw MEG data or MEG sensor coil positions.
+    While this extension is still valid, it has been succeeded by `.con` for raw MEG data and `.mrk` for
+    marker information.
+
+    Used by KIT, Yokogawa, and Ricoh MEG systems.
+.tif:
+  name: Tag Image File Format
+  description: |
+    A [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) file.
+.trg:
+  name: KRISS TRG
+  description: |
+    A file generated by KRISS MEG systems containing the event markers.
+
+    Each experimental run on the KRISS system produces a file with extension `.kdf`.
+    Additional files that may be available in the same folder include
+    the digitized positions of the head points (`\_digitizer.txt`),
+    the position of the center of the MEG coils (`.chn`),
+    and the event markers (`.trg`).
+.tsv:
+  name: Tab-Delimited
+  description: |
+    A tab-delimited file.
+.tsv.gz:
+  name: Compressed Tab-Delimited
+  description: |
+    A gzipped tab-delimited file.
+    This file extension is only used for very large tabular data, such as physiological recordings.
+    For smaller data, the unzipped `.tsv` extension is preferred.
+.txt:
+  name: Text
+  description: |
+    A free-form text file.
+
+    Tab-delimited files should have the `.tsv` extension rather than a `.txt` extension.
+.vhdr:
+  name: BrainVision Text Header
+  description: |
+    A text header file in the
+    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
+    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
+.vmrk:
+  name: BrainVision Marker
+  description: |
+    A text marker file in the
+    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
+    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
+/:
+  name: Folder
+  description: |
+    A folder with no extension.
+    Corresponds to BTi/4D data.
+None:
+  name: No extension
+  description: |
+    A file with no extension.
diff --git a/src/schema/rules/datatypes/meg.yaml b/src/schema/rules/datatypes/meg.yaml
index 104689b7f1..6231204d51 100644
--- a/src/schema/rules/datatypes/meg.yaml
+++ b/src/schema/rules/datatypes/meg.yaml
@@ -15,6 +15,8 @@
   - .mrk
   - .kdf
   - .mhd
+  - .trg
+  - .chn
   entities:
     subject: required
     session: optional
@@ -58,7 +60,8 @@
 - suffixes:
   - headshape
   extensions:
-  - "*"
+  - .*
+  - .pos
   entities:
     subject: required
     session: optional

From 280074a212d1e4b89456252c4127582c2da00a2a Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 31 Mar 2022 14:23:16 -0400
Subject: [PATCH 225/347] ENH: allow for .png and .tif in eeg/ieeg/meg as
 allowed for micr

Discovered while working on https://github.com/bids-standard/bids-specification/issues/1047
---
 src/schema/rules/datatypes/eeg.yaml  | 2 ++
 src/schema/rules/datatypes/ieeg.yaml | 2 ++
 src/schema/rules/datatypes/meg.yaml  | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/src/schema/rules/datatypes/eeg.yaml b/src/schema/rules/datatypes/eeg.yaml
index 6b112e343d..094de8aeac 100644
--- a/src/schema/rules/datatypes/eeg.yaml
+++ b/src/schema/rules/datatypes/eeg.yaml
@@ -66,6 +66,8 @@
   - photo
   extensions:
   - .jpg
+  - .png
+  - .tif
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/ieeg.yaml b/src/schema/rules/datatypes/ieeg.yaml
index 37c02963f5..07355cc825 100644
--- a/src/schema/rules/datatypes/ieeg.yaml
+++ b/src/schema/rules/datatypes/ieeg.yaml
@@ -67,6 +67,8 @@
   - photo
   extensions:
   - .jpg
+  - .png
+  - .tif
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/meg.yaml b/src/schema/rules/datatypes/meg.yaml
index 104689b7f1..0652991a97 100644
--- a/src/schema/rules/datatypes/meg.yaml
+++ b/src/schema/rules/datatypes/meg.yaml
@@ -119,6 +119,8 @@
   - photo
   extensions:
   - .jpg
+  - .png
+  - .tif
   entities:
     subject: required
     session: optional

From 4428fd332100545cf36a8828d665590457797d03 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 31 Mar 2022 14:48:37 -0400
Subject: [PATCH 226/347] [FIX] PET Spec; added known DICOM tags, fixed tag
 error, updated citation, clarified scale factor. (#1021)

* PET citation update

* DICOM tag error fix

* scale factor should be 1 (does it work as 'array')

* added all DICOM tags we know

* Update 09-positron-emission-tomography.md

Added dicom tag description for `InjectionStart`

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Fixed markdown formatting, removed dicom tag desc

- Fixed markdown formatting in src/01-introduction.md
- Removed dicom tag description for InjectionTimeStart in src/04-modality-specific-files/09-positron-emission-tomography.md
  as there is some disagreement on whether dicom tag Radiopharmaceutical Start Time (0018, 1072) should be referenced.

* added back tag to description, dropped reference to timezero

* Update metadata.yaml

Update Scale Factor description to consensus

* removed trailing spaces.

* update text "recommended" to "RECOMMENDED"

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

Co-authored-by: CPernet <wamcyril@gmail.com>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
Co-authored-by: Martin Norgaard <martin.noergaard@nru.dk>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/01-introduction.md                        | 14 ++++++--
 .../09-positron-emission-tomography.md        | 36 +++++++++----------
 src/schema/objects/metadata.yaml              |  6 ++--
 3 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/src/01-introduction.md b/src/01-introduction.md
index 79ce0831d2..507a1fd74c 100644
--- a/src/01-introduction.md
+++ b/src/01-introduction.md
@@ -113,12 +113,22 @@ For example:
 
 #### PET
 
+-   Norgaard, M., Matheson, G.J., Hansen, H.D., Thomas, A., Searle, G., Rizzo, G.,
+    Veronese, M., Giacomel, A., Yaqub, M., Tonietto, M., Funck, T., Gillman, A., Boniface,
+    H., Routier, A., Dalenberg, J.R.., Betthauser, T., Feingold, F., Markiewicz, C.J.,
+    Gorgolewski, K.J., Blair, R.W., Appelhoff, S., Gau, R., Salo, T., Niso, G., Pernet, C.,
+    Phillips, C., Oostenveld, R., Gallezot, J-D., Carson, R.E., Knudsen, G.M.,
+    Innis R.B. & Ganz M. (2021).
+    **PET-BIDS, an extension to the brain imaging data structure for positron emission tomography**.
+    Scientific Data, 9 (65).
+    [doi:10.1038/s41597-022-01164-1](https://doi.org/10.1038/s41597-022-01164-1)
+
 -   Knudsen GM, Ganz M, Appelhoff S, Boellaard R, Bormans G, Carson RE, Catana C,
     Doudet D, Gee AD, Greve DN, Gunn RN, Halldin C, Herscovitch P, Huang H, Keller SH,
     Lammertsma AA, Lanzenberger R, Liow JS, Lohith TG, Lubberink M, Lyoo CH, Mann JJ,
     Matheson GJ, Nichols TE, Nørgaard M, Ogden T, Parsey R, Pike VW, Price J, Rizzo G,
-    Rosa-Neto P, Schain M, Scott PJH, Searle G, Slifstein M, Suhara T, Talbot PS,
-    Thomas A, Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. (2020).
+    Rosa-Neto P, Schain M, Scott PJH, Searle G, Slifstein M, Suhara T, Talbot PS, Thomas A,
+    Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. (2020).
     **Guidelines for Content and Format of PET Brain Data in Publications and in Archives: A Consensus Paper**.
     Journal of Cerebral Blood Flow and Metabolism, 2020 Aug; 40(8): 1576-1585.
     [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433)
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 81d6babe01..04c6524c98 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -154,8 +154,8 @@ which we divide into several categories:
 
 {{ MACROS___make_metadata_table(
    {
-      "TracerName": "REQUIRED",
-      "TracerRadionuclide": "REQUIRED",
+      "TracerName": ("REQUIRED", "Corresponds to DICOM Tags (0008,0105) `Mapping Resource` and (0008,0122) `Mapping Resource Name`."),
+      "TracerRadionuclide": ("REQUIRED", "Corresponds to DICOM Tags (0008,0104) `CodeValue` and (0008,0104) `CodeMeaning`."),
       "InjectedRadioactivity": "REQUIRED",
       "InjectedRadioactivityUnits": "REQUIRED",
       "InjectedMass": "REQUIRED",
@@ -186,11 +186,11 @@ which we divide into several categories:
 
 {{ MACROS___make_metadata_table(
    {
-      "PharmaceuticalName": "RECOMMENDED",
-      "PharmaceuticalDoseAmount": "RECOMMENDED",
+      "PharmaceuticalName": ("RECOMMENDED", "Corresponds to DICOM Tag (0008,0034) `Intervention Drug Name`."),
+      "PharmaceuticalDoseAmount": ("RECOMMENDED", "Corresponds to DICOM Tag (0008,0028) `Intervention Drug Dose`."),
       "PharmaceuticalDoseUnits": "RECOMMENDED",
       "PharmaceuticalDoseRegimen": "RECOMMENDED",
-      "PharmaceuticalDoseTime": "RECOMMENDED",
+      "PharmaceuticalDoseTime": ("RECOMMENDED", "Corresponds to a combination of DICOM Tags (0008,0027) `Intervention Drug Stop Time` and (0008,0035) `Intervention Drug Start Time`."),
       "Anaesthesia": "OPTIONAL",
    }
 ) }}
@@ -201,11 +201,11 @@ which we divide into several categories:
    {
       "TimeZero": "REQUIRED",
       "ScanStart": "REQUIRED",
-      "InjectionStart": "REQUIRED",
+      "InjectionStart": ("REQUIRED", "This corresponds to DICOM Tag (0018,1072) `Radiopharmaceutical Start Time`."),
       "FrameTimesStart": "REQUIRED",
       "FrameDuration": "REQUIRED",
-      "InjectionEnd": "RECOMMENDED",
-      "ScanDate": "DEPRECATED",
+      "InjectionEnd": ("RECOMMENDED", "This corresponds to DICOM Tag (0018,1073) `Radiopharmaceutical Stop Time` converted to seconds relative to TimeZero."),
+      "ScanDate": ("DEPRECATED", "This corresponds to DICOM Tag (0008,0022) `Acquisition Date`."),
    }
 ) }}
 
@@ -218,19 +218,19 @@ We refer to the common principles for the standards for describing dates and tim
       "AcquisitionMode": "REQUIRED",
       "ImageDecayCorrected": "REQUIRED",
       "ImageDecayCorrectionTime": "REQUIRED",
-      "ReconMethodName": "REQUIRED",
-      "ReconMethodParameterLabels": "REQUIRED",
-      "ReconMethodParameterUnits": "REQUIRED",
-      "ReconMethodParameterValues": "REQUIRED",
-      "ReconFilterType": "REQUIRED",
-      "ReconFilterSize": "REQUIRED",
-      "AttenuationCorrection": "REQUIRED",
+      "ReconMethodName": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterLabels": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterUnits": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterValues": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconFilterType": ("REQUIRED", "This partly matches the DICOM Tag (0018,1210) `Convolution Kernel`."),
+      "ReconFilterSize": ("REQUIRED", "This partly matches the DICOM Tag (0018,1210) `Convolution Kernel`."),
+      "AttenuationCorrection": ("REQUIRED", "This corresponds to DICOM Tag (0054,1101) `Attenuation Correction Method`."),
       "ReconMethodImplementationVersion": "RECOMMENDED",
       "AttenuationCorrectionMethodReference": "RECOMMENDED",
       "ScaleFactor": "RECOMMENDED",
-      "ScatterFraction": "RECOMMENDED",
-      "DecayCorrectionFactor": "RECOMMENDED",
-      "DoseCalibrationFactor": "RECOMMENDED",
+      "ScatterFraction": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1323) `Scatter Fraction Factor`."),
+      "DecayCorrectionFactor": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1321) `Decay Factor`."),
+      "DoseCalibrationFactor": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1322) `Dose Calibration Factor`."),
       "PromptRate": "RECOMMENDED",
       "RandomRate": "RECOMMENDED",
       "SinglesRate": "RECOMMENDED",
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index aca8e8ad0a..2f182ae71c 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -1247,7 +1247,7 @@ InjectionStart:
   description: |
     Time of start of injection with respect to `"TimeZero"` in the default unit
     seconds.
-    This corresponds to DICOM Tag 0018, 1042 `Contrast/Bolus Start Time`
+    This corresponds to DICOM Tag 0018, 1072 `Contrast/Bolus Start Time`
     converted to seconds relative to `"TimeZero"`.
   type: number
   unit: s
@@ -2293,7 +2293,9 @@ SamplingFrequency:
 ScaleFactor:
   name: ScaleFactor
   description: |
-    Scale factor for each frame.
+    Scale factor for each frame. This field MUST be defined if the imaging data (`.nii[.gz]`) are scaled.
+    If this field is not defined, then it is assumed that the scaling factor is 1. Defining this field
+    when the scaling factor is 1 is RECOMMENDED, for the sake of clarity.
   type: array
   items:
     type: number

From e311eec6e37b546c2eb1611f2f4568fa385ed1ce Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 4 Apr 2022 10:50:02 -0400
Subject: [PATCH 227/347] Define file_relative format. (#1046)

---
 src/schema/objects/formats.yaml                  | 9 +++++++++
 tools/schemacode/schemacode/tests/test_schema.py | 8 ++++++++
 2 files changed, 17 insertions(+)

diff --git a/src/schema/objects/formats.yaml b/src/schema/objects/formats.yaml
index dab370d2c7..67a78be33f 100644
--- a/src/schema/objects/formats.yaml
+++ b/src/schema/objects/formats.yaml
@@ -67,6 +67,15 @@ datetime:
     where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
     and [Z] is an optional, valid timezone code.
   pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?'
+file_relative:
+  name: Path relative to the parent file
+  description: |
+    A path to a file, relative to the file in which the field is defined.
+
+    The validation for this format is minimal.
+    It simply ensures that the value is a string with any characters that may appear in a valid path,
+    without starting with "/" (an absolute path).
+  pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
 participant_relative:
   name: Path relative to the participant folder
   description: |
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
index 9e169d0f1c..3f71542a81 100644
--- a/tools/schemacode/schemacode/tests/test_schema.py
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -62,6 +62,11 @@ def test_formats(schema_obj):
             "9:00:00",  # leading zeros are not required for hours
         ],
         "unit": ["any string is valid."],
+        "file_relative": [
+            "file_in_same_directory.txt",
+            "../../relative/path/file.txt",
+            "sub-01/path/file.txt",
+        ],
         "stimuli_relative": ["any/arbitrary/path/file.txt"],
         "dataset_relative": ["any/arbitrary/path/file.txt"],
         "participant_relative": ["any/arbitrary/path/file.txt"],
@@ -108,6 +113,9 @@ def test_formats(schema_obj):
             "01:23",  # lacks either hours or seconds
         ],
         "unit": [],
+        "file_relative": [
+            "/path/with/starting/slash/file.txt",
+        ],
         "stimuli_relative": [
             "/path/with/starting/slash/file.txt",
             "stimuli/path/file.txt",

From 4d1bae52e21aaa9a7ba36b38dae4bf55942e1c40 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Apr 2022 16:50:26 +0200
Subject: [PATCH 228/347] fix typo rawdata (#1045)

---
 src/02-common-principles.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index d993224cd5..ec2c4aba5a 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -270,7 +270,9 @@ Alternatively one can organize their data in the following way
     "my_dataset-1": {
             "sourcedata": "",
             "...": "",
-            "sourcedata": {
+            "rawdata": {
+                "dataset_description.json": "",
+                "participants.tsv": "",
                 "sub-01": {},
                 "sub-02": {},
                 "...": "",

From d9eeb6d3606b1e52ee1282b09a581aab93273395 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Apr 2022 16:50:56 +0200
Subject: [PATCH 229/347] [MISC] consistently use "directory" instead of
 "folder" as a term (#1044)

* sub-directory -> subdirectory

* [fF]older[s]{0,1} --> [dD]irector[yies]*

* ci: bump GH actions

* markdown: fix table pipes
---
 .github/workflows/codespell.yml               |  2 +-
 .github/workflows/markdown_style.yml          |  2 +-
 .github/workflows/no-bad-latin.yml            |  4 +-
 .github/workflows/schemacode_ci.yml           | 10 ++---
 .github/workflows/yml_lint.yml                |  4 +-
 CONTRIBUTING.md                               |  4 +-
 macros_doc.md                                 |  8 ++--
 src/01-introduction.md                        |  2 +-
 src/02-common-principles.md                   | 44 +++++++++----------
 src/03-modality-agnostic-files.md             |  4 +-
 .../01-magnetic-resonance-imaging-data.md     |  2 +-
 .../02-magnetoencephalography.md              |  6 +--
 .../04-intracranial-electroencephalography.md |  2 +-
 .../05-task-events.md                         | 10 ++---
 .../07-behavioral-experiments.md              |  6 +--
 .../10-microscopy.md                          |  2 +-
 src/99-appendices/06-meg-file-formats.md      | 20 ++++-----
 src/99-appendices/11-qmri.md                  | 10 ++---
 src/CHANGES.md                                |  8 ++--
 src/schema/README.md                          | 34 +++++++-------
 src/schema/objects/associated_data.yaml       | 12 ++---
 src/schema/objects/columns.yaml               |  4 +-
 src/schema/objects/formats.yaml               | 16 +++----
 src/schema/objects/metadata.yaml              |  4 +-
 src/schema/rules/associated_data.yaml         |  4 +-
 tools/examplecode/example.py                  |  4 +-
 tools/filetree_example.ipynb                  |  8 ++--
 tools/mkdocs_macros_bids/macros.py            |  6 +--
 tools/schemacode/schemacode/render.py         |  4 +-
 tools/schemacode/schemacode/schema.py         |  4 +-
 .../schemacode/tests/test_schema.py           |  2 +-
 tools/schemacode/schemacode/utils.py          |  4 +-
 32 files changed, 128 insertions(+), 128 deletions(-)

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
index 3609c21cfd..db5f92e7d6 100644
--- a/.github/workflows/codespell.yml
+++ b/.github/workflows/codespell.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: codespell-project/actions-codespell@master
         with:
           skip: js,*.svg
diff --git a/.github/workflows/markdown_style.yml b/.github/workflows/markdown_style.yml
index 578c6e8cf5..ecc5d6403f 100644
--- a/.github/workflows/markdown_style.yml
+++ b/.github/workflows/markdown_style.yml
@@ -6,7 +6,7 @@ jobs:
   markdown-style:
     runs-on : ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Setup NodeJS
       uses: actions/setup-node@v2
       with:
diff --git a/.github/workflows/no-bad-latin.yml b/.github/workflows/no-bad-latin.yml
index 8a67e45ae3..da5bf72ac7 100644
--- a/.github/workflows/no-bad-latin.yml
+++ b/.github/workflows/no-bad-latin.yml
@@ -31,10 +31,10 @@ jobs:
     # This section collects together the steps involved in running the test
     steps:
     # Checkout the repository. Relies on another GH-Action.
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     # Set up the Python version. Relies on another GH-Action.
     - name: Setup Python 3.7
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: 3.7
     # Install Python dependencies
diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 51f0334e5a..2bcb2c96d3 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -20,7 +20,7 @@ jobs:
     outputs:
       skip: ${{ steps.result_step.outputs.ci-skip }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - id: result_step
@@ -43,10 +43,10 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: "Set up Python"
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
             python-version: ${{ matrix.python-version }}
 
@@ -74,10 +74,10 @@ jobs:
     name: Lint schemacode
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: "3.7"
 
diff --git a/.github/workflows/yml_lint.yml b/.github/workflows/yml_lint.yml
index 9f5609afa6..99e534c78b 100644
--- a/.github/workflows/yml_lint.yml
+++ b/.github/workflows/yml_lint.yml
@@ -6,9 +6,9 @@ jobs:
   yml-lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
     - name: Install dependencies
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 807f7f345a..a8f740e19b 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -415,7 +415,7 @@ specification, do not hesitate to make a suggestion by showing a draft in a GitH
 After discussion and approval by the community, you can then submit your image
 in a pull request.
 
-Images should be added to an `images` folder that is at the same level as the Markdown file
+Images should be added to an `images` directory that is at the same level as the Markdown file
 where your image will be added. For example if you want to add a figure `figure01.png` to
 `src/05-derivatives/01-introduction.md` then your image should go to
 `src/05-derivatives/images/figure01.png`.
@@ -629,7 +629,7 @@ reviewer as a co-author.
 ## Making a change to the BIDS-schema
 
 Several aspects of the specification are defined in a set of YAML files in the
-`src/schema` folder. The content of those files is described in a dedicated
+`src/schema` directory. The content of those files is described in a dedicated
 [README file](./src/schema/README.md).
 
 ### 1. Ensure that changes to the specification are matched in the schema
diff --git a/macros_doc.md b/macros_doc.md
index b130b961cd..c202891717 100644
--- a/macros_doc.md
+++ b/macros_doc.md
@@ -17,7 +17,7 @@ in the BIDS specification.
    - [Do I need learn how to program to use those macros?](#do-i-need-learn-how-to-program-to-use-those-macros)
    - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call)
    - [How-To and Examples](#how-to-and-examples)
-      - [Writing folder content examples](#writing-folder-content-examples)
+      - [Writing directory content examples](#writing-directory-content-examples)
       - [Generating tables](#generating-tables)
          - [Modifying a term in the table](#modifying-a-term-in-the-table)
          - [Why would you NOT want to modify the content of the yml file directly ?](#why-would-you-not-want-to-modify-the-content-of-the-yml-file-directly-)
@@ -113,7 +113,7 @@ correct terms in the schema. This process is illustrated in the next section.
 
 Note that under the hood the macros themselves call python code that can be
 found in the
-[`tools` folder](https://github.com/bids-standard/bids-specification/tree/master/tools).
+[`tools` directory](https://github.com/bids-standard/bids-specification/tree/master/tools).
 If you are interested in creating a new macro for users, this would be useful.
 
 ## Anything else I need to know if I need to insert a new macro call?
@@ -146,7 +146,7 @@ and a guide for editing at <link>.
 
 ## How-To and Examples
 
-### Writing folder content examples
+### Writing directory content examples
 
 One of the simplest macro we use helps us create consistent "file tree" examples
 that would look like this in the final document:
@@ -173,7 +173,7 @@ To do this get this output, your macro call would look like this:
 ) }}
 ```
 
-When you have complex files and folder structure, we suggest you use this
+When you have complex files and directory structure, we suggest you use this
 [Jupyter notebook](tools/filetree_example.ipynb) for sandboxing your example
 before you insert the macro call into the markdown document.
 
diff --git a/src/01-introduction.md b/src/01-introduction.md
index 507a1fd74c..f3342ba00a 100644
--- a/src/01-introduction.md
+++ b/src/01-introduction.md
@@ -40,7 +40,7 @@ and the INCF Neuroimaging Data Sharing (NIDASH) Task Force.
 While working on BIDS we consulted
 many neuroscientists to make sure it covers most common experiments, but at the
 same time is intuitive and easy to adopt. The specification is intentionally
-based on simple file formats and folder structures to reflect current lab
+based on simple file formats and directory structures to reflect current lab
 practices and make it accessible to a wide range of scientists coming from
 different backgrounds.
 
diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index ec2c4aba5a..ca238fa64c 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -140,7 +140,7 @@ T2 volume does not need to be included, but when it is available it should be
 saved under a particular filename specified in the standard. This standard
 aspires to describe a majority of datasets, but acknowledges that there will be
 cases that do not fit. In such cases one can include additional files and
-subfolders to the existing folder structure following common sense. For example
+subdirectories to the existing directory structure following common sense. For example
 one may want to include eye tracking data in a vendor specific format that is
 not covered by this standard. The most sensible place to put it is next to the
 continuous recording file with the same naming scheme but different extensions.
@@ -156,7 +156,7 @@ Two prominent examples of entities are `subject` and `session`.
 
 For a data file that was collected in a given `session` from a given
 `subject`, the filename MUST begin with the string `sub-<label>_ses-<label>`.
-If the `session` level is omitted in the folder structure, the filename MUST begin
+If the `session` level is omitted in the directory structure, the filename MUST begin
 with the string `sub-<label>`, without `ses-<label>`.
 
 Note that `sub-<label>` corresponds to the `subject` entity because it has
@@ -165,10 +165,10 @@ correspond to a unique identifier of that subject, such as `01`.
 The same holds for the `session` entity with its `ses-` key and its `<label>`
 value.
 
-The extra session layer (at least one `/ses-<label>` subfolder) SHOULD
+The extra session layer (at least one `/ses-<label>` subdirectory) SHOULD
 be added for all subjects if at least one subject in the dataset has more than
 one session.
-If a `/ses-<label>` subfolder is included as part of the directory hierarchy,
+If a `/ses-<label>` subdirectory is included as part of the directory hierarchy,
 then the same [`ses-<label>`](./99-appendices/09-entities.md#ses)
 key/value pair MUST also be included as part of the filenames themselves.
 Acquisition time of session can
@@ -252,16 +252,16 @@ recommending a particular naming scheme for including different types of
 source data (such as the raw event logs or parameter files, before conversion to BIDS).
 However, in the case that these data are to be included:
 
-1.  These data MUST be kept in separate `sourcedata` folder with a similar
-    folder structure as presented below for the BIDS-managed data. For example:
+1.  These data MUST be kept in separate `sourcedata` directory with a similar
+    directory structure as presented below for the BIDS-managed data. For example:
     `sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz` or
     `sourcedata/sub-01/ses-pre/func/MyEvent.sce`.
 
-1.  A README file SHOULD be found at the root of the `sourcedata` folder or the
-    `derivatives` folder, or both.
+1.  A README file SHOULD be found at the root of the `sourcedata` directory or the
+    `derivatives` directory, or both.
     This file should describe the nature of the raw data or the derived data.
     We RECOMMEND including the PDF print-out with the actual sequence
-    parameters generated by the scanner in the `sourcedata`  folder.
+    parameters generated by the scanner in the `sourcedata`  directory.
 
 Alternatively one can organize their data in the following way
 
@@ -287,17 +287,17 @@ Alternatively one can organize their data in the following way
 ) }}
 
 In this example, where `sourcedata` and `derivatives` are not nested inside
-`rawdata`, **only the `rawdata` subfolder** needs to be a BIDS-compliant
+`rawdata`, **only the `rawdata` subdirectory** needs to be a BIDS-compliant
 dataset.
-The subfolders of `derivatives` MAY be BIDS-compliant derivatives datasets
+The subdirectories of `derivatives` MAY be BIDS-compliant derivatives datasets
 (see [Non-compliant derivatives](#non-compliant-derivatives) for further discussion).
 This specification does not prescribe anything about the contents of `sourcedata`
-folders in the above example - nor does it prescribe the `sourcedata`,
-`derivatives`, or `rawdata` folder names.
+directories in the above example - nor does it prescribe the `sourcedata`,
+`derivatives`, or `rawdata` directory names.
 The above example is just a convention that can be useful for organizing raw,
 source, and derived data while maintaining BIDS compliance of the raw data
-folder. When using this convention it is RECOMMENDED to set the `SourceDatasets`
-field in `dataset_description.json` of each subfolder of `derivatives` to:
+directory. When using this convention it is RECOMMENDED to set the `SourceDatasets`
+field in `dataset_description.json` of each subdirectory of `derivatives` to:
 
 ```JSON
 {
@@ -309,18 +309,18 @@ field in `dataset_description.json` of each subfolder of `derivatives` to:
 
 Derivatives can be stored/distributed in two ways:
 
-1.  Under a `derivatives/` subfolder in the root of the source BIDS dataset
-    folder to make a clear distinction between raw data and results of data
+1.  Under a `derivatives/` subdirectory in the root of the source BIDS dataset
+    directory to make a clear distinction between raw data and results of data
     processing.
     A data processing pipeline will typically have a dedicated directory
     under which it stores all of its outputs.
     Different components of a pipeline can, however, also be stored under different
-    subfolders.
+    subdirectories.
     There are few restrictions on the directory names;
     it is RECOMMENDED to use the format `<pipeline>-<variant>` in cases where
     it is anticipated that the same pipeline will output more than one variant
     (for example, `AFNI-blurring` and `AFNI-noblurring`).
-    For the sake of consistency, the subfolder name SHOULD be
+    For the sake of consistency, the subdirectory name SHOULD be
     the `GeneratedBy.Name` field in `data_description.json`,
     optionally followed by a hyphen and a suffix (see
     [Derived dataset and pipeline description][derived-dataset-description]).
@@ -397,7 +397,7 @@ session subdirectory within the corresponding subject directory; and so on.
 
 Nothing in this specification should be interpreted to disallow the
 storage/distribution of non-compliant derivatives of BIDS datasets.
-In particular, if a BIDS dataset contains a `derivatives/` sub-directory,
+In particular, if a BIDS dataset contains a `derivatives/` subdirectory,
 the contents of that directory may be a heterogeneous mix of BIDS Derivatives
 datasets and non-compliant derivatives.
 
@@ -819,7 +819,7 @@ Describing dates and timestamps:
 
 ### Single session example
 
-This is an example of the folder and file structure. Because there is only one
+This is an example of the directory and file structure. Because there is only one
 session, the session level is not required by the format. For details on
 individual files see descriptions in the next section:
 
@@ -864,7 +864,7 @@ individual files see descriptions in the next section:
 
 ## Unspecified data
 
-Additional files and folders containing raw data MAY be added as needed for
+Additional files and directories containing raw data MAY be added as needed for
 special cases.
 All non-standard file entities SHOULD conform to BIDS-style naming conventions, including
 alphabetic entities and suffixes and alphanumeric labels/indices.
diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 822bb197c7..f46cca8615 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -105,8 +105,8 @@ In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
    }
 ) }}
 
-If a derived dataset is stored as a subfolder of the raw dataset, then the `Name` field
-of the first `GeneratedBy` object MUST be a substring of the derived dataset folder name.
+If a derived dataset is stored as a subdirectory of the raw dataset, then the `Name` field
+of the first `GeneratedBy` object MUST be a substring of the derived dataset directory name.
 That is, in a directory `<dataset>/derivatives/<pipeline>[-<variant>]/`, the first
 `GeneratedBy` object should have a `Name` of `<pipeline>`.
 
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 41969de679..4c3d47dd13 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -161,7 +161,7 @@ diffusion and functional MRI may also be *intended for* estimating the
 *B<sub>0</sub>* field nonuniformity inside the scanner (in other words,
 *mapping the field*) without the acquisition of additional MRI schemes
 such as gradient-recalled echo (GRE) sequences that are stored under the
-`fmap/` folder of the BIDS structure.
+`fmap/` directory of the BIDS structure.
 
 The modality labels `dwi` (under `dwi/`), `bold` (under `func/`),
 `asl` (under `perf/`), `sbref` (under `dwi/`, `func/` or `perf/`), and
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 7ba79f7c45..e1d03756a5 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -44,8 +44,8 @@ If multiple *Tasks* were performed within a single *Run*,
 the task description can be set to `task-multitask`.
 The `*_meg.json` file SHOULD contain details on the *Tasks*.
 
-Some manufacturers' data storage conventions use folders which contain data
-files of various nature: for example, CTF's `.ds` format, or BTi/4D's data folder.
+Some manufacturers' data storage conventions use directories which contain data
+files of various nature: for example, CTF's `.ds` format, or BTi/4D's data directory.
 Yet other manufacturers split their files once they exceed a certain size
 limit.
 For example Neuromag/Elekta/Megin, which can produce several files
@@ -475,7 +475,7 @@ Empty-room MEG recordings capture the environmental and recording system's
 noise.
 In the context of BIDS it is RECOMMENDED to perform an empty-room recording for
 each experimental session.
-It is RECOMMENDED to store the empty-room recording inside a subject folder
+It is RECOMMENDED to store the empty-room recording inside a subject directory
 named `sub-emptyroom`.
 The label for the [`task-<label>`](../99-appendices/09-entities.md#task) entity in the empty-room recording SHOULD be
 set to `noise`.
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index e4d1b0cbf8..85ca8fbc78 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -525,7 +525,7 @@ other task events. Electrical stimulation parameters can be described in columns
 called `electrical_stimulation_<label>`, with labels chosen by the researcher and
 optionally defined in more detail in an accompanying `_events.json` file (as
 per the main BIDS spec). Functions for complex stimulation patterns can, similar
-as when a video is presented, be stored in a folder in the `/stimuli/` folder.
+as when a video is presented, be stored in a directory in the `/stimuli/` directory.
 For example: `/stimuli/electrical_stimulation_functions/biphasic.tsv`
 
 Example:
diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md
index 5188a8c1ae..cdda5e2e3b 100644
--- a/src/04-modality-specific-files/05-task-events.md
+++ b/src/04-modality-specific-files/05-task-events.md
@@ -127,17 +127,17 @@ for additional information and examples.
 Additional information about the stimuli can be added in the `events.tsv`
 and `events.json` files.
 
-This can be done by using a `/stimuli` folder or by reference to a stimuli database.
+This can be done by using a `/stimuli` directory or by reference to a stimuli database.
 
-### Stimuli folder
+### Stimuli directory
 
-The stimulus files can be added in a `/stimuli` folder
-(under the root folder of the dataset; with optional subfolders) AND using a
+The stimulus files can be added in a `/stimuli` directory
+(under the root directory of the dataset; with optional subdirectories) AND using a
 `stim_file` column in `events.tsv` mentioning which stimulus file was used
 for a given event,
 
 There are no restrictions on the file formats of the stimuli files,
-but they should be stored in the `/stimuli` folder.
+but they should be stored in the `/stimuli` directory.
 
 {{ MACROS___make_columns_table(
    {
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
index 0406871b15..23747807d1 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -5,7 +5,7 @@
 In addition to logs from behavioral experiments performed alongside imaging data
 acquisitions, one can also include data from experiments performed with no neural
 recordings.
-The results of those experiments can be stored in the `beh` folder using the same
+The results of those experiments can be stored in the `beh` directory using the same
 formats for event timing (`_events.tsv`), metadata (`_events.json`),
 physiological (`_physio.tsv.gz`, `_physio.json`)
 and other continuous recordings (`_stim.tsv.gz`, `_stim.json`)
@@ -31,10 +31,10 @@ In addition to the metadata that is either:
 
 -   RECOMMENDED for sidecar JSON files for [tabular data](../02-common-principles.md#tabular-data), or
 
--   REQUIRED for some data that can be found in the `beh` folder
+-   REQUIRED for some data that can be found in the `beh` directory
     (for example `SamplingFrequency` and `StartTime` for `*_<physio|stim>.tsv.gz` files),
 
-it is RECOMMENDED to add the following metadata to the JSON files of this folder:
+it is RECOMMENDED to add the following metadata to the JSON files of this directory:
 
 {{ MACROS___make_metadata_table(
    {
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 4c03988744..cb9f486081 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -208,7 +208,7 @@ JSON metadata may be defined per sample or per chunk as appropriate, as per the
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,
 only the higher resolution file is present in the raw data.
-Lower resolutions files MUST be placed under the `derivatives` folder and use the
+Lower resolutions files MUST be placed under the `derivatives` directory and use the
 [`res-<label>`](../99-appendices/09-entities.md#res) entity.
 
 For example:
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 7036eb32a0..b00cee525a 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -5,9 +5,9 @@ RECOMMENDED values for `manufacturer_specific_extensions`:
 
 | **Value**                                           | **Description**                                                                       |
 | --------------------------------------------------- | ------------------------------------------------------------------------------------- |
-| [`ctf`](06-meg-file-formats.md#ctf)                 | CTF (folder with `.ds` extension)                                                     |
+| [`ctf`](06-meg-file-formats.md#ctf)                 | CTF (directory with `.ds` extension)                                                  |
 | [`fif`](06-meg-file-formats.md#neuromagelektamegin) | Neuromag / Elekta / MEGIN and BabyMEG (file with extension `.fif`)                    |
-| [`4d`](06-meg-file-formats.md#bti4d-neuroimaging)   | BTi / 4D Neuroimaging (folder containing multiple files without extensions)           |
+| [`4d`](06-meg-file-formats.md#bti4d-neuroimaging)   | BTi / 4D Neuroimaging (directory containing multiple files without extensions)        |
 | [`kit`](06-meg-file-formats.md#kityokogawaricoh)    | KIT / Yokogawa / Ricoh (file with extension `.sqd`, `.con`, `.raw`, `.ave` or `.mrk`) |
 | [`kdf`](06-meg-file-formats.md#kriss)               | KRISS (file with extension `.kdf`)                                                    |
 | [`itab`](06-meg-file-formats.md#itab)               | Chieti system (file with extension `.raw` and `.mhd`)                                 |
@@ -16,10 +16,10 @@ Below are specifications for each system brand.
 
 ## CTF
 
-Each experimental run with a CTF system yields a folder with a `.ds` extension,
+Each experimental run with a CTF system yields a directory with a `.ds` extension,
 containing several files. The OPTIONAL digitized positions of the head points
 are usually stored in a separate `.pos` file, not necessarily within the `.ds`
-folder.
+directory.
 
 ```Text
 [sub-<label>[_ses-<label>]_headshape.pos]
@@ -90,10 +90,10 @@ entity.
 Note that cross-talk files MUST be denoted using `acq-crosstalk` and
 fine-calibration files MUST be denoted using `acq-calibration`.
 
-The cross-talk and fine-calibration data MUST be stored in the subject-level `meg` folder,
-which may be nested inside a `ses-<label>` folder, as shown in the following examples.
+The cross-talk and fine-calibration data MUST be stored in the subject-level `meg` directory,
+which may be nested inside a `ses-<label>` directory, as shown in the following examples.
 
-#### Example with single session (omitted session folder)
+#### Example with single session (omitted session directory)
 
 {{ MACROS___make_filetree_example(
    {
@@ -155,7 +155,7 @@ which may be nested inside a `ses-<label>` folder, as shown in the following exa
 
 After applying SSS (for example, by using the MaxFilter software),
 files SHOULD be renamed with the corresponding label (for example, `proc-sss`)
-and placed in a `derivatives` subfolder.
+and placed in a `derivatives` subdirectory.
 
 Example:
 
@@ -230,7 +230,7 @@ support recording dates earlier than `1901-12-13T08:45:53.000000` UTC or later t
 
 ## BTi/4D neuroimaging
 
-Each experimental run on a 4D neuroimaging/BTi system results in a folder
+Each experimental run on a 4D neuroimaging/BTi system results in a directory
 containing multiple files without extensions.
 
 ```Text
@@ -329,7 +329,7 @@ More about the KIT/Yokogawa/Ricoh data organization at:
 ## KRISS
 
 Each experimental run on the KRISS system produces a file with extension
-`.kdf`. Additional files can be available in the same folder: the digitized
+`.kdf`. Additional files can be available in the same directory: the digitized
 positions of the head points (`\_digitizer.txt`), the position of the center of
 the MEG coils (`.chn`) and the event markers (`.trg`).
 
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 6c4a349907..b58f410df7 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -40,7 +40,7 @@ application by creating logical groups of input files through `suffix` and certa
 representing acquisition parameters (`echo`, `flip`, `inv`, `mt`) or file parts (`part`).
 
 If a qMRI file collection is intended for creating structural quantitative maps (for example, `T1map`),
-files belonging to that collection are stored in the `anat` subfolder.
+files belonging to that collection are stored in the `anat` subdirectory.
 Below is an example file collection for `MP2RAGE`:
 
 {{ MACROS___make_filetree_example(
@@ -60,7 +60,7 @@ Below is an example file collection for `MP2RAGE`:
 
 Commonly, RF fieldmaps (`B1+` and `B1-` maps) are used for the correction of structural quantitative maps.
 As these images do not convey substantial structural information,
-respective file collections of RF fieldmaps are stored in the `fmap` subfolder.
+respective file collections of RF fieldmaps are stored in the `fmap` subdirectory.
 Below is an example file collection for RF transmit field map `TB1EPI`:
 
 {{ MACROS___make_filetree_example(
@@ -84,7 +84,7 @@ Please visit the [file collections appendix](./10-file-collections.md#magnetic-r
 
 ### Quantitative maps are derivatives
 
-Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the `derivatives` folder.
+Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the `derivatives` directory.
 For example a `T1map` can be generated from an `MP2RAGE` file collection using either options.
 
 If the map is post-generated:
@@ -194,7 +194,7 @@ Explanation of the table:
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
 [derived datasets](../03-modality-agnostic-files.md#derived-dataset-and-pipeline-description).
 
-An example `dataset_description.json` for a qMRI map derivatives folder:
+An example `dataset_description.json` for a qMRI map derivatives directory:
 
 {{ MACROS___make_filetree_example(
    {
@@ -416,7 +416,7 @@ raw dataset directory along with the `MP2RAGE` file collection and to be used as
 for quantifying a `T1map`.
 
 If an additional `UNIT1` image is calculated offline, then the output is to be stored in the
-`derivatives` folder with necessary provenance information.
+`derivatives` directory with necessary provenance information.
 
 ##### `NumberShots` metadata field
 
diff --git a/src/CHANGES.md b/src/CHANGES.md
index 2988478002..bffffb8630 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -130,7 +130,7 @@
 -   \[FIX] Mix up (typo) between ficiduals and landmarks in EEG spec [#754](https://github.com/bids-standard/bids-specification/pull/754) ([rob-luke](https://github.com/rob-luke))
 -   \[INFRA] updating remark, CIs, contributor docs [#745](https://github.com/bids-standard/bids-specification/pull/745) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] schema for i/eeg coordsys+elecs: sub-ses-acq-space are allowed entities [#743](https://github.com/bids-standard/bids-specification/pull/743) ([sappelhoff](https://github.com/sappelhoff))
--   \[DOC] move schema documentation into the schema folder [#740](https://github.com/bids-standard/bids-specification/pull/740) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[DOC] move schema documentation into the schema directory [#740](https://github.com/bids-standard/bids-specification/pull/740) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] standardize string examples format in tables [#739](https://github.com/bids-standard/bids-specification/pull/739) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] Clarify participant_id in participants.tsv file if it exists [#738](https://github.com/bids-standard/bids-specification/pull/738) ([adam2392](https://github.com/adam2392))
 -   \[FIX] split MEG files should be listed separately in scans.tsv [#735](https://github.com/bids-standard/bids-specification/pull/735) ([eort](https://github.com/eort))
@@ -302,7 +302,7 @@
 -   \[FIX] Clarify channels.tsv is RECOMMENDED consistently across ephys [#347](https://github.com/bids-standard/bids-specification/pull/347) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase))
 -   \[MISC] rm TOC.md - seems no longer pertinent/used [#341](https://github.com/bids-standard/bids-specification/pull/341) ([yarikoptic](https://github.com/yarikoptic))
--   \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta))
+-   \[MISC] Move the PR template to a separate directory and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta))
 -   \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Clarify phenotypic and assessment data in new section [#331](https://github.com/bids-standard/bids-specification/pull/331) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] add information about continuous integration checks to PR template [#330](https://github.com/bids-standard/bids-specification/pull/330) ([sappelhoff](https://github.com/sappelhoff))
@@ -366,7 +366,7 @@
 -   \[FIX] make MEG section headings and ToC consistent to the EEG and iEEG specs [#181](https://github.com/bids-standard/bids-specification/pull/181) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[FIX] make section headings and ToC consistent between meg and eeg specs [#180](https://github.com/bids-standard/bids-specification/pull/180) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[MISC] Spelling fixes [#179](https://github.com/bids-standard/bids-specification/pull/179) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
--   \[ENH] Alternative folder organization for raw, derived, and source data [#178](https://github.com/bids-standard/bids-specification/pull/178) ([chrisgorgo](https://github.com/chrisgorgo))
+-   \[ENH] Alternative directory organization for raw, derived, and source data [#178](https://github.com/bids-standard/bids-specification/pull/178) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[INFRA] Adding instructions for naming PRs [#177](https://github.com/bids-standard/bids-specification/pull/177) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Introducing Stefan Appelhoff as the first Maintainer [#176](https://github.com/bids-standard/bids-specification/pull/176) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[FIX] Clarify name of "BrainVision" format [#175](https://github.com/bids-standard/bids-specification/pull/175) ([JegouA](https://github.com/JegouA))
@@ -440,7 +440,7 @@
 -   \[MISC] corrected link that is shown for CC0 [#31](https://github.com/bids-standard/bids-specification/pull/31) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[INFRA] added linter integration via travis [#30](https://github.com/bids-standard/bids-specification/pull/30) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Cleanup [#29](https://github.com/bids-standard/bids-specification/pull/29) ([chrisgorgo](https://github.com/chrisgorgo))
--   \[MISC] split intro, commons, mr, and meg into folder from specification.md [#28](https://github.com/bids-standard/bids-specification/pull/28) ([teonbrooks](https://github.com/teonbrooks))
+-   \[MISC] split intro, commons, mr, and meg into directory from specification.md [#28](https://github.com/bids-standard/bids-specification/pull/28) ([teonbrooks](https://github.com/teonbrooks))
 -   \[MISC] Add some bids starter kit contributors [#27](https://github.com/bids-standard/bids-specification/pull/27) ([KirstieJane](https://github.com/KirstieJane))
 -   \[MISC] Embedded footnotes into text [#25](https://github.com/bids-standard/bids-specification/pull/25) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Making HED Strategy Guide link prettier [#24](https://github.com/bids-standard/bids-specification/pull/24) ([fake-filo](https://github.com/fake-filo))
diff --git a/src/schema/README.md b/src/schema/README.md
index c3d142cba6..04bdca0a7c 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -32,14 +32,14 @@ The types of objects currently supported in the schema are:
 -   suffixes,
 -   metadata,
 -   top-level files,
--   and non-BIDS associated folders.
+-   and non-BIDS associated directories.
 
-Each of these object types has a single file in the `objects/` folder.
+Each of these object types has a single file in the `objects/` directory.
 
 -   `modalities.yaml`: The modalities, or types of technology, used to acquire data in a BIDS dataset.
     These modalities are not reflected directly in the specification.
     For example, while both fMRI and DWI data are acquired with an MRI,
-    in a BIDS dataset they are stored in different folders reflecting the two different `datatypes`.
+    in a BIDS dataset they are stored in different directories reflecting the two different `datatypes`.
 
 -   `datatypes.yaml`: Data types supported by the specification.
     The only information provided in the file is:
@@ -48,7 +48,7 @@ Each of these object types has a single file in the `objects/` folder.
     1.  each datatype's full name
     1.  a free text description of the datatype.
 
--   `entities.yaml`: Entities (key/value pairs in folder and filenames).
+-   `entities.yaml`: Entities (key/value pairs in directory and filenames).
 
 -   `metadata.yaml`: All valid metadata fields that are explicitly supported in BIDS sidecar JSON files.
 
@@ -58,7 +58,7 @@ Each of these object types has a single file in the `objects/` folder.
 
 -   `top_level_files.yaml`: Valid top-level files which may appear in a BIDS dataset.
 
--   `associated_data.yaml`: Folders that may appear within a dataset folder without following BIDS rules.
+-   `associated_data.yaml`: Directories that may appear within a dataset directory without following BIDS rules.
 
 ### On re-used objects with different definitions
 
@@ -115,7 +115,7 @@ The `description` field is a freeform description of the modality.
 ### `datatypes.yaml`
 
 This file contains a dictionary in which each datatype is defined.
-Keys are the folder names associated with each datatype (for example, `anat` for anatomical MRI),
+Keys are the directory names associated with each datatype (for example, `anat` for anatomical MRI),
 and each associated value is a dictionary with two keys: `name` and `description`.
 
 The `name` field is the full name of the datatype.
@@ -218,7 +218,7 @@ There are additional fields which may define rules that apply to a given type.
 
        -   `dataset_relative` (relative paths from dataset root),
 
-       -   `participant_relative` (relative paths from participant folder).
+       -   `participant_relative` (relative paths from participant directory).
 
     -   `enum` defines a list of valid values for the field.
         The minimum string length (`minLength`) defaults to 1.
@@ -388,21 +388,21 @@ The `description` field is a freeform description of the file.
 
 ### `associated_data.yaml`
 
-This file contains a dictionary in which each non-BIDS folder is defined.
-Keys are folder names, and each associated value is a dictionary with two keys: `name` and `description`.
+This file contains a dictionary in which each non-BIDS directory is defined.
+Keys are directory names, and each associated value is a dictionary with two keys: `name` and `description`.
 
-The `name` field is the full name of the folder.
-The `description` field is a freeform description of the folder.
+The `name` field is the full name of the directory.
+The `description` field is a freeform description of the directory.
 
 ## Rule files
 
-The files in the `rules/` folder are less standardized than the files in `objects/`,
+The files in the `rules/` directory are less standardized than the files in `objects/`,
 because rules governing how different object types interact in a valid dataset are more variable
 than the object definitions.
 
 -   `modalities.yaml`: This file simply groups `datatypes` under their associated modality.
 
--   `datatypes/*.yaml`: Files in the `datatypes` folder contain information about valid filenames within a given datatype.
+-   `datatypes/*.yaml`: Files in the `datatypes` directory contain information about valid filenames within a given datatype.
     Specifically, each datatype's YAML file contains a list of dictionaries.
     Each dictionary contains a list of suffixes, entities, and file extensions which may constitute a valid BIDS filename.
 
@@ -410,7 +410,7 @@ than the object definitions.
 
 -   `top_level_files.yaml`: Requirement levels and valid file extensions of top-level files.
 
--   `associated_data.yaml`: Requirement levels of associated non-BIDS folders.
+-   `associated_data.yaml`: Requirement levels of associated non-BIDS directories.
 
 ### `modalities.yaml`
 
@@ -419,7 +419,7 @@ The `datatypes` dictionary contains a list of datatypes that fall under that mod
 
 ### `datatypes/*.yaml`
 
-The files in this folder are currently the least standardized of any part of the schema.
+The files in this directory are currently the least standardized of any part of the schema.
 
 Each file corresponds to a single `datatype`.
 Within the file is a list of dictionaries.
@@ -496,5 +496,5 @@ In cases where there is a data file and a metadata file, the `.json` extension f
 
 ### `associated_data.yaml`
 
-This file contains a dictionary in which each key is a folder and the value is a dictionary with one key: `required`.
-The `required` entry contains a boolean value to indicate if that folder is required for BIDS datasets or not.
+This file contains a dictionary in which each key is a directory and the value is a dictionary with one key: `required`.
+The `required` entry contains a boolean value to indicate if that directory is required for BIDS datasets or not.
diff --git a/src/schema/objects/associated_data.yaml b/src/schema/objects/associated_data.yaml
index 901e17bdac..1541da72e7 100644
--- a/src/schema/objects/associated_data.yaml
+++ b/src/schema/objects/associated_data.yaml
@@ -1,12 +1,12 @@
 ---
-# This file describes folders that may appear within a dataset folder
+# This file describes directories that may appear within a dataset directory
 # without following BIDS rules.
-# Information about whether these folders are required or not is present in
+# Information about whether these directories are required or not is present in
 # `rules/associated_data.yaml`.
 code:
   name: Code
   description: |
-    A folder in which to store any code used to generate the derivatives from the
+    A directory in which to store any code used to generate the derivatives from the
     source data.
 derivatives:
   name: Derivative data
@@ -20,10 +20,10 @@ sourcedata:
 stimuli:
   name: Stimulus files
   description: |
-    The stimulus files can be added in a `/stimuli` folder
-    (under the root folder of the dataset; with optional subfolders)
+    The stimulus files can be added in a `/stimuli` directory
+    (under the root directory of the dataset; with optional subdirectories)
     AND using a stim_file column in *_events.tsv mentioning which stimulus file was
     used for a given event.
 
     There are no restrictions on the file formats of the stimuli files, but they should be
-    stored in the `/stimuli` folder.
+    stored in the `/stimuli` directory.
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 1c34c936bd..36e93fe308 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -423,8 +423,8 @@ stim_file:
     Represents the location of the stimulus file (such as an image, video, or
     audio file) presented at the given onset time.
     There are no restrictions on the file formats of the stimuli files,
-    but they should be stored in the `/stimuli` folder
-    (under the root folder of the dataset; with optional subfolders).
+    but they should be stored in the `/stimuli` directory
+    (under the root directory of the dataset; with optional subdirectories).
     The values under the `stim_file` column correspond to a path relative to
     `/stimuli`.
     For example `images/cat03.jpg` will be translated to `/stimuli/images/cat03.jpg`.
diff --git a/src/schema/objects/formats.yaml b/src/schema/objects/formats.yaml
index 67a78be33f..4abc02fa84 100644
--- a/src/schema/objects/formats.yaml
+++ b/src/schema/objects/formats.yaml
@@ -46,9 +46,9 @@ bids_uri:
     starting with "bids:".
   pattern: 'bids:[0-9a-zA-Z/#:\?\_\-\.]+'
 dataset_relative:
-  name: Path relative to the BIDS dataset folder
+  name: Path relative to the BIDS dataset directory
   description: |
-    A path to a file, relative to the dataset folder.
+    A path to a file, relative to the dataset directory.
 
     The validation for this format is minimal.
     It simply ensures that the value is a string with any characters that may appear in a valid path,
@@ -77,14 +77,14 @@ file_relative:
     without starting with "/" (an absolute path).
   pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
 participant_relative:
-  name: Path relative to the participant folder
+  name: Path relative to the participant directory
   description: |
-    A path to a file, relative to the participant's folder in the dataset.
+    A path to a file, relative to the participant's directory in the dataset.
 
     The validation for this format is minimal.
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path) or "sub/"
-    (a relative path starting with the participant folder, rather than relative to that folder).
+    (a relative path starting with the participant directory, rather than relative to that directory).
   pattern: '(?!/)(?!sub-)[0-9a-zA-Z/\_\-\.]+'
 rrid:
   name: Research resource identifier
@@ -92,14 +92,14 @@ rrid:
     A [research resource identifier](https://scicrunch.org/resources).
   pattern: 'RRID:.+_.+'
 stimuli_relative:
-  name: Path relative to the stimuli folder
+  name: Path relative to the stimuli directory
   description: |
-    A path to a stimulus file, relative to a `/stimuli` folder somewhere.
+    A path to a stimulus file, relative to a `/stimuli` directory somewhere.
 
     The validation for this format is minimal.
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path) or "stimuli/"
-    (a relative path starting with the stimuli folder, rather than relative to that folder).
+    (a relative path starting with the stimuli directory, rather than relative to that directory).
   pattern: '(?!/)(?!stimuli/)[0-9a-zA-Z/\_\-\.]+'
 time:
   name: Time
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 2f182ae71c..61bf8dcc6a 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -134,7 +134,7 @@ ArterialSpinLabelingType:
 AssociatedEmptyRoom:
   name: AssociatedEmptyRoom
   description: |
-    Relative path in BIDS folder structure to empty-room file associated with
+    Relative path in BIDS directory structure to empty-room file associated with
     the subject's MEG recording.
     The path needs to use forward slashes instead of backward slashes
     (for example,
@@ -1279,7 +1279,7 @@ IntendedFor:
   description: |
     The paths to files for which the associated file is intended to be used.
     Contains one or more filenames with paths relative to the participant
-    subfolder.
+    subdirectory.
     Paths need to use forward slashes instead of backward slashes,
     regardless of operating system.
   anyOf:
diff --git a/src/schema/rules/associated_data.yaml b/src/schema/rules/associated_data.yaml
index 609fcafaa5..b855bf9a25 100644
--- a/src/schema/rules/associated_data.yaml
+++ b/src/schema/rules/associated_data.yaml
@@ -1,6 +1,6 @@
 ---
-# This file describes the requirement levels of folders which may appear
-# within a dataset folder without following BIDS format.
+# This file describes the requirement levels of directories which may appear
+# within a dataset directory without following BIDS format.
 code:
   required: false
 derivatives:
diff --git a/tools/examplecode/example.py b/tools/examplecode/example.py
index 95be6c19c1..abaac4663b 100644
--- a/tools/examplecode/example.py
+++ b/tools/examplecode/example.py
@@ -45,7 +45,7 @@ def build_tree(self):
 
     def _tree_body(self, directory, prefix=""):
         """
-        Loops through the dictionary content representing a folder
+        Loops through the dictionary content representing a directory
         and append the content to the tree.
         This is done recursively any time a new dictionary is encountered.
         """
@@ -54,7 +54,7 @@ def _tree_body(self, directory, prefix=""):
 
         for index, entry in enumerate(directory):
 
-            # change connector if this is the last item in this folder
+            # change connector if this is the last item in this directory
             connector = self.ELBOW if index == entries_count - 1 else self.TEE
             self._add_dictionary(
                 directory, entry, index, entries_count, prefix, connector
diff --git a/tools/filetree_example.ipynb b/tools/filetree_example.ipynb
index 3c02f18a8f..81d7876d5e 100644
--- a/tools/filetree_example.ipynb
+++ b/tools/filetree_example.ipynb
@@ -34,7 +34,7 @@
    "outputs": [],
    "source": [
     "directory_dict =  {\n",
-    "                    \"sub-01\": { # use nested dictionaries to represent folders\n",
+    "                    \"sub-01\": { # use nested dictionaries to represent directories\n",
     "                        \"sub-01_part-mag_T1w.nii.gz\" : \"\",\n",
     "                        \"sub-01_part-mag_T1w.json\" : \"\",\n",
     "                        \"sub-01_part-phase_T1w.nii.gz\" : \"\",\n",
@@ -58,7 +58,7 @@
    "source": [
     "nested_directory_dict =  {\n",
     "                        \"sub-01\" : {\n",
-    "                            \"anat\": { # you can represent subfolders by nesting directories\n",
+    "                            \"anat\": { # you can represent subdirectories by nesting directories\n",
     "                                \"sub-01_part-mag_T1w.nii.gz\" : \"\",\n",
     "                                \"sub-01_part-mag_T1w.json\" : \"\",\n",
     "                                \"sub-01_part-phase_T1w.nii.gz\" : \"\",\n",
@@ -86,7 +86,7 @@
     "                    \"...\" : \"\",\n",
     "                },\n",
     "                \"sourcedata\": {\n",
-    "                    \"sub-01\" : {}, # use empty dictionaries to represent folders without specifying their content\n",
+    "                    \"sub-01\" : {}, # use empty dictionaries to represent directories without specifying their content\n",
     "                    \"sub-02\" : {},\n",
     "                    \"...\" : \"\",\n",
     "                },\n",
@@ -107,7 +107,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# you can also represent files and folders on the same level\n",
+    "# you can also represent files and directories on the same level\n",
     "\n",
     "directory = {\n",
     "            \"dataset_description.json\" : \"\",\n",
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index 6f4363fbff..d27aef4f6d 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -113,7 +113,7 @@ def make_metadata_table(field_info):
     ----------
     field_names : dict
         A list of the field names.
-        Field names correspond to filenames in the "metadata" folder of the
+        Field names correspond to filenames in the "metadata" directory of the
         schema.
         Until requirement levels can be codified in the schema,
         this argument will be dictionary, with the field names as keys and
@@ -138,7 +138,7 @@ def make_columns_table(column_info):
     ----------
     column_info : dict
         A list of the column names.
-        Column names correspond to filenames in the "columns" folder of the
+        Column names correspond to filenames in the "columns" directory of the
         schema.
         Until requirement levels can be codified in the schema,
         this argument will be a dictionary, with the column names as keys and
@@ -162,7 +162,7 @@ def make_filetree_example(filetree_info, use_pipe=True):
     Parameters
     ----------
     filetree_info : dict
-        Dictionary to represent the folder content.
+        Dictionary to represent the directory content.
     use_pipe : bool
         Set to ``False`` to avoid using pdf unfriendly pipes: "│ └─ ├─"
 
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index ea4f0fd1f9..c1b8872142 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -176,7 +176,7 @@ def make_filename_template(schema, n_dupes_to_combine=6, **kwargs):
     entity_order = schema["rules"]["entities"]
 
     paragraph = ""
-    # Parent folders
+    # Parent directories
     paragraph += "{}-<{}>/\n\t[{}-<{}>/]\n".format(
         schema["objects"]["entities"]["subject"]["entity"],
         schema["objects"]["entities"]["subject"]["format"],
@@ -263,7 +263,7 @@ def make_entity_table(schema, tablefmt="github", **kwargs):
     Parameters
     ----------
     schema_path : str
-        Folder containing schema, which is stored in yaml files.
+        Directory containing schema, which is stored in yaml files.
     entities_file : str, optional
         File in which entities are described.
         This is used for hyperlinks in the table, so the path to the file
diff --git a/tools/schemacode/schemacode/schema.py b/tools/schemacode/schemacode/schema.py
index 1748c3a5aa..54d668d051 100644
--- a/tools/schemacode/schemacode/schema.py
+++ b/tools/schemacode/schemacode/schema.py
@@ -66,7 +66,7 @@ def load_schema(schema_path):
     Parameters
     ----------
     schema_path : str
-        Folder containing yaml files or yaml file.
+        Directory containing yaml files or yaml file.
 
     Returns
     -------
@@ -98,7 +98,7 @@ def load_schema(schema_path):
         dict_ = yaml.safe_load(rule_group_file.read_text())
         schema["rules"][rule_group_file.stem] = dereference_yaml(dict_, dict_)
 
-    # Load folders of rule subgroups.
+    # Load directories of rule subgroups.
     for rule_group_file in sorted(rules_dir.glob("*/*.yaml")):
         rule = schema["rules"].setdefault(rule_group_file.parent.name, {})
         lgr.debug(f"Loading {rule_group_file.stem} rules.")
diff --git a/tools/schemacode/schemacode/tests/test_schema.py b/tools/schemacode/schemacode/tests/test_schema.py
index 3f71542a81..f058b7e1e2 100644
--- a/tools/schemacode/schemacode/tests/test_schema.py
+++ b/tools/schemacode/schemacode/tests/test_schema.py
@@ -6,7 +6,7 @@
 
 def test_load_schema(schema_dir):
     """Smoke test for schemacode.schema.load_schema."""
-    # Pointing to a nonexistent folder should raise a ValueError
+    # Pointing to a nonexistent directory should raise a ValueError
     bad_path = "/path/to/nowhere"
     with pytest.raises(ValueError):
         schema.load_schema(bad_path)
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 6d2cfcabe5..c2eadc5244 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -7,12 +7,12 @@
 
 
 def get_schema_path():
-    """Get the path to the schema folder.
+    """Get the path to the schema directory.
 
     Returns
     -------
     str
-        Absolute path to the folder containing schema-related files.
+        Absolute path to the directory containing schema-related files.
     """
     return op.abspath(op.join(op.dirname(__file__), "data", "schema"))
 

From ee9e8b539f582e0171f7a365127b9dab80c58cb4 Mon Sep 17 00:00:00 2001
From: Mateusz Pawlik <mateusz.pawlik@plus.ac.at>
Date: Mon, 4 Apr 2022 16:51:07 +0200
Subject: [PATCH 230/347] [ENH] Allow README file extensions. (#1033)

* Fixed contributing link

* Modified README description.

Used REQUIRED for consistency with the schema.

* Added optional file extensions.

* Added line break because 'Lint yml files' check failed.

* Applied feedback to README description.

* Removed 'free-form' from README description

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Removed "(unstructured text)" at "txt" in README

* Polishing README description.

Added fogotten changes propagation to src/03-modality-agnostic-files.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
---
 src/03-modality-agnostic-files.md       | 14 ++++++++++++--
 src/99-appendices/14-glossary.md        |  2 +-
 src/schema/objects/top_level_files.yaml | 17 ++++++++++++++---
 src/schema/rules/top_level_files.yaml   |  3 +++
 4 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index f46cca8615..014e5e6726 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -143,8 +143,18 @@ Example:
 
 ### `README`
 
-Every BIDS dataset SHOULD come with a free form text file (`README`) describing the dataset in more detail.
-The `README` file MUST be either in ASCII or UTF-8 encoding.
+A REQUIRED text file, `README`, SHOULD describe the dataset in more detail.
+The `README` file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions:
+`.md` ([Markdown](https://www.markdownguide.org/)),
+`.rst` ([reStructuredText](https://docutils.sourceforge.io/rst.html)),
+or `.txt`.
+A BIDS dataset MUST NOT contain more than one `README` file (with or without extension)
+at its root directory.
+BIDS does not make any recommendations with regards to the
+[Markdown flavor](https://www.markdownguide.org/extended-syntax/#lightweight-markup-languages)
+and does not validate the syntax of Markdown and reStructuredText.
+The `README` file SHOULD be structured such that its contents can be easily understood
+even if the used format is not rendered.
 A guideline for creating a good `README` file can be found in the
 [bids-starter-kit](https://github.com/bids-standard/bids-starter-kit/blob/master/templates/README).
 
diff --git a/src/99-appendices/14-glossary.md b/src/99-appendices/14-glossary.md
index 8f9affb6f1..e56ff9381f 100644
--- a/src/99-appendices/14-glossary.md
+++ b/src/99-appendices/14-glossary.md
@@ -4,6 +4,6 @@ This section compiles the object definitions in the schema.
 
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
-  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-BIDS-schema
 -->
 {{ MACROS___make_glossary() }}
diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 79eab838c0..4a3df6121d 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_files.yaml
@@ -21,9 +21,20 @@ LICENSE:
 README:
   name: README
   description: |
-    In addition a free form text file (`README`) describing the dataset in more details SHOULD be
-    provided.
-    The `README` file MUST be either in ASCII or UTF-8 encoding.
+    A REQUIRED text file, `README`, SHOULD describe the dataset in more detail.
+    The `README` file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions:
+    `.md` ([Markdown](https://www.markdownguide.org/)),
+    `.rst` ([reStructuredText](https://docutils.sourceforge.io/rst.html)),
+    or `.txt`.
+    A BIDS dataset MUST NOT contain more than one `README` file (with or without extension)
+    at its root directory.
+    BIDS does not make any recommendations with regards to the
+    [Markdown flavor](https://www.markdownguide.org/extended-syntax/#lightweight-markup-languages)
+    and does not validate the syntax of Markdown and reStructuredText.
+    The `README` file SHOULD be structured such that its contents can be easily understood
+    even if the used format is not rendered.
+    A guideline for creating a good `README` file can be found in the
+    [bids-starter-kit](https://github.com/bids-standard/bids-starter-kit/blob/master/templates/README).
 dataset_description:
   name: Dataset Description
   description: |
diff --git a/src/schema/rules/top_level_files.yaml b/src/schema/rules/top_level_files.yaml
index f24133deba..cc776648cf 100644
--- a/src/schema/rules/top_level_files.yaml
+++ b/src/schema/rules/top_level_files.yaml
@@ -3,6 +3,9 @@ README:
   required: true
   extensions:
   - None
+  - .md
+  - .rst
+  - .txt
 CHANGES:
   required: true
   extensions:

From 252e2c4bfd4fcdfa8bd1f92af0ff35dacd6c0915 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 6 Apr 2022 10:25:47 +0200
Subject: [PATCH 231/347] [DOC] Preface each macro call with comment (#1052)

* [DATALAD RUNCMD] add filetree macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_filetree_example/i \\<!-- This block generates a file tree.\\nA guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/**/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add filetree macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_filetree_example/i \\<!-- This block generates a file tree.\\nA guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add metadata table macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_metadata_table/i \\<!-- This block generates a metadata table.\\nThe definitions of these fields can be found in\\n  src/schema/objects/metadata.yaml\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add metadata table macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_metadata_table/i \\<!-- This block generates a metadata table.\\nThe definitions of these fields can be found in\\n  src/schema/objects/metadata.yaml\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/**/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add columns table macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_columns_table/i \\<!-- This block generates a columns table.\\nThe definitions of these fields can be found in\\n  src/schema/objects/columns.yaml\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add columns table macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_columns_table/i \\<!-- This block generates a columns table.\\nThe definitions of these fields can be found in\\n  src/schema/objects/columns.yaml\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/**/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add suffix macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_suffix_table/i \\<!--\\nThis block generates a suffix table.\\nThe definitions of these fields can be found in\\n  src/schema/rules/datatypes\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/**/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] add filename template macro comment

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i '/^.*make_filename_template/i \\<!--\\nThis block generates a filename templates.\\nThe inputs for this macro can be found in the folder\\n  src/schema/rules/datatypes\\nand a guide for using macros can be found at\\n https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md\\n-->' ./src/**/*.md",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* update other macros with comments

* indent comment
---
 src/02-common-principles.md                   |  34 +++
 src/03-modality-agnostic-files.md             |  42 +++
 .../01-magnetic-resonance-imaging-data.md     | 268 ++++++++++++++++++
 .../02-magnetoencephalography.md              | 121 ++++++++
 .../03-electroencephalography.md              | 107 +++++++
 .../04-intracranial-electroencephalography.md | 115 ++++++++
 .../05-task-events.md                         |  36 +++
 ...logical-and-other-continuous-recordings.md |  30 ++
 .../07-behavioral-experiments.md              |  13 +
 .../08-genetic-descriptor.md                  |  12 +
 .../09-positron-emission-tomography.md        |  62 ++++
 .../10-microscopy.md                          |  65 +++++
 src/05-derivatives/02-common-data-types.md    |  32 +++
 src/05-derivatives/03-imaging.md              |  72 +++++
 src/06-longitudinal-and-multi-site-studies.md |   4 +
 src/99-appendices/04-entity-table.md          |   2 +
 src/99-appendices/06-meg-file-formats.md      |  40 +++
 src/99-appendices/09-entities.md              |   2 +
 src/99-appendices/10-file-collections.md      |  14 +
 src/99-appendices/11-qmri.md                  |  42 +++
 src/99-appendices/14-glossary.md              |   2 +
 21 files changed, 1115 insertions(+)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index ca238fa64c..5e1379b163 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -265,6 +265,10 @@ However, in the case that these data are to be included:
 
 Alternatively one can organize their data in the following way
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "my_dataset-1": {
@@ -360,6 +364,10 @@ Derivatives can be stored/distributed in two ways:
 
     Example of a derivative dataset including the raw dataset as source:
 
+    <!-- This block generates a file tree.
+    A guide for using macros can be found at
+    https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+    -->
     {{ MACROS___make_filetree_example(
         {
         "my_processed_data": {
@@ -461,6 +469,12 @@ Note that if a field name included in the data dictionary matches a column name
 then that field MUST contain a description of the corresponding column,
 using an object containing the following fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
         "LongName": "OPTIONAL",
@@ -592,6 +606,10 @@ Corollaries:
 
 Example 1: Demonstration of inheritance principle
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
@@ -635,6 +653,10 @@ absence in the metadata file at the lower level (rule 5.b; corollary 3).
 
 Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
@@ -656,6 +678,10 @@ Example 2: Impermissible use of multiple metadata files at one directory level (
 Example 3: Modification of filesystem structure from Example 2 to satisfy inheritance
 principle requirements
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
@@ -676,6 +702,10 @@ principle requirements
 
 Example 4: Single metadata file applying to multiple data files (corollary 2)
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-01": {
@@ -823,6 +853,10 @@ This is an example of the directory and file structure. Because there is only on
 session, the session level is not required by the format. For details on
 individual files see descriptions in the next section:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-control01": {
diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 014e5e6726..82bdc20af0 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -14,6 +14,12 @@ Templates:
 The file `dataset_description.json` is a JSON file describing the dataset.
 Every dataset MUST include this file with the following fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Name": "REQUIRED",
@@ -99,6 +105,12 @@ top level of every derived dataset:
 In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
 `GeneratedBy` key:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "GeneratedBy": "REQUIRED"
@@ -209,6 +221,12 @@ Commonly used *optional* columns in `participants.tsv` files are `age`, `sex`,
 of these columns, and in case that you do use them, we RECOMMEND to use the
 following values for them:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "participant_id": ("REQUIRED", "There MUST be exactly one row for each participant."),
@@ -288,6 +306,12 @@ The purpose of this file is to describe properties of samples, indicated by the
 This file is REQUIRED if `sample-<label>` is present in any filename within the dataset.
 Each sample MUST be described by one and only one row.
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "sample_id": ("REQUIRED", "The combination of `sample_id` and `participant_id` MUST be unique."),
@@ -358,6 +382,12 @@ MAY be accompanied by a JSON file describing the columns in detail
 
 In addition to the column descriptions, the JSON file MAY contain the following fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "MeasurementToolMetadata": "OPTIONAL",
@@ -424,6 +454,12 @@ Some recordings consist of multiple parts, that span several files,
 for example through `echo-`, `part-`, or `split-` entities.
 Such recordings MUST be documented with one row per file.
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "filename": ("REQUIRED", "There MUST be exactly one row for each file."),
@@ -467,6 +503,12 @@ These files MUST include a `session_id` column and describe each session by one
 Column names in `sessions.tsv` files MUST be different from group level participant key column names in the
 [`participants.tsv` file](./03-modality-agnostic-files.md#participants-file).
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "session_id": ("REQUIRED", "There MUST be exactly one row for each session."),
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 4c3d47dd13..917b0d03aa 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -12,6 +12,12 @@ by Ben Inglis.
 
 ### Scanner Hardware
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Manufacturer": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0070 `Manufacturer`."),
@@ -50,6 +56,12 @@ that a given scan was collected with the intended coil elements selected
 
 ### Sequence Specifics
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PulseSequenceType": "RECOMMENDED",
@@ -76,6 +88,12 @@ that a given scan was collected with the intended coil elements selected
 
 ### In-Plane Spatial Encoding
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "NumberShots": "RECOMMENDED",
@@ -117,6 +135,12 @@ and the center of the last "effective" echo, sometimes called the "FSL definitio
 
 ### Timing Parameters
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EchoTime": "RECOMMENDED, but REQUIRED if corresponding fieldmap data is present, or the data comes from a multi echo sequence or Arterial Spin Labeling",
@@ -129,6 +153,12 @@ and the center of the last "effective" echo, sometimes called the "FSL definitio
 
 ### RF & Contrast
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "FlipAngle": "RECOMMENDED, but REQUIRED if `LookLocker` is set `true`",
@@ -138,6 +168,12 @@ and the center of the last "effective" echo, sometimes called the "FSL definitio
 
 ### Slice Acceleration
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "MultibandAccelerationFactor": "RECOMMENDED",
@@ -148,6 +184,12 @@ and the center of the last "effective" echo, sometimes called the "FSL definitio
 
 Useful for multimodal co-registration with MEG, (S)EEG, TMS, and so on.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "AnatomicalLandmarkCoordinates__mri": "RECOMMENDED",
@@ -168,6 +210,12 @@ The modality labels `dwi` (under `dwi/`), `bold` (under `func/`),
 any modality under `fmap/` are allowed to encode the MR protocol intent for
 fieldmap estimation using the following metadata:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "B0FieldIdentifier": "RECOMMENDED",
@@ -177,6 +225,12 @@ fieldmap estimation using the following metadata:
 
 ### Institution information
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "InstitutionName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0080 `InstitutionName`."),
@@ -192,10 +246,24 @@ whenever possible. See also
 
 ## Anatomy imaging data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["anat"]) }}
 
 Currently supported non-parametric structural MR images include:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "T1w",
@@ -256,6 +324,12 @@ JSON file. See [Common metadata fields](#common-metadata-fields) for a
 list of terms and their definitions. There are also some OPTIONAL JSON
 fields specific to anatomical scans:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "ContrastBolusIngredient": "OPTIONAL",
@@ -273,6 +347,10 @@ which are typically used in `part-mag`/`part-phase` or `part-real`/`part-imag`
 pairs of files.
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -307,6 +385,13 @@ different reconstruction algorithms (for example ones using motion correction).
 Structural MR images whose intensity is represented in a non-arbitrary scale
 constitute parametric maps. Currently supported parametric maps include:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "T1map",
@@ -352,6 +437,13 @@ They are, however, still valid suffixes, to maintain backwards compatibility.
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
 datasets (created after version 1.5.0.):
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "T2star",
@@ -365,6 +457,13 @@ datasets (created after version 1.5.0.):
 
 Currently supported image contrasts include:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "bold",
@@ -374,6 +473,13 @@ Currently supported image contrasts include:
    )
 }}
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["func"]) }}
 
 Functional imaging consists of techniques that support rapid temporal repetition.
@@ -426,6 +532,10 @@ for more information on `dir` field specification.
 Multi-echo data MUST be split into one file per echo using the
 [`echo-<index>`](../99-appendices/09-entities.md#echo) key-value pair. For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -456,6 +566,10 @@ name with the exception of the `part-<mag|phase>` or `part-<real|imag>` key/valu
 
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -478,6 +592,12 @@ JSON file.
 
 ### Required fields
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "RepetitionTime": "REQUIRED",
@@ -495,6 +615,12 @@ combined image rather than an image from each coil.
 
 #### Timing Parameters
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "NumberOfVolumesDiscardedByScanner": "RECOMMENDED",
@@ -526,6 +652,12 @@ sparse sequences.
 
 #### fMRI task information
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Instructions": ("RECOMMENDED", "This is especially important in context of resting state recordings and distinguishing between eyes open and eyes closed paradigms."),
@@ -540,6 +672,10 @@ additional terms and their definitions.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -589,6 +725,13 @@ and that can be used for practical guidance when curating a new dataset:
 Diffusion-weighted imaging data acquired for a participant.
 Currently supported image types include:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "dwi",
@@ -597,6 +740,13 @@ Currently supported image types include:
    )
 }}
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["dwi"]) }}
 
 If more than one run of the same acquisition and direction has been acquired, the
@@ -688,6 +838,12 @@ not be able to be directly concatenated.
 BIDS permits defining arbitrary groupings of these multipart scans with the
 following metadata:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "MultipartID": "REQUIRED",
@@ -707,6 +863,10 @@ two runs each, and the intent of the researcher is that all of them are
 part of a unique multipart scan, then they will tag all four runs with the
 same `MultipartID` (shown at the right-hand side of the file listing):
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-1": {
@@ -723,6 +883,10 @@ same `MultipartID` (shown at the right-hand side of the file listing):
 If, conversely, the researcher wanted to store two multipart scans, one possibility
 is to combine matching phase-encoding directions:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-1": {
@@ -739,6 +903,10 @@ is to combine matching phase-encoding directions:
 Alternatively, the researcher's intent could be combining opposed phase-encoding
 runs instead:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-1": {
@@ -755,6 +923,10 @@ runs instead:
 The `MultipartID` metadata MAY be used with the
 [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair, for example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-1": {
@@ -792,6 +964,13 @@ Several [example ASL datasets](https://github.com/bids-standard/bids-examples#as
 have been formatted using this specification
 and can be used for practical guidance when curating a new dataset.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["perf"]) }}
 
 The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order,
@@ -850,6 +1029,12 @@ See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#summary-i
 
 #### Common metadata fields applicable to both (P)CASL and PASL
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "ArterialSpinLabelingType": "REQUIRED",
@@ -875,6 +1060,12 @@ See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#summary-i
 
 These fields can only be used when `ArterialSpinLabelingType` is `"CASL"` or `"PCASL"`. See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#pcasl-sequence) for more information on the (P)CASL sequence and the Labeling Pulse fields.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "LabelingDuration": "REQUIRED",
@@ -893,6 +1084,12 @@ These fields can only be used when `ArterialSpinLabelingType` is `"CASL"` or `"P
 
 These fields can only be used when `ArterialSpinLabelingType` is `PASL`. See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#pasl-sequence) for more information on the PASL sequence and the BolusCutOff fields.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "BolusCutOffFlag": "REQUIRED",
@@ -907,6 +1104,12 @@ These fields can only be used when `ArterialSpinLabelingType` is `PASL`. See [Ap
 
 Some common metadata fields are REQUIRED for the `*_m0scan.json`: `EchoTime`, `RepetitionTimePreparation`, and `FlipAngle` in case `LookLocker` is `true`.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "IntendedFor": (
@@ -952,6 +1155,13 @@ The current version of this standard considers four different scenarios:
 These four different types of field mapping strategies can be encoded
 using the following image types:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "magnitude",
@@ -997,6 +1207,12 @@ tools that support older datasets.
 Fieldmap data MAY be linked to the specific scan(s) it was acquired for by
 filling the `IntendedFor` field in the corresponding JSON file.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "IntendedFor": (
@@ -1029,6 +1245,13 @@ containing that type of fieldmap can be found here:
 -   [`genetics_ukbb`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
 -   [`ds000117`](https://github.com/bids-standard/bids-examples/tree/master/ds000117)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["phasediff", "magnitude1", "magnitude2"]) }}
 
 where
@@ -1038,6 +1261,12 @@ the OPTIONAL `_magnitude2` image to the longer echo time.
 
 Required fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EchoTime1": "REQUIRED",
@@ -1065,10 +1294,23 @@ Similar to case 1, but instead of a precomputed phase-difference map, two
 separate phase images and two magnitude images corresponding to first and
 second echos are available.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["phase1", "phase2", "magnitude1", "magnitude2"]) }}
 
 Required fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EchoTime__fmap": "REQUIRED",
@@ -1089,10 +1331,23 @@ For example, `sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.json`
 In some cases (for example GE), the scanner software will directly reconstruct a
 *B<sub>0</sub>* field map along with a magnitude image used for anatomical reference.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["fieldmap", "magnitude"]) }}
 
 Required fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Units": (
@@ -1131,6 +1386,13 @@ in the latter case, all timepoints share the same scanning parameters.
 Examples of software tools using these kinds of images are FSL TOPUP,
 AFNI `3dqwarp`, and SPM.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["epi"]) }}
 
 The [`dir-<label>`](../99-appendices/09-entities.md#dir) entity is REQUIRED
@@ -1141,6 +1403,12 @@ the REQUIRED `PhaseEncodingDirection` metadata field
 
 Required fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PhaseEncodingDirection": "REQUIRED",
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index e1d03756a5..c7a0c76cda 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -16,6 +16,13 @@ the [BIDS examples repository](https://github.com/bids-standard/bids-examples).
 
 ## MEG recording data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
    datatypes=["meg"],
    suffixes=["meg", "markers", "events", "physio", "stim"])
@@ -91,6 +98,12 @@ systems (see [coordinates section](#coordinate-system-json-_coordsystemjson) bel
 
 Generic fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TaskName": ("REQUIRED", "A RECOMMENDED convention is to name resting state task using labels beginning with `rest`."),
@@ -101,6 +114,12 @@ SHOULD be present: For consistency between studies and institutions, we
 encourage users to extract the values of these fields from the actual raw data.
 Whenever possible, please avoid using ad-hoc wording.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "InstitutionName": "RECOMMENDED",
@@ -130,6 +149,12 @@ Whenever possible, please avoid using ad-hoc wording.
 
 Specific MEG fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "SamplingFrequency": ("REQUIRED", "The sampling frequency of data channels that deviate from the main sampling frequency SHOULD be specified in the `channels.tsv` file."),
@@ -143,6 +168,12 @@ Specific MEG fields MUST be present:
 
 SHOULD be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "MEGChannelCount": "RECOMMENDED",
@@ -171,6 +202,12 @@ Specific EEG fields
 (if recorded with MEG, see [Recording EEG simultaneously with MEG](#recording-eeg-simultaneously-with-meg)
 SHOULD be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EEGPlacementScheme": "OPTIONAL",
@@ -219,6 +256,13 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 ## Channels description (`*_channels.tsv`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["channels"]) }}
 
 This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
@@ -231,6 +275,12 @@ The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
@@ -241,6 +291,12 @@ MUST be present **in this specific order**:
 
 SHOULD be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "description": "OPTIONAL",
@@ -313,6 +369,13 @@ UADC001 AUDIO V envelope of audio signal presented to participant
 
 ## Coordinate System JSON (`*_coordsystem.json`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["coordsystem"]) }}
 
 OPTIONAL. A JSON document specifying the coordinate system(s) used for the MEG,
@@ -320,6 +383,12 @@ EEG, head localization coils, and anatomical landmarks.
 
 MEG and EEG sensors:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "MEGCoordinateSystem": "REQUIRED",
@@ -340,6 +409,12 @@ MEG and EEG sensors:
 
 Head localization coils:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "HeadCoilCoordinates": "OPTIONAL",
@@ -351,6 +426,12 @@ Head localization coils:
 
 Digitized head points:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "DigitizedHeadPoints": "OPTIONAL",
@@ -362,6 +443,12 @@ Digitized head points:
 
 Anatomical MRI:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "IntendedFor": (
@@ -375,6 +462,12 @@ Anatomical MRI:
 
 Anatomical landmarks:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "AnatomicalLandmarkCoordinates": "OPTIONAL",
@@ -402,6 +495,12 @@ session-specific labels for example, "NAS-session1": `[127,213,139]`,"NAS-sessio
 
 Fiducials information:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "FiducialsDescription": "OPTIONAL",
@@ -421,6 +520,13 @@ or:
 Photos of the anatomical landmarks and/or head localization coils
 (`*_photo.jpg`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["photo"]) }}
 
 Photos of the anatomical landmarks and/or head localization coils on the
@@ -441,6 +547,13 @@ actual anatomical nasion: `sub-0001_ses-001_acq-NAS_photo.jpg`
 
 ## Head shape and electrode description (`*_headshape.<ext>`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["headshape"]) }}
 
 This file is RECOMMENDED.
@@ -454,6 +567,10 @@ manufacturer (see [Appendix VI](../99-appendices/06-meg-file-formats.md)).
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {
@@ -492,6 +609,10 @@ SHOULD be present as well.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {},
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 2df55c6a54..95bdeb7850 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -12,6 +12,13 @@ and can be used for practical guidance when curating a new dataset.
 
 ## EEG recording data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
    datatypes=["eeg"],
    suffixes=["eeg", "events", "physio", "stim"])
@@ -79,6 +86,12 @@ be specified.
 
 Generic fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TaskName": ("REQUIRED", "A RECOMMENDED convention is to name resting state task using labels beginning with `rest`."),
@@ -89,6 +102,12 @@ SHOULD be present: For consistency between studies and institutions, we
 encourage users to extract the values of these fields from the actual raw data.
 Whenever possible, please avoid using ad hoc wording.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "InstitutionName": "RECOMMENDED",
@@ -107,6 +126,12 @@ Whenever possible, please avoid using ad hoc wording.
 
 Specific EEG fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EEGReference": "REQUIRED",
@@ -118,6 +143,12 @@ Specific EEG fields MUST be present:
 
 SHOULD be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "CapManufacturer": "RECOMMENDED",
@@ -185,6 +216,13 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 ## Channels description (`*_channels.tsv`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["channels"]) }}
 
 This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
@@ -205,6 +243,12 @@ The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
@@ -215,6 +259,12 @@ MUST be present **in this specific order**:
 
 SHOULD be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "description": "OPTIONAL",
@@ -270,6 +320,13 @@ UADC001  MISC  n/a    envelope of audio signal        n/a           good    n/a
 
 ## Electrodes description (`*_electrodes.tsv`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["electrodes"]) }}
 
 File that gives the location of EEG electrodes. Note that coordinates are
@@ -281,6 +338,12 @@ file MUST be specified as well**. The order of the required columns in the
 
 MUST be present **in this specific order**:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "name__electrodes": "REQUIRED",
@@ -292,6 +355,12 @@ MUST be present **in this specific order**:
 
 SHOULD be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "type__electrodes": "RECOMMENDED",
@@ -322,6 +391,13 @@ the recording.
 
 ## Coordinate System JSON (`*_coordsystem.json`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["coordsystem"]) }}
 
 A `*_coordsystem.json` file is used to specify the fiducials, the location of
@@ -360,6 +436,12 @@ head.
 
 General fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "IntendedFor": (
@@ -372,6 +454,12 @@ General fields:
 
 Fields relating to the EEG electrode positions:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "EEGCoordinateSystem": "REQUIRED",
@@ -382,6 +470,12 @@ Fields relating to the EEG electrode positions:
 
 Fields relating to the position of fiducials measured during an EEG session/run:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "FiducialsDescription": "OPTIONAL",
@@ -394,6 +488,12 @@ Fields relating to the position of fiducials measured during an EEG session/run:
 
 Fields relating to the position of anatomical landmark measured during an EEG session/run:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "AnatomicalLandmarkCoordinates": "RECOMMENDED",
@@ -430,6 +530,13 @@ Example:
 
 Photos of the anatomical landmarks and/or fiducials.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["photo"]) }}
 
 Photos of the anatomical landmarks and/or fiducials are OPTIONAL.
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index 85ca8fbc78..a79387f0e2 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -12,6 +12,13 @@ and can be used for practical guidance when curating a new dataset.
 
 ## iEEG recording data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
    datatypes=["ieeg"],
    suffixes=["ieeg", "events", "physio", "stim"])
@@ -92,6 +99,12 @@ please avoid using ad hoc wording.
 
 Generic fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TaskName": ("REQUIRED", "A RECOMMENDED convention is to name resting state task using labels beginning with `rest`."),
@@ -104,6 +117,12 @@ SHOULD be present: For consistency between studies and institutions, we
 encourage users to extract the values of these fields from the actual raw data.
 Whenever possible, please avoid using ad hoc wording.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "InstitutionName": "RECOMMENDED",
@@ -122,6 +141,12 @@ Whenever possible, please avoid using ad hoc wording.
 
 Specific iEEG fields MUST be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "iEEGReference": "REQUIRED",
@@ -133,6 +158,12 @@ Specific iEEG fields MUST be present:
 
 Specific iEEG fields SHOULD be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "DCOffsetCorrection": "DEPRECATED",
@@ -159,6 +190,12 @@ Specific iEEG fields SHOULD be present:
 
 Specific iEEG fields MAY be present:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "ElectricalStimulation": "OPTIONAL",
@@ -205,6 +242,13 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri
 
 ## Channels description (`*_channels.tsv`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["channels"]) }}
 
 A channel represents one time series recorded with the recording system
@@ -221,6 +265,12 @@ The columns of the channels description table stored in `*_channels.tsv` are:
 
 MUST be present **in this specific order**:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "name__channels": ("REQUIRED", "When a corresponding electrode is specified in `_electrodes.tsv`, "
@@ -235,6 +285,12 @@ MUST be present **in this specific order**:
 
 SHOULD be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "reference__ieeg": "OPTIONAL",
@@ -291,6 +347,13 @@ Example of free-form text for field `description`:
 
 ## Electrode description (`*_electrodes.tsv`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["electrodes"]) }}
 
 File that gives the location, size and other properties of iEEG electrodes. Note
@@ -321,6 +384,10 @@ correspond.
 
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -337,6 +404,12 @@ Units are specified in `space-<label>_coordsystem.json`.
 
 MUST be present **in this specific order**:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "name__electrodes": "REQUIRED",
@@ -349,6 +422,12 @@ MUST be present **in this specific order**:
 
 SHOULD be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "material": "RECOMMENDED",
@@ -360,6 +439,12 @@ SHOULD be present:
 
 MAY be present:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "type__electrodes": "OPTIONAL",
@@ -379,6 +464,13 @@ H01   27  -42  -21  5      AdTech
 
 ## Coordinate System JSON (`*_coordsystem.json`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["coordsystem"]) }}
 
 This `_coordsystem.json` file contains the coordinate system in which electrode
@@ -387,6 +479,12 @@ also be specified.
 
 General fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "IntendedFor": (
@@ -409,6 +507,12 @@ General fields:
 
 Fields relating to the iEEG electrode positions:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "iEEGCoordinateSystem": "REQUIRED",
@@ -462,6 +566,13 @@ Example:
 
 ## Photos of the electrode positions (`*_photo.jpg`)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["photo"]) }}
 
 These can include photos of the electrodes on the brain surface, photos of
@@ -489,6 +600,10 @@ Example of the operative photo of ECoG electrodes (here is an annotated example
 which electrodes and vasculature are marked, taken from Hermes et al.,
 JNeuroMeth 2010).
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md
index cdda5e2e3b..407f9ebc86 100644
--- a/src/04-modality-specific-files/05-task-events.md
+++ b/src/04-modality-specific-files/05-task-events.md
@@ -34,6 +34,12 @@ file describing the columns in detail (see
 The tabular files consists of one row per event and a set of REQUIRED
 and OPTIONAL columns:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "onset": "REQUIRED",
@@ -62,6 +68,10 @@ SHOULD be documented in an accompanying JSON sidecar file.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {
@@ -102,6 +112,10 @@ sake of brevity.
 For multi-echo files, the `events.tsv` file is applicable to all echos of
 a particular run:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -139,6 +153,12 @@ for a given event,
 There are no restrictions on the file formats of the stimuli files,
 but they should be stored in the `/stimuli` directory.
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "stim_file": "OPTIONAL",
@@ -153,6 +173,10 @@ The following example includes references to the
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {
@@ -202,6 +226,12 @@ sake of brevity.
 It is RECOMMENDED to include details of the stimulus presentation software,
 when applicable:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "StimulusPresentation": "RECOMMENDED",
@@ -210,6 +240,12 @@ when applicable:
 
 The object supplied for `StimulusPresentation` SHOULD include the following key-value pairs:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "OperatingSystem": "RECOMMENDED",
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
index 3bf43c7532..06a90f3f3a 100644
--- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
@@ -48,6 +48,12 @@ and a JSON file for storing the following metadata fields.
 Note that when supplying a `*_<physio|stim>.tsv.gz` file, an accompanying
 `*_<physio|stim>.json` MUST be supplied as well.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "SamplingFrequency": "REQUIRED",
@@ -68,6 +74,10 @@ as well as to make support for other file formats possible in the future.
 
 Example `*_physio.tsv.gz`:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {
@@ -88,6 +98,10 @@ Example `*_physio.tsv.gz`:
 
 Example `*_physio.json`:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-control01": {
@@ -114,6 +128,12 @@ Example `*_physio.json`:
 To store pulse or breathing measurements, or the scanner trigger signal, the
 following naming conventions SHOULD be used for the column names:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "cardiac": "OPTIONAL",
@@ -140,6 +160,10 @@ For multi-echo data, a given `physio.tsv` file is applicable to all echos of
 a particular run.
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -158,6 +182,12 @@ For example:
 The following RECOMMENDED metadata can also be added in the side-car JSON files
 of any `*_<physio>.tsv.gz` file.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Manufacturer": "RECOMMENDED",
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
index 23747807d1..1d32f45eb9 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -1,5 +1,12 @@
 # Behavioral experiments (with no neural recordings)
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["beh"]) }}
 
 In addition to logs from behavioral experiments performed alongside imaging data
@@ -36,6 +43,12 @@ In addition to the metadata that is either:
 
 it is RECOMMENDED to add the following metadata to the JSON files of this directory:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TaskName": "RECOMMENDED",
diff --git a/src/04-modality-specific-files/08-genetic-descriptor.md b/src/04-modality-specific-files/08-genetic-descriptor.md
index bdd7d3fa08..08986ef578 100644
--- a/src/04-modality-specific-files/08-genetic-descriptor.md
+++ b/src/04-modality-specific-files/08-genetic-descriptor.md
@@ -27,6 +27,12 @@ Datasets linked to a genetic database entry include the following REQUIRED or OP
 `dataset_description.json` keys (a dot in the key name denotes a key in a sub-[object][],
 see the example further below):
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Genetics.Dataset": "REQUIRED",
@@ -90,6 +96,12 @@ Datasets containing the `Genetics` field in `dataset_description.json` or the
 `genetic_id` column in `participants.tsv` MUST include this file with the following
 fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "GeneticLevel": "REQUIRED",
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 04c6524c98..e7661be71b 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -60,6 +60,13 @@ In this example, tracer injection coincides with scan start.
 
 ## PET recording data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
    datatypes=["pet"],
    suffixes=["pet", "events", "physio", "stim"])
@@ -133,6 +140,12 @@ which we divide into several categories:
 
 #### Scanner Hardware
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Manufacturer": ("REQUIRED", "Corresponds to DICOM Tag 0008, 0070 `Manufacturer`."),
@@ -152,6 +165,12 @@ which we divide into several categories:
 
 #### Radiochemistry
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TracerName": ("REQUIRED", "Corresponds to DICOM Tags (0008,0105) `Mapping Resource` and (0008,0122) `Mapping Resource Name`."),
@@ -184,6 +203,12 @@ which we divide into several categories:
 
 #### Pharmaceuticals
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PharmaceuticalName": ("RECOMMENDED", "Corresponds to DICOM Tag (0008,0034) `Intervention Drug Name`."),
@@ -197,6 +222,12 @@ which we divide into several categories:
 
 #### Time
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "TimeZero": "REQUIRED",
@@ -213,6 +244,12 @@ We refer to the common principles for the standards for describing dates and tim
 
 #### Reconstruction
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "AcquisitionMode": "REQUIRED",
@@ -309,6 +346,13 @@ ses-02 59
 
 ## Blood recording data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["pet"], suffixes=["blood"]) }}
 
 If collected, blood measurements of radioactivity are be stored in
@@ -330,6 +374,12 @@ Innis et al. 2007 ([doi:10.1038/sj.jcbfm.9600493](https://doi.org/10.1038/sj.jcb
 Some metadata about the recording MUST be provided in an additional JSON
 file.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PlasmaAvail": "REQUIRED",
@@ -347,6 +397,12 @@ file.
 
 The following metadata SHOULD or MUST be provided if corresponding flags are `true`.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PlasmaFreeFraction": "RECOMMENDED if `PlasmaAvail` is `true`",
@@ -359,6 +415,12 @@ The following metadata SHOULD or MUST be provided if corresponding flags are `tr
 The following columns are defined for `_blood.tsv` files.
 The `time` column MUST always be the first column.
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "time": "REQUIRED",
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index cb9f486081..5515559fdc 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -18,6 +18,13 @@ Further Microscopy datasets are available:
 
 ## Microscopy imaging data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
 "PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }}
 
@@ -57,6 +64,13 @@ as a successor to OME-TIFF for better remote sharing of large datasets.
 ### Modality suffixes
 Microscopy data currently support the following imaging modalities:
 
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_suffix_table(
       [
          "TEM",
@@ -94,6 +108,10 @@ The label MUST be unique per subject and is RECOMMENDED to be unique throughout
 For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`,
 imaged by scanning electron microscopy (SEM) in PNG format
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -126,6 +144,10 @@ For example: One brain slice (`sample-01`) extracted from subject `sub-01` with
 stains (`stain-01`, `stain-02` and `stain-03`) in three separate files, imaged by selective plane
 illumination microscopy (SPIM) in OME-TIFF format
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -179,6 +201,10 @@ Figure 1: Examples of chunks configurations.
 For example: Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`)
 of subject `sub-01`, imaged by confocal microscopy (CONF) in OME-TIFF format
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -213,6 +239,10 @@ Lower resolutions files MUST be placed under the `derivatives` directory and use
 
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "my_dataset": {
@@ -245,6 +275,12 @@ Microscopy data MUST be described by metadata fields, stored in sidecar JSON fil
 
 #### Device Hardware
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Manufacturer": "RECOMMENDED",
@@ -260,6 +296,12 @@ Microscopy data MUST be described by metadata fields, stored in sidecar JSON fil
 
 #### Image Acquisition
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "PixelSize": "REQUIRED",
@@ -274,6 +316,12 @@ Microscopy data MUST be described by metadata fields, stored in sidecar JSON fil
 
 #### Sample
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "BodyPart": ("RECOMMENDED", "From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example `\"BRAIN\"`)."),
@@ -308,6 +356,12 @@ of the same sample in an implicit coordinate system.
 
 -   Other transformations should be described in derivatives.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "ChunkTransformationMatrix": "RECOMMENDED if `<chunk-index>` is used in filenames",
@@ -409,6 +463,13 @@ Photos of the tissue sample, overview microscopy scans or blockface images from
 MAY be included for visualization of large samples or to indicate the location of chunks
 in a sample.
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
@@ -418,6 +479,10 @@ acquisition of different photos of the same sample.
 
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
diff --git a/src/05-derivatives/02-common-data-types.md b/src/05-derivatives/02-common-data-types.md
index 9dbe604706..4e1b800b49 100644
--- a/src/05-derivatives/02-common-data-types.md
+++ b/src/05-derivatives/02-common-data-types.md
@@ -10,6 +10,12 @@ JSON file is also REQUIRED.
 Each derivative type defines their own set of fields, but all of them
 share the following (non-required) ones:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
         "Description": (
@@ -28,6 +34,10 @@ The location of the file in the original datasets is encoded in the `RawSources`
 and [`_desc-<label>`](../99-appendices/09-entities.md#desc)
 is used to prevent clashing with the original filename.
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -85,6 +95,12 @@ If the [`space` entity](../99-appendices/09-entities.md#space) is omitted,
 or the space is not in the [Standard template identifiers][templates] table,
 then the `SpatialReference` metadata is REQUIRED.
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "SpatialReference": "RECOMMENDED if the derivative is aligned to a standard template listed in [Standard template identifiers][templates]. REQUIRED otherwise.",
@@ -107,6 +123,10 @@ For CIFTI-2 images, the relevant structures are BrainStructure values defined in
 Preprocessed `bold` NIfTI file in `individual` coordinate space. Please mind
 that in this case `SpatialReference` key is REQUIRED.
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -130,6 +150,10 @@ In this example, because all volumetric structures are sampled to the same
 reference, the `VolumeReference` key is used as a default, and only the
 surface references need to be specified by BrainStructure names.
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
    "sub-01": {
@@ -187,6 +211,10 @@ processing for the same input data.
 
 Examples of preprocessed data:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline1": {
@@ -204,6 +232,10 @@ Examples of preprocessed data:
    }
 ) }}
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline2": {
diff --git a/src/05-derivatives/03-imaging.md b/src/05-derivatives/03-imaging.md
index 6814889c6c..1b0fc9da47 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/05-derivatives/03-imaging.md
@@ -32,6 +32,10 @@ to present both [`res`](../99-appendices/09-entities.md#res) and
 
 Examples:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline1": {
@@ -48,6 +52,12 @@ Examples:
 
 The following metadata JSON fields are defined for preprocessed images:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "SkullStripped": "REQUIRED",
@@ -94,6 +104,10 @@ Example of CIFTI-2 files (a format that combines regularly sampled data
 and non-parametric surfaces) having both [`res`](../99-appendices/09-entities.md#res)
 and [`den`](../99-appendices/09-entities.md#den) entities:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline1": {
@@ -146,6 +160,12 @@ and the `Atlas` metadata SHOULD be defined.
 
 JSON metadata fields:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "RawSources": "REQUIRED",
@@ -158,6 +178,10 @@ JSON metadata fields:
 
 Examples:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "func_loc": {
@@ -171,6 +195,10 @@ Examples:
    }
 ) }}
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "manual_masks": {
@@ -213,6 +241,12 @@ Probabilistic segmentations of surfaces are currently [unspecified][].
 
 The following metadata fields apply to all segmentation files:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "Manual": "OPTIONAL",
@@ -240,6 +274,10 @@ Template:
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -264,6 +302,10 @@ the [`atlas` entity](../99-appendices/09-entities.md#atlas) and the
 
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -297,6 +339,10 @@ Template:
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -316,6 +362,10 @@ for reserved key values for [`label`](../99-appendices/09-entities.md#label).
 A 4D probabilistic segmentation, in which each frame corresponds to a different
 tissue class, must provide a label mapping in its JSON sidecar. For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -365,6 +415,10 @@ The [`hemi-<label>`](../99-appendices/09-entities.md#hemi) entity is REQUIRED fo
 a structure that is restricted to a hemibrain.
 For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -380,6 +434,10 @@ For example:
 
 The REQUIRED extension for CIFTI parcellations is `.dlabel.nii`. For example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -420,6 +478,10 @@ filename.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -438,6 +500,10 @@ segmentations in relative subdirectories.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "pipeline": {
@@ -453,6 +519,12 @@ Example:
 
 These TSV lookup tables contain the following columns:
 
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/objects/columns.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_columns_table(
    {
       "index": "REQUIRED",
diff --git a/src/06-longitudinal-and-multi-site-studies.md b/src/06-longitudinal-and-multi-site-studies.md
index 568c80c9c7..e7abffbe40 100644
--- a/src/06-longitudinal-and-multi-site-studies.md
+++ b/src/06-longitudinal-and-multi-site-studies.md
@@ -5,6 +5,10 @@ and [filenames](02-common-principles.md#file-name-structure)
 in the form of a session (for example `ses-<label>`) and
 with a [`*_sessions.tsv` file](03-modality-agnostic-files.md#sessions-file).
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
     {
     "sub-control01": {
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 3056eb326d..de13336818 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -16,6 +16,8 @@ while entity definitions are in [Appendix IX](09-entities.md).
 <!--
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-bids-schema
+  and a guide for using macros can be found at
+  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 
 ## Magnetic Resonance Imaging
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index b00cee525a..cd3244ae82 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -36,6 +36,10 @@ such as the CTF newDs command-line application or
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -95,6 +99,10 @@ which may be nested inside a `ses-<label>` directory, as shown in the following
 
 #### Example with single session (omitted session directory)
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -122,6 +130,10 @@ which may be nested inside a `ses-<label>` directory, as shown in the following
 
 #### Example with multiple sessions
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -159,6 +171,10 @@ and placed in a `derivatives` subdirectory.
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -200,6 +216,10 @@ for the `acq_time` column in `scans.tsv` MUST all be identical, as described in
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -243,6 +263,10 @@ files for each run inside (for example, `c,rfhp0.1Hz`, `config` and `hs_file`).
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -262,6 +286,10 @@ Example:
 
 Where:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01_ses-001_task-rest_run-01_meg": {
@@ -286,6 +314,10 @@ Head points and marker points in *head space* are acquired using third-party har
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -343,6 +375,10 @@ sub-<label>[_ses-<label>]_task-<label>[_acq-<label>]_digitizer.txt
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
@@ -377,6 +413,10 @@ information).
 
 Example:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-control01": {
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 64d9700033..1f63bc707e 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -12,5 +12,7 @@ be specified for a given file type, is specified in the [Entity Table](04-entity
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-bids-schema
+  and a guide for using macros can be found at
+  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_entity_definitions() }}
diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 004c2a33dd..ce95bd8146 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -22,6 +22,13 @@ included in this appendix:
 
 ### Anatomy imaging data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
     datatypes=["anat"],
     suffixes=[
@@ -49,6 +56,13 @@ included in this appendix:
 
 ### Fieldmap data
 
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the folder
+  src/schema/rules/datatypes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filename_template(
     datatypes=["fmap"],
     suffixes=[
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index b58f410df7..608c70dbc0 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -43,6 +43,10 @@ If a qMRI file collection is intended for creating structural quantitative maps
 files belonging to that collection are stored in the `anat` subdirectory.
 Below is an example file collection for `MP2RAGE`:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -63,6 +67,10 @@ As these images do not convey substantial structural information,
 respective file collections of RF fieldmaps are stored in the `fmap` subdirectory.
 Below is an example file collection for RF transmit field map `TB1EPI`:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -89,6 +97,10 @@ For example a `T1map` can be generated from an `MP2RAGE` file collection using e
 
 If the map is post-generated:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "ds-example": {
@@ -110,6 +122,10 @@ If the map is post-generated:
 
 If the map is pre-generated, for example, by a Siemens scanner:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "ds-example": {
@@ -196,6 +212,10 @@ As qMRI maps are stored as derivatives, they are subjected to the metadata requi
 
 An example `dataset_description.json` for a qMRI map derivatives directory:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "ds-example": {
@@ -262,6 +282,12 @@ For example, without the information of `MagneticFieldStrength`, white-matter T1
 -   The JSON file accompanying a qMRI map which is obtained by using open-source software is RECOMMENDED
     to include additional metadata fields listed in the following table:
 
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_metadata_table(
    {
       "BasedOn": "RECOMMENDED",
@@ -500,6 +526,10 @@ files:
 To properly identify constituents of this particular method, values of the `echo`
 entity MUST index the images as follows:
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -534,6 +564,10 @@ and MAY be followed by freeform entries:
 | `_acq-tr1Test`   | `_acq-tr2Test`   | Acquisition `Test`   |
 | `_acq-tr1Retest` | `_acq-tr2Retest` | Acquisition `Retest` |
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -562,6 +596,10 @@ values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be
 | `_acq-anatTest`             | `_acq-fampTest`           | Acquisition `Test`   |
 | `_acq-anatRetest`           | `_acq-fampRetest`         | Acquisition `Retest` |
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
@@ -594,6 +632,10 @@ entries:
 | `_acq-bodyPDw` | `_acq-headPDw` | `PDw` for `MPM`    |
 | `_acq-bodyT1w` | `_acq-headT1w` | `T1w` for `MPM`    |
 
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
 {{ MACROS___make_filetree_example(
    {
     "sub-01": {
diff --git a/src/99-appendices/14-glossary.md b/src/99-appendices/14-glossary.md
index e56ff9381f..92bc5540a2 100644
--- a/src/99-appendices/14-glossary.md
+++ b/src/99-appendices/14-glossary.md
@@ -5,5 +5,7 @@ This section compiles the object definitions in the schema.
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#making-a-change-to-the-BIDS-schema
+  and a guide for using macros can be found at
+  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_glossary() }}

From 0b543805ebdc9897226d6a65e1ac532487328d89 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 6 Apr 2022 05:18:12 -0400
Subject: [PATCH 232/347] [FIX] Add coordsystem-specific definition of
 DigitizedHeadPoints (#1023)

* Add coordsystem-specific definition of DigitizedHeadpoints.

* Use new file_relative format.
---
 .../02-magnetoencephalography.md                         | 2 +-
 src/schema/objects/metadata.yaml                         | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index c7a0c76cda..b49c9ae556 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -434,7 +434,7 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_metadata_table(
    {
-      "DigitizedHeadPoints": "OPTIONAL",
+      "DigitizedHeadPoints__coordsystem": "OPTIONAL",
       "DigitizedHeadPointsCoordinateSystem": "OPTIONAL",
       "DigitizedHeadPointsCoordinateUnits": "OPTIONAL",
       "DigitizedHeadPointsCoordinateSystemDescription": "OPTIONAL, but REQUIRED if `DigitizedHeadPointsCoordinateSystem` is `Other`",
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 61bf8dcc6a..7f584f9760 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -533,6 +533,15 @@ DigitizedHeadPoints:
     `true` or `false` value indicating whether head points outlining the
     scalp/face surface are contained within this recording.
   type: boolean
+DigitizedHeadPoints__coordsystem:
+  name: DigitizedHeadPoints
+  description: |
+    Relative path to the file containing the locations of digitized head points
+    collected during the session (for example, `"sub-01_headshape.pos"`).
+    RECOMMENDED for all MEG systems, especially for CTF and BTi/4D.
+    For Elekta/Neuromag the head points will be stored in the fif file.
+  type: string
+  format: file_relative
 DigitizedHeadPointsCoordinateSystem:
   name: DigitizedHeadPointsCoordinateSystem
   description: |

From e140f35e749c3f5a4205e033ffe0a7f368a303f4 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed, 6 Apr 2022 05:29:07 -0400
Subject: [PATCH 233/347] [FIX] run entity - "scans" -> "data samples" (#760)

* [FIX] run entity - "scans" -> "data samples"

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* use Taylor's proposal: data samples -> data acquisitions

* Update src/schema/objects/entities.yaml

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/schema/objects/entities.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 657b835eed..5ed45c866d 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -240,7 +240,8 @@ run:
   name: Run
   entity: run
   description: |
-    If several scans with the same acquisition parameters are acquired in the same session,
+    If several data acquisitions (for example, MRI scans or EEG recordings)
+    with the same acquisition parameters are acquired in the same session,
     they MUST be indexed with the [`run-<index>`](../99-appendices/09-entities.md#run) entity:
     `_run-1`, `_run-2`, `_run-3`, and so on (only nonnegative integers are allowed as
     run labels).

From 4c6571c02cffcdf58d2963e8276db637b65f5e28 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 7 Apr 2022 15:14:40 -0400
Subject: [PATCH 234/347] [SCHEMA] Define YAML tables for
 DWI/ASL/(i)EEG/micr/beh metadata (#1029)

* Draft ASL and DWI metadata table rules.

* Add description addendum.

* Define metadata for the behavioral modality.

* Whoops, separate beh and continuous data.

* Add EEG.

* Add iEEG.

* Fix.

* Add microscopy.

* Split up the existing sidecars file.

* Fix issues.

* Update micr.yaml

* Update entities.yaml
---
 src/schema/rules/sidecars/anat.yaml           |  18 ++
 src/schema/rules/sidecars/asl.yaml            | 197 ++++++++++++++++++
 src/schema/rules/sidecars/beh.yaml            |  21 ++
 src/schema/rules/sidecars/continuous.yaml     |  26 +++
 src/schema/rules/sidecars/dwi.yaml            |  25 +++
 src/schema/rules/sidecars/eeg.yaml            | 164 +++++++++++++++
 src/schema/rules/sidecars/entities.yaml       |  81 +++++++
 src/schema/rules/sidecars/ieeg.yaml           | 143 +++++++++++++
 src/schema/rules/sidecars/micr.yaml           |  79 +++++++
 .../rules/{sidecars.yml => sidecars/mri.yaml} |  84 --------
 10 files changed, 754 insertions(+), 84 deletions(-)
 create mode 100644 src/schema/rules/sidecars/anat.yaml
 create mode 100644 src/schema/rules/sidecars/asl.yaml
 create mode 100644 src/schema/rules/sidecars/beh.yaml
 create mode 100644 src/schema/rules/sidecars/continuous.yaml
 create mode 100644 src/schema/rules/sidecars/dwi.yaml
 create mode 100644 src/schema/rules/sidecars/eeg.yaml
 create mode 100644 src/schema/rules/sidecars/entities.yaml
 create mode 100644 src/schema/rules/sidecars/ieeg.yaml
 create mode 100644 src/schema/rules/sidecars/micr.yaml
 rename src/schema/rules/{sidecars.yml => sidecars/mri.yaml} (80%)

diff --git a/src/schema/rules/sidecars/anat.yaml b/src/schema/rules/sidecars/anat.yaml
new file mode 100644
index 0000000000..ec79389d8d
--- /dev/null
+++ b/src/schema/rules/sidecars/anat.yaml
@@ -0,0 +1,18 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Anatomy imaging data
+
+MRIAnatomyCommonMetadataFields:
+    selectors:
+    - modality == "MRI"
+    - datatype == "anat"
+    fields:
+        ContrastBolusIngredient: OPTIONAL
+        RepetitionTimeExcitation: OPTIONAL
+        RepetitionTimePreparation: OPTIONAL
diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
new file mode 100644
index 0000000000..4a81ecbfbb
--- /dev/null
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -0,0 +1,197 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Fields described in text, but not in tables
+MRIASLTextOnly:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    fields:
+        MagneticFieldStrength: REQUIRED
+        MRAcquisitionType: REQUIRED
+        EchoTime: REQUIRED
+        SliceTiming:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `MRAcquisitionType` is defined as `2D`
+        RepetitionTimePreparation: REQUIRED
+        FlipAngle:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `LookLocker` is `true`
+
+MRIASLTextOnlySliceTiming:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.MRAcquisitionType == "2D"
+    fields:
+        SliceTiming: REQUIRED
+
+MRIASLTextOnlyFlipAngle:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.LookLocker == true
+    fields:
+        FlipAngle: REQUIRED
+
+# Common metadata fields applicable to both (P)CASL and PASL
+MRIASLCommonMetadataFields:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    fields:
+        ArterialSpinLabelingType: REQUIRED
+        PostLabelingDelay: REQUIRED
+        BackgroundSuppression: REQUIRED
+        M0Type: REQUIRED
+        TotalAcquiredPairs: REQUIRED
+        VascularCrushing: RECOMMENDED
+        AcquisitionVoxelSize: RECOMMENDED
+        M0Estimate:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `M0Type` is `Estimate`
+        BackgroundSuppressionNumberPulses:
+            level: OPTIONAL
+            level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
+        BackgroundSuppressionPulseTime:
+            level: OPTIONAL
+            level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
+        VascularCrushingVENC:
+            level: OPTIONAL
+            level_addendum: RECOMMENDED if `VascularCrushing` is `true`
+        LabelingOrientation: RECOMMENDED
+        LabelingDistance: RECOMMENDED
+        LabelingLocationDescription: RECOMMENDED
+        LookLocker: OPTIONAL
+        LabelingEfficiency: OPTIONAL
+
+MRIASLCommonMetadataFieldsM0Type:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.M0Type == "Estimate"
+    fields:
+        M0Estimate: REQUIRED
+
+MRIASLCommonMetadataFieldsBackgroundSuppression:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.BackgroundSuppression == true
+    fields:
+        BackgroundSuppressionNumberPulses: RECOMMENDED
+        BackgroundSuppressionPulseTime: RECOMMENDED
+
+MRIASLCommonMetadataFieldsVascularCrushing:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.VascularCrushing == true
+    fields:
+        VascularCrushingVENC: RECOMMENDED
+
+MRIASLPCASLSpecific:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.ArterialSpinLabelingType in ["CASL", "PCASL"]
+    fields:
+        LabelingDuration: REQUIRED
+        LabelingPulseAverageGradient: RECOMMENDED
+        LabelingPulseMaximumGradient: RECOMMENDED
+        LabelingPulseAverageB1: RECOMMENDED
+        LabelingPulseDuration: RECOMMENDED
+        LabelingPulseFlipAngle: RECOMMENDED
+        LabelingPulseInterval: RECOMMENDED
+
+MRIASLPCASLSpecific2:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.ArterialSpinLabelingType == "PCASL"
+    fields:
+        PCASLType: RECOMMENDED
+
+MRIASLCASLSpecific:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.ArterialSpinLabelingType == "CASL"
+    fields:
+        CASLType: RECOMMENDED
+
+MRIASLPASLSpecific:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.ArterialSpinLabelingType == "PASL"
+    fields:
+        BolusCutOffFlag: REQUIRED
+        PASLType: RECOMMENDED
+        LabelingSlabThickness: RECOMMENDED
+        BolusCutOffDelayTime:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `BolusCutOffFlag` is `true`
+        BolusCutOffTechnique:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `BolusCutOffFlag` is `true`
+
+MRIASLPASLSpecificBolusCutOffFlag:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "asl"
+    - sidecar.ArterialSpinLabelingType == "PASL"
+    - sidecar.BolusCutOffFlag == true
+    fields:
+        BolusCutOffDelayTime: REQUIRED
+        BolusCutOffTechnique: REQUIRED
+
+# m0scan metadata fields
+MRIASLM0ScanTextOnly:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "m0scan"
+    fields:
+        EchoTime: REQUIRED
+        RepetitionTimePreparation: REQUIRED
+        FlipAngle:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `LookLocker` is `true`
+
+MRIASLM0ScanTextOnlyFlipAngle:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "m0scan"
+    - sidecar.LookLocker == true
+    fields:
+        FlipAngle: REQUIRED
+
+MRIASLM0Scan:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "m0scan"
+    fields:
+        IntendedFor:
+            level: REQUIRED
+            addendum: This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
+        AcquisitionVoxelSize: RECOMMENDED
diff --git a/src/schema/rules/sidecars/beh.yaml b/src/schema/rules/sidecars/beh.yaml
new file mode 100644
index 0000000000..74052ff92a
--- /dev/null
+++ b/src/schema/rules/sidecars/beh.yaml
@@ -0,0 +1,21 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Metadata for either beh or events files
+BEHTabularData:
+    selectors:
+    - suffix in ["beh", "events"]
+    fields:
+        TaskName: RECOMMENDED
+        Instructions: RECOMMENDED
+        TaskDescription: RECOMMENDED
+        CogAtlasID: RECOMMENDED
+        CogPOID: RECOMMENDED
+        InstitutionName: RECOMMENDED
+        InstitutionAddress: RECOMMENDED
+        InstitutionalDepartmentName: RECOMMENDED
diff --git a/src/schema/rules/sidecars/continuous.yaml b/src/schema/rules/sidecars/continuous.yaml
new file mode 100644
index 0000000000..9325f4daf0
--- /dev/null
+++ b/src/schema/rules/sidecars/continuous.yaml
@@ -0,0 +1,26 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Metadata for either physio or stim files
+Continuous:
+    selectors:
+    - suffix in ["physio", "stim"]
+    fields:
+        SamplingFrequency: REQUIRED
+        StartTime: REQUIRED
+        Columns: REQUIRED
+
+# Other RECOMMENDED metadata for physiological data
+Physio:
+    selectors:
+    - suffix == "physio"
+    fields:
+        Manufacturer: RECOMMENDED
+        ManufacturersModelName: RECOMMENDED
+        SoftwareVersions: RECOMMENDED
+        DeviceSerialNumber: RECOMMENDED
diff --git a/src/schema/rules/sidecars/dwi.yaml b/src/schema/rules/sidecars/dwi.yaml
new file mode 100644
index 0000000000..aea15ca5e2
--- /dev/null
+++ b/src/schema/rules/sidecars/dwi.yaml
@@ -0,0 +1,25 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Multipart (split) DWI schemes
+# NOTE: I don't think this can be schemafied, since it depends on owner intent.
+MRIDiffusionMultipart:
+    selectors:
+    - modality == "MRI"
+    - datatype == "dwi"
+    fields:
+        MultipartID: REQUIRED
+
+# Other RECOMMENDED metadata
+MRIDiffusionOtherMetadata:
+    selectors:
+    - modality == "MRI"
+    - datatype == "dwi"
+    fields:
+        PhaseEncodingDirection: RECOMMENDED
+        TotalReadoutTime: RECOMMENDED
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
new file mode 100644
index 0000000000..4b1902bd23
--- /dev/null
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -0,0 +1,164 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+
+EEGGeneric:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "eeg"
+    fields:
+        TaskName:
+            level: REQUIRED
+            addendum: |
+                A RECOMMENDED convention is to name resting state task using labels
+                beginning with `rest`.
+
+EEGRecommended:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "eeg"
+    fields:
+        InstitutionName: RECOMMENDED
+        InstitutionAddress: RECOMMENDED
+        InstitutionalDepartmentName: RECOMMENDED
+        Manufacturer: RECOMMENDED
+        ManufacturersModelName: RECOMMENDED
+        SoftwareVersions: RECOMMENDED
+        TaskDescription: RECOMMENDED
+        Instructions:
+            level: RECOMMENDED
+            addendum: |
+                This is especially important in context of resting state recordings and
+                distinguishing between eyes open and eyes closed paradigms.
+        CogAtlasID: RECOMMENDED
+        CogPOID: RECOMMENDED
+        DeviceSerialNumber: RECOMMENDED
+
+EEGRequired:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "eeg"
+    fields:
+        EEGReference: REQUIRED
+        SamplingFrequency:
+            level: REQUIRED
+            addendum: |
+                The sampling frequency of data channels that deviate from the main sampling
+                frequency SHOULD be specified in the `channels.tsv` file.
+        PowerLineFrequency: REQUIRED
+        SoftwareFilters": REQUIRED
+
+EEGMoreRecommended:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "eeg"
+    fields:
+        CapManufacturer: RECOMMENDED
+        CapManufacturersModelName: RECOMMENDED
+        EEGChannelCount: RECOMMENDED
+        ECGChannelCount: RECOMMENDED
+        EMGChannelCount: RECOMMENDED
+        EOGChannelCount: RECOMMENDED
+        MiscChannelCount: RECOMMENDED
+        TriggerChannelCount: RECOMMENDED
+        RecordingDuration: RECOMMENDED
+        RecordingType: RECOMMENDED
+        EpochLength: RECOMMENDED
+        EEGGround: RECOMMENDED
+        HeadCircumference: RECOMMENDED
+        EEGPlacementScheme: RECOMMENDED
+        HardwareFilters: RECOMMENDED
+        SubjectArtefactDescription: RECOMMENDED
+
+# General fields
+EEGCoordsystemGeneral:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    fields:
+        IntendedFor:
+            level: OPTIONAL
+            addendum: |
+                This identifies the MRI or CT scan associated with the electrodes,
+                landmarks, and fiducials.
+
+# Fields relating to the EEG electrode positions
+EEGCoordsystemPositions:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    fields:
+        EEGCoordinateSystem: REQUIRED
+        EEGCoordinateUnits: REQUIRED
+        EEGCoordinateSystemDescription:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `EEGCoordinateSystem` is `"Other"`
+
+EEGCoordsystemOther:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - sidecar.EEGCoordinateSystem == "Other"
+    fields:
+        EEGCoordinateSystemDescription: REQUIRED
+
+# Fields relating to the position of fiducials measured during an EEG session/run
+EEGCoordsystemFiducials:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    fields:
+        FiducialsDescription: OPTIONAL
+        FiducialsCoordinates: RECOMMENDED
+        FiducialsCoordinateSystem: RECOMMENDED
+        FiducialsCoordinateUnits: RECOMMENDED
+        FiducialsCoordinateSystemDescription:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `FiducialsCoordinateSystem` is `"Other"`
+
+EEGCoordsystemOtherFiducialCoordinateSystem:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - FiducialsCoordinateSystem == "Other"
+    fields:
+        FiducialsCoordinateSystemDescription: REQUIRED
+
+# Fields relating to the position of anatomical landmark measured during an EEG session/run
+EEGCoordsystemLandmark:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    fields:
+        AnatomicalLandmarkCoordinates: RECOMMENDED
+        AnatomicalLandmarkCoordinateSystem:
+            level: RECOMMENDED
+            addendum: Preferably the same as the `EEGCoordinateSystem`.
+        AnatomicalLandmarkCoordinateUnits: RECOMMENDED
+        AnatomicalLandmarkCoordinateSystemDescription:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `AnatomicalLandmarkCoordinateSystem` is `"Other"`
+
+EEGCoordsystemAnatomicalLandmarkCoordinateSystemDescription:
+    selectors:
+    - modality == "eeg"
+    - datatype == "eeg"
+    - suffix == "coordsystem"
+    - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
+    fields:
+        AnatomicalLandmarkCoordinateSystemDescription: REQUIRED
diff --git a/src/schema/rules/sidecars/entities.yaml b/src/schema/rules/sidecars/entities.yaml
new file mode 100644
index 0000000000..3fcc796da6
--- /dev/null
+++ b/src/schema/rules/sidecars/entities.yaml
@@ -0,0 +1,81 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+
+# Entities
+
+EntitiesTaskMetadata:
+    selectors:
+    - entities contains "task"
+    fields:
+        TaskName: RECOMMENDED
+
+EntitiesCeMetadata:
+    selectors:
+    - entities contains "ce"
+    fields:
+        ContrastBolusIngredient: OPTIONAL
+
+EntitiesTrcMetadata:
+    selectors:
+    - entities contains "trc"
+    fields:
+        TracerName: REQUIRED
+
+EntitiesStainMetadata:
+    selectors:
+    - entities contains "stain"
+    fields:
+        SampleStaining: RECOMMENDED
+        SamplePrimaryAntibodies: RECOMMENDED
+        SampleSecondaryAntibodies: RECOMMENDED
+
+EntitiesEchoMetadata:
+    selectors:
+    - entities contains "echo"
+    fields:
+        EchoTime: REQUIRED
+
+EntitiesFlipMetadata:
+    selectors:
+    - entities contains "flip"
+    fields:
+        FlipAngle: REQUIRED
+
+EntitiesInvMetadata:
+    selectors:
+    - entities contains "inv"
+    fields:
+        InversionTime: REQUIRED
+
+EntitiesMTMetadata:
+    selectors:
+    - entities contains "mt"
+    fields:
+        MTState: REQUIRED
+
+EntitiesPartMetadata:
+    selectors:
+    - entities.part == "phase"
+    fields:
+        Units:
+            level: REQUIRED
+            rules:
+            - value in ["rad", "arbitrary"]
+
+EntitiesResMetadata:
+    selectors:
+    - entities contains "res"
+    fields:
+        Resolution: REQUIRED
+
+EntitiesDenMetadata:
+    selectors:
+    - entities contains "den"
+    fields:
+        Density: REQUIRED
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
new file mode 100644
index 0000000000..90b43db4ca
--- /dev/null
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -0,0 +1,143 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+
+iEEGGeneric:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "ieeg"
+    fields:
+        TaskName:
+            level: REQUIRED
+            addendum: |
+                A RECOMMENDED convention is to name resting state task using labels
+                beginning with `rest`.
+
+iEEGRecommended:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "ieeg"
+    fields:
+        InstitutionName: RECOMMENDED
+        InstitutionAddress: RECOMMENDED
+        InstitutionalDepartmentName: RECOMMENDED
+        Manufacturer:
+            level: RECOMMENDED
+            addendum: For example, `"TDT"`, `"Blackrock"`.
+        ManufacturersModelName: RECOMMENDED
+        SoftwareVersions: RECOMMENDED
+        TaskDescription: RECOMMENDED
+        Instructions:
+            level: RECOMMENDED
+            addendum: |
+                This is especially important in context of resting state recordings and
+                distinguishing between eyes open and eyes closed paradigms.
+        CogAtlasID: RECOMMENDED
+        CogPOID: RECOMMENDED
+        DeviceSerialNumber: RECOMMENDED
+
+# Specific iEEG fields MUST be present
+iEEGRequired:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "ieeg"
+    fields:
+        iEEGReference: REQUIRED
+        SamplingFrequency:
+            level: REQUIRED
+            addendum: |
+                The sampling frequency of data channels that deviate from the main sampling
+                frequency SHOULD be specified in the `channels.tsv` file.
+        PowerLineFrequency: REQUIRED
+        SoftwareFilters": REQUIRED
+
+# Specific iEEG fields SHOULD be present
+iEEGMoreRecommended:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "ieeg"
+    fields:
+        DCOffsetCorrection: DEPRECATED
+        HardwareFilters: RECOMMENDED
+        ElectrodeManufacturer: RECOMMENDED
+        ElectrodeManufacturersModelName: RECOMMENDED
+        ECOGChannelCount: RECOMMENDED
+        SEEGChannelCount: RECOMMENDED
+        EEGChannelCount: RECOMMENDED
+        EOGChannelCount: RECOMMENDED
+        ECGChannelCount: RECOMMENDED
+        EMGChannelCount: RECOMMENDED
+        MiscChannelCount: RECOMMENDED
+        TriggerChannelCount: RECOMMENDED
+        RecordingDuration: RECOMMENDED
+        RecordingType: RECOMMENDED
+        EpochLength: RECOMMENDED
+        iEEGGround: RECOMMENDED
+        iEEGPlacementScheme: RECOMMENDED
+        iEEGElectrodeGroups: RECOMMENDED
+        SubjectArtefactDescription: RECOMMENDED
+
+# Specific iEEG fields MAY be present
+iEEGOptional:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "ieeg"
+    fields:
+        ElectricalStimulation: OPTIONAL
+        ElectricalStimulationParameters: OPTIONAL
+
+# General fields
+iEEGCoordsystemGeneral:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+    fields:
+        IntendedFor:
+            level: OPTIONAL
+            addendum: |
+                If only a surface reconstruction is available, this should point to
+                the surface reconstruction file.
+                Note that this file should have the same coordinate system
+                specified in `iEEGCoordinateSystem`.
+                For example, **T1**: `'sub-<label>/ses-<label>/anat/sub-01_T1w.nii.gz'`
+                **Surface**: `'/derivatives/surfaces/sub-<label>/ses-<label>/anat/
+                sub-01_hemi-R_desc-T1w_pial.surf.gii'`
+                **Operative photo**: `'/sub-<label>/ses-<label>/ieeg/
+                sub-0001_ses-01_acq-photo1_photo.jpg'`
+                **Talairach**: `'/derivatives/surfaces/sub-Talairach/ses-01/anat/
+                sub-Talairach_hemi-R_pial.surf.gii'`
+
+# Fields relating to the iEEG electrode positions
+iEEGCoordsystemPositions:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+    fields:
+        iEEGCoordinateSystem: REQUIRED
+        iEEGCoordinateUnits: REQUIRED
+        iEEGCoordinateSystemDescription:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if `iEEGCoordinateSystem` is `"Other"`
+        iEEGCoordinateProcessingDescription: RECOMMENDED
+        iEEGCoordinateProcessingReference: RECOMMENDED
+
+iEEGCoordsystemOther:
+    selectors:
+    - modality == "ieeg"
+    - datatype == "ieeg"
+    - suffix == "coordsystem"
+    - sidecar.iEEGCoordinateSystem == "Other"
+    fields:
+        iEEGCoordinateSystemDescription: REQUIRED
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
new file mode 100644
index 0000000000..c4fd7d41ed
--- /dev/null
+++ b/src/schema/rules/sidecars/micr.yaml
@@ -0,0 +1,79 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Device Hardware
+MicroscopyDeviceHardware:
+    selectors:
+    - modality == "MICR"
+    - datatype == "micr"
+    fields:
+        Manufacturer: RECOMMENDED
+        ManufacturersModelName: RECOMMENDED
+        DeviceSerialNumber: RECOMMENDED
+        StationName: RECOMMENDED
+        SoftwareVersions: RECOMMENDED
+        InstitutionName: RECOMMENDED
+        InstitutionAddress: RECOMMENDED
+        InstitutionalDepartmentName: RECOMMENDED
+
+# Image Acquisition
+MicroscopyImageAcquisition:
+    selectors:
+    - modality == "MICR"
+    - datatype == "micr"
+    fields:
+        PixelSize: REQUIRED
+        PixelSizeUnits: REQUIRED
+        Immersion: OPTIONAL
+        NumericalAperture: OPTIONAL
+        Magnification: OPTIONAL
+        ImageAcquisitionProtocol: OPTIONAL
+        OtherAcquisitionParameters: OPTIONAL
+
+# Sample
+MicroscopySample:
+    selectors:
+    - modality == "MICR"
+    - datatype == "micr"
+    fields:
+        BodyPart:
+            level: RECOMMENDED
+            addendum: |
+                From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/
+                output/chtml/part16/chapter_L.html#chapter_L)
+                (for example `"BRAIN"`).
+        BodyPartDetails: RECOMMENDED
+        BodyPartDetailsOntology: OPTIONAL
+        SampleEnvironment: RECOMMENDED
+        SampleEmbedding: OPTIONAL
+        SampleFixation: OPTIONAL
+        SampleStaining: RECOMMENDED
+        SamplePrimaryAntibody: RECOMMENDED
+        SampleSecondaryAntibody: RECOMMENDED
+        SliceThickness: OPTIONAL
+        TissueDeformationScaling: OPTIONAL
+        SampleExtractionProtocol: OPTIONAL
+        SampleExtractionInstitution: OPTIONAL
+
+# Chunk Transformations
+MicroscopyChunkTransformations:
+    selectors:
+    - modality == "MICR"
+    - datatype == "micr"
+    - entities contains "chunk"
+    fields:
+        ChunkTransformationMatrix: RECOMMENDED
+
+MicroscopyChunkTransformationsMatrixAxis:
+    selectors:
+    - modality == "MICR"
+    - datatype == "micr"
+    - entities contains "chunk"
+    - sidecar contains "ChunkTransformationMatrix"
+    fields:
+        ChunkTransformationMatrixAxis: REQUIRED
diff --git a/src/schema/rules/sidecars.yml b/src/schema/rules/sidecars/mri.yaml
similarity index 80%
rename from src/schema/rules/sidecars.yml
rename to src/schema/rules/sidecars/mri.yaml
index e321c6a9f8..3cbbebfacd 100644
--- a/src/schema/rules/sidecars.yml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -216,87 +216,3 @@ MRIInstitutionInformation:
         InstitutionalDepartmentName:
             level: RECOMMENDED
             addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
-
-# Anatomy imaging data
-
-MRIAnatomyCommonMetadataFields:
-    selectors:
-    - modality == "MRI"
-    - datatype == "anat"
-    fields:
-        ContrastBolusIngredient: OPTIONAL
-        RepetitionTimeExcitation: OPTIONAL
-        RepetitionTimePreparation: OPTIONAL
-
-# Entities
-
-EntitiesTaskMetadata:
-    selectors:
-    - entities contains "task"
-    fields:
-        TaskName: RECOMMENDED
-
-EntitiesCeMetadata:
-    selectors:
-    - entities contains "ce"
-    fields:
-        ContrastBolusIngredient: OPTIONAL
-
-EntitiesTrcMetadata:
-    selectors:
-    - entities contains "trc"
-    fields:
-        TracerName: REQUIRED
-
-EntitiesStainMetadata:
-    selectors:
-    - entities contains "stain"
-    fields:
-        SampleStaining: RECOMMENDED
-        SamplePrimaryAntibodies: RECOMMENDED
-        SampleSecondaryAntibodies: RECOMMENDED
-
-EntitiesEchoMetadata:
-    selectors:
-    - entities contains "echo"
-    fields:
-        EchoTime: REQUIRED
-
-EntitiesFlipMetadata:
-    selectors:
-    - entities contains "flip"
-    fields:
-        FlipAngle: REQUIRED
-
-EntitiesInvMetadata:
-    selectors:
-    - entities contains "inv"
-    fields:
-        InversionTime: REQUIRED
-
-EntitiesMTMetadata:
-    selectors:
-    - entities contains "mt"
-    fields:
-        MTState: REQUIRED
-
-EntitiesPartMetadata:
-    selectors:
-    - entities.part == "phase"
-    fields:
-        Units:
-            level: REQUIRED
-            rules:
-            - value in ["rad", "arbitrary"]
-
-EntitiesResMetadata:
-    selectors:
-    - entities contains "res"
-    fields:
-        Resolution: REQUIRED
-
-EntitiesDenMetadata:
-    selectors:
-    - entities contains "den"
-    fields:
-        Density: REQUIRED

From e332798a497eaa144629e6098971d4d09c1f5e45 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 7 Apr 2022 17:00:58 -0400
Subject: [PATCH 235/347] Merge gh-1027

Squashed commit of the following:

commit ee5ff05a20f951df806ed4baedd660140d660aae
Author: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Thu Apr 7 15:48:02 2022 -0400

    moved pet stuff to src/schema/rules/sidecars/pet.yaml

commit d00e6839a56068acda1fdfc488cc22965870d917
Author: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Fri Mar 18 09:40:55 2022 -0400

    Update src/schema/rules/sidecars.yml

commit 928eea281eb47ce0f7951e4f13da6bd507758b0c
Author: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Thu Mar 17 15:42:10 2022 -0400

    Add backticks

    Added backticks

commit 50b0ae0c6575bc05984777a917baa6d8b4f47c58
Author: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Tue Mar 15 12:34:42 2022 -0400

    fixed level addendum's, removed quotes for selector in PETMRISequenceSpecifics to make linter happy

commit 4a177c08cf7c49b9da4d1b17d624029b899a2a9f
Author: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Mon Mar 14 15:59:54 2022 -0400

    fixed n - 1 yaml errors, 1 remaining

commit 6e403184ad82e2763b145729a58a476bcf01ac5e
Author: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Mon Mar 14 15:49:29 2022 -0400

    Update src/schema/rules/sidecars.yml

    change addendum -> level_addendum per commit suggestion.

    Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

commit a4fb3774f0baf615555a86d29de68f509944dd36
Merge: 41bc8165 c5f89c60
Author: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Mon Mar 14 15:17:00 2022 -0400

    Merge branch 'schema/sidecar_validation' into bendhouseart-tables

commit 41bc81652a11567519dc78188e62875f92bd8e7a
Author: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date:   Thu Mar 10 15:49:58 2022 -0500

    fixed yaml formatting
---
 src/schema/rules/sidecars/pet.yaml | 183 +++++++++++++++++++++++++++++
 1 file changed, 183 insertions(+)
 create mode 100644 src/schema/rules/sidecars/pet.yaml

diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
new file mode 100644
index 0000000000..0a8a509450
--- /dev/null
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -0,0 +1,183 @@
+---
+# PET common metadata fields
+PETScannerHardware:
+    selectors:
+    - modality == "PET"
+    fields:
+        Manufacturer:
+            level: REQUIRED
+            addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
+        ManufacturersModelName:
+            level: REQUIRED
+            addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
+        Units:
+            level: REQUIRED
+            addendum: |
+                SI unit for radioactivity (Becquerel) should be used (for example, "Bq/mL").
+                Corresponds to DICOM Tag 0054, 1001 `Units`.
+        InstitutionName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
+        InstitutionAddress:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
+        InstitutionalDepartmentName:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
+        BodyPart:
+            level: RECOMMENDED
+            addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
+
+PETRadioChemistry:
+    selectors:
+    - modality == "PET"
+    fields:
+        TracerName:
+            level: REQUIRED
+        TracerRadionuclide:
+            level: REQUIRED
+        InjectedRadioactivity:
+            level: REQUIRED
+        InjectedRadioactivityUnits:
+            level: REQUIRED
+        InjectedMass:
+            level: REQUIRED
+        InjectedMassUnits:
+            level: REQUIRED
+        SpecificRadioactivity:
+            level: REQUIRED
+        SpecificRadioactivityUnits:
+            level: REQUIRED
+        ModeOfAdministration:
+            level: REQUIRED
+        TracerRadLex:
+            level: RECOMMENDED
+        TracerSNOMED:
+            level: RECOMMENDED
+        TracerMolecularWeight:
+            level: RECOMMENDED
+        TracerMolecularWeightUnits:
+            level: RECOMMENDED
+        InjectedMassPerWeight:
+            level: RECOMMENDED
+        InjectedMassPerWeightUnits:
+            level: RECOMMENDED
+        SpecificRadioactivityMeasTime:
+            level: RECOMMENDED
+        MolarActivity:
+            level: RECOMMENDED
+        MolarActivityUnits:
+            level: RECOMMENDED
+        MolarActivityMeasTime:
+            level: RECOMMENDED
+        InfusionRadioactivity:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+        InfusionStart:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+        InfusionSpeed:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+        InfusionSpeedUnits:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+        InjectedVolume:
+            level: RECOMMENDED
+            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+        Purity:
+            level: RECOMMENDED
+
+# PET Infusion conditionally REQUIRED entities
+EntitiesBolusMetadata:
+    selectors:
+    - modality == 'PET'
+    - sidecar.ModeOfAdministration == 'bolus-infusion'
+    fields:
+        InfusionRadioactivity:
+            level: REQUIRED
+        InfusionStart:
+            level: REQUIRED
+        InfusionSpeed:
+            level: REQUIRED
+        InfusionSpeedUnits:
+            level: REQUIRED
+        InjectedVolume:
+            level: REQUIRED
+
+PETPharmaceuticals:
+    selectors:
+    - modality == "PET"
+    fields:
+        PharmaceuticalName:
+            level: RECOMMENDED
+        PharmaceuticalDoseAmount:
+            level: RECOMMENDED
+        PharmaCeuticalDoseUnits:
+            level: RECOMMENDED
+        PharmaCeuticalDoseRegimen:
+            level: RECOMMENDED
+        PharmaCeuticalDoseTime:
+            level: RECOMMENDED
+        Anaesthesia:
+            level: OPTIONAL
+
+PETTime:
+    selectors:
+    - modality == "PET"
+    fields:
+        TimeZero:
+            level: REQUIRED
+        ScanStart:
+            level: REQUIRED
+        InjectionStart:
+            level: REQUIRED
+        FramesTimesStart:
+            level: REQUIRED
+        FrameDuration:
+            level: REQUIRED
+        InjectionEnd:
+            level: RECOMMENDED
+        ScanDate:
+            level: DEPRECATED
+
+PETReconstruction:
+    selectors:
+    - modality == "PET"
+    fields:
+        AcquisitionMode:
+            level: REQUIRED
+        ImageDecayCorrected:
+            level: REQUIRED
+        ImageDecayCorrectionTime:
+            level: REQUIRED
+        ReconMethodName:
+            level: REQUIRED
+        ReconMethodParameterLabels:
+            level: REQUIRED
+        ReconMethodParameterUnits:
+            level: REQUIRED
+        ReconMethodParameterValues:
+            level: REQUIRED
+        ReconFilterType:
+            level: REQUIRED
+        ReconFilterSize:
+            level: REQUIRED
+        AttenuationCorrection:
+            level: REQUIRED
+        ReconMethodImplementationVersion:
+            level: RECOMMENDED
+        AttenuationCorrectionMethodReference:
+            level: RECOMMENDED
+        ScaleFactor:
+            level: RECOMMENDED
+        ScatterFraction:
+            level: RECOMMENDED
+        DecayCorrectionFactor:
+            level: RECOMMENDED
+        DoseCalibrationFactor:
+            level: RECOMMENDED
+        PromptRate:
+            level: RECOMMENDED
+        SinglesRate:
+            level: RECOMMENDED

From 30d8250ed706ce48594aa8e3ca5771e45f3165f6 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 8 Apr 2022 12:33:43 -0400
Subject: [PATCH 236/347] [SCHEMA] Add MEG, func, and fmap metadata tables
 (#1054)

* Add MEG.

* Add fmap file.

* Add func file.

* Fix a couple of things.

* Update func.yaml
---
 src/schema/rules/sidecars/fmap.yaml |  87 ++++++++++
 src/schema/rules/sidecars/func.yaml | 106 ++++++++++++
 src/schema/rules/sidecars/meg.yaml  | 256 ++++++++++++++++++++++++++++
 3 files changed, 449 insertions(+)
 create mode 100644 src/schema/rules/sidecars/fmap.yaml
 create mode 100644 src/schema/rules/sidecars/func.yaml
 create mode 100644 src/schema/rules/sidecars/meg.yaml

diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
new file mode 100644
index 0000000000..8eaec2707a
--- /dev/null
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -0,0 +1,87 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Fieldmap data
+MRIFieldmapB0FieldIdentifier:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    fields:
+        B0FieldIdentifier: RECOMMENDED
+
+MRIFieldmapIntendedFor:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    fields:
+        IntendedFor:
+            level: OPTIONAL
+            addendum: |
+                This field is OPTIONAL, and in case the fieldmaps do not correspond
+                to any particular scans, it does not have to be filled.
+
+# Case 1: Phase-difference map and at least one magnitude image
+MRIFieldmapPhaseDifferencePhasediff:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix == "phasediff"
+    fields:
+        EchoTime1: REQUIRED
+        EchoTime2: REQUIRED
+
+MRIFieldmapPhaseDifferenceMagnitude1:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix == "magnitude1"
+    fields:
+        EchoTime1: REQUIRED
+
+MRIFieldmapPhaseDifferenceMagnitude2:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix == "magnitude2"
+    fields:
+        EchoTime2: REQUIRED
+
+# Case 2: Two phase maps and two magnitude images
+# NOTE: Need to check for presence of related files.
+# For example, magnitude1 needs EchoTime__fmap only if phase1 file exists,
+# but EchoTime1 if phasediff exists.
+MRIFieldmapTwoPhase:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix in ["phase1", "phase2", "magnitude1", "magnitude2"]
+    fields:
+        EchoTime__fmap: REQUIRED
+
+# Case 3: Direct field mapping
+MRIFieldmapDirectFieldMapping:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix in ["phase", "fieldmap"]
+    fields:
+        Units:
+            level: REQUIRED
+            addendum: |
+                Fieldmaps must be in units of Hertz (`"Hz"`),
+                radians per second (`"rad/s"`), or Tesla (`"T"`).
+
+# Case 4: Multiple phase encoded directions ("pepolar")
+MRIFieldmapPepolar:
+    selectors:
+    - modality == "MRI"
+    - datatype == "fmap"
+    - suffix == "epi"
+    fields:
+        PhaseEncodingDirection: REQUIRED
+        TotalReadoutTime: REQUIRED
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
new file mode 100644
index 0000000000..03714fc44e
--- /dev/null
+++ b/src/schema/rules/sidecars/func.yaml
@@ -0,0 +1,106 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Task imaging data
+
+# Required fields
+MRIFuncRequired:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    fields:
+        RepetitionTime: REQUIRED
+        VolumeTiming: REQUIRED
+        TaskName:
+            level: REQUIRED
+            addendum: |
+                A RECOMMENDED convention is to name resting state task using labels
+                beginning with `rest`.
+
+# Timing Parameters
+MRIFuncTimingParameters:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    fields:
+        NumberOfVolumesDiscardedByScanner: RECOMMENDED
+        NumberOfVolumesDiscardedByUser: RECOMMENDED
+        DelayTime: RECOMMENDED
+        AcquisitionDuration:
+            level: RECOMMENDED
+            level_addendum: |
+                REQUIRED for sequences that are described with the `VolumeTiming`
+                field and that do not have the `SliceTiming` field set to allow for
+                accurate calculation of "acquisition time"
+        DelayAfterTrigger: RECOMMENDED
+
+# The mutual exclusion table, spread across 5 definitions
+# NOTE: This introduces a PROHIBITED level
+MRIFuncTimingParametersMutualExclusion1:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    - sidecar contains "RepetitionTime"
+    fields:
+        AcquisitionDuration: PROHIBITED
+        VolumeTiming: PROHIBITED
+
+MRIFuncTimingParametersMutualExclusion2:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    - sidecar contains "SliceTiming"
+    - sidecar contains "VolumeTiming"
+    fields:
+        RepetitionTime: PROHIBITED
+        DelayTime: PROHIBITED
+
+MRIFuncTimingParametersMutualExclusion3:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    - sidecar contains "AcquisitionDuration"
+    - sidecar contains "VolumeTiming"
+    fields:
+        RepetitionTime: PROHIBITED
+        DelayTime: PROHIBITED
+
+MRIFuncTimingParametersMutualExclusion4:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    - sidecar contains "RepetitionTime"
+    - sidecar contains "SliceTiming"
+    fields:
+        AcquisitionDuration: PROHIBITED
+        VolumeTiming: PROHIBITED
+
+MRIFuncTimingParametersMutualExclusion5:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    - sidecar contains "RepetitionTime"
+    - sidecar contains "DelayTime"
+    fields:
+        AcquisitionDuration: PROHIBITED
+        VolumeTiming: PROHIBITED
+
+# fMRI task information
+MRIFuncTaskInformation:
+    selectors:
+    - modality == "MRI"
+    - datatype == "func"
+    fields:
+        Instructions:
+            level: RECOMMENDED
+            addendum: |
+                This is especially important in context of resting state recordings and
+                distinguishing between eyes open and eyes closed paradigms.
+        TaskDescription: RECOMMENDED
+        CogAtlasID: RECOMMENDED
+        CogPOID: RECOMMENDED
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
new file mode 100644
index 0000000000..804d9e11e3
--- /dev/null
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -0,0 +1,256 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+
+---
+# Magnetoencephalography
+
+# Sidecar JSON (*_meg.json)
+MEGGeneric:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "meg"
+    fields:
+        TaskName:
+            level: REQUIRED
+            addendum: |
+                A RECOMMENDED convention is to name resting state task using labels
+                beginning with `rest`.
+
+MEGRecommended:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "meg"
+    fields:
+        InstitutionName: RECOMMENDED
+        InstitutionAddress: RECOMMENDED
+        InstitutionalDepartmentName: RECOMMENDED
+        Manufacturer:
+            level: RECOMMENDED
+            addendum: |
+                For MEG scanners, this must be one of:
+                `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
+                `"ITAB"`, `"KRISS"`, `"Other"`.
+                See [Appendix VII](/99-appendices/07-meg-systems.html) for
+                preferred names.
+        ManufacturersModelName:
+            level: RECOMMENDED
+            addendum: |
+                See [Appendix VII](/99-appendices/07-meg-systems.html) for
+                preferred names.
+        SoftwareVersions: RECOMMENDED
+        TaskDescription: RECOMMENDED
+        Instructions:
+            level: RECOMMENDED
+            addendum: |
+                This is especially important in context of resting state recordings and
+                distinguishing between eyes open and eyes closed paradigms.
+        CogAtlasID: RECOMMENDED
+        CogPOID: RECOMMENDED
+        DeviceSerialNumber: RECOMMENDED
+
+# Specific MEG fields MUST be present
+MEGRequired:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "meg"
+    fields:
+        SamplingFrequency:
+            level: REQUIRED
+            addendum: |
+                The sampling frequency of data channels that deviate from the main sampling
+                frequency SHOULD be specified in the `channels.tsv` file.
+        PowerLineFrequency: REQUIRED
+        DewarPosition: REQUIRED
+        SoftwareFilters: REQUIRED
+        DigitizedLandmarks: REQUIRED
+        DigitizedHeadPoints: REQUIRED
+
+# Specific MEG fields SHOULD be present
+MEGMoreRecommended:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "meg"
+    fields:
+        MEGChannelCount: RECOMMENDED
+        MEGREFChannelCount: RECOMMENDED
+        EEGChannelCount: RECOMMENDED
+        ECOGChannelCount: RECOMMENDED
+        SEEGChannelCount: RECOMMENDED
+        EOGChannelCount: RECOMMENDED
+        ECGChannelCount: RECOMMENDED
+        EMGChannelCount: RECOMMENDED
+        MiscChannelCount: RECOMMENDED
+        TriggerChannelCount: RECOMMENDED
+        RecordingDuration: RECOMMENDED
+        RecordingType: RECOMMENDED
+        EpochLength: RECOMMENDED
+        ContinuousHeadLocalization: RECOMMENDED
+        HeadCoilFrequency: RECOMMENDED
+        MaxMovement: RECOMMENDED
+        SubjectArtefactDescription: RECOMMENDED
+        AssociatedEmptyRoom: RECOMMENDED
+        HardwareFilters: RECOMMENDED
+
+# Specific EEG fields
+# NOTE: I'm not sure if "EEG is present" is enough to indicate simultaneous EEG/MEG.
+MEGwithEEG:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "meg"
+    - dataset.modalities contains "EEG"
+    fields:
+        EEGPlacementScheme: OPTIONAL
+        CapManufacturer: OPTIONAL
+        CapManufacturersModelName: OPTIONAL
+        EEGReference: OPTIONAL
+
+# MEG and EEG sensors
+MEGCoordsystemWithEEG:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    fields:
+        MEGCoordinateSystem: REQUIRED
+        MEGCoordinateUnits: REQUIRED
+        MEGCoordinateSystemDescription:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `MEGCoordinateSystem` is `Other`
+        EEGCoordinateSystem:
+            level: OPTIONAL
+            addendum: |
+                See [Recording EEG simultaneously with MEG]
+                (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+                Preferably the same as the `MEGCoordinateSystem`.
+        EEGCoordinateUnits: OPTIONAL
+        EEGCoordinateSystemDescription:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `EEGCoordinateSystem` is `Other`
+            addendum: |
+                See [Recording EEG simultaneously with MEG]
+                (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+
+# NOTE: The JSON isn't really a sidecar, so "sidecar.MEGCoordinateSystem" is misleading.
+MEGCoordsystemWithEEGMEGCoordinateSystem:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - sidecar.MEGCoordinateSystem == "Other"
+    fields:
+        MEGCoordinateSystemDescription: REQUIRED
+
+# NOTE: Not sure if this requires simult. EEG
+MEGCoordsystemWithEEGEEGCoordinateSystem:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - sidecar.EEGCoordinateSystem == "Other"
+    fields:
+        EEGCoordinateSystemDescription: REQUIRED
+
+# Head localization coils
+MEGCoordsystemHeadLocalizationCoils:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    fields:
+        HeadCoilCoordinates: OPTIONAL
+        HeadCoilCoordinateSystem: OPTIONAL
+        HeadCoilCoordinateUnits: OPTIONAL
+        HeadCoilCoordinateSystemDescription:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `HeadCoilCoordinateSystem` is `Other`
+
+MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - sidecar.HeadCoilCoordinateSystem == "Other"
+    fields:
+        HeadCoilCoordinateSystemDescription: REQUIRED
+
+# Digitized head points
+MEGCoordsystemDigitizedHeadPoints:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    fields:
+        DigitizedHeadPoints: OPTIONAL
+        DigitizedHeadPointsCoordinateSystem: OPTIONAL
+        DigitizedHeadPointsCoordinateUnits: OPTIONAL
+        DigitizedHeadPointsCoordinateSystemDescription:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `DigitizedHeadPointsCoordinateSystem` is `Other`
+
+MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - sidecar.DigitizedHeadPointsCoordinateSystem == "Other"
+    fields:
+        DigitizedHeadPointsCoordinateSystemDescription: REQUIRED
+
+# Anatomical MRI
+MEGCoordsystemAnatomicalMRI:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - dataset.modalities contains "anat"
+    fields:
+        IntendedFor:
+            level: OPTIONAL
+            addendum: |
+                This is used to identify the structural MRI(s),
+                possibly of different types if a list is specified,
+                to be used with the MEG recording.
+
+# Anatomical landmarks
+MEGCoordsystemAnatomicalLandmarks:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    fields:
+        AnatomicalLandmarkCoordinates: OPTIONAL
+        AnatomicalLandmarkCoordinateSystem:
+            level: OPTIONAL
+            addendum: |
+                Preferably the same as the `MEGCoordinateSystem`.
+        AnatomicalLandmarkCoordinateUnits: OPTIONAL
+        AnatomicalLandmarkCoordinateSystemDescription:
+            level: OPTIONAL
+            level_addendum: REQUIRED if `AnatomicalLandmarkCoordinateSystem` is `Other`
+
+MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
+    fields:
+        AnatomicalLandmarkCoordinateSystemDescription: REQUIRED
+
+# Fiducials information
+MEGCoordsystemFiducialsInformation:
+    selectors:
+    - modality == "meg"
+    - datatype == "meg"
+    - suffix == "coordsystem"
+    fields:
+        FiducialsDescription: OPTIONAL

From 1909cac90e899b5e136dbf53dbafc6cd6a0f7187 Mon Sep 17 00:00:00 2001
From: Ghislain Vaillant <ghisvail@users.noreply.github.com>
Date: Sat, 9 Apr 2022 21:56:48 +0200
Subject: [PATCH 237/347] [FIX] Change recording entity to REQUIRED for
 pet/blood modality (#1005)

* Fix REQUIRED recording entity for pet/blood

* Default to manual if sampling method is unknown

* Update src/04-modality-specific-files/09-positron-emission-tomography.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 .../09-positron-emission-tomography.md                       | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index e7661be71b..d221b43218 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -359,13 +359,12 @@ If collected, blood measurements of radioactivity are be stored in
 [Tabular files](../02-common-principles.md#tabular-files) and located in
 the `pet/` directory along with the corresponding PET data.
 
-The OPTIONAL `recording` entity is used to distinguish sampling methods.
+The REQUIRED `recording` entity is used to distinguish sampling methods.
 For example, if an autosampler is used to record continuous blood samples,
 and manual measurements are also taken,
 then the files may have recording labels `autosampler` and `manual`,
 respectively.
-If multiple recording methods are used on the same PET acquisition,
-the `recording` entity MUST be used to distinguish them.
+If the sampling method is unknown, then recording SHOULD be set as `manual`.
 All blood measurements should be reported according to a single time-scale
 in relation to time zero defined by the PET data (Figure 1).
 All definitions used below are in accordance with

From 341a73bec9ef1d114e0b8508ca9125d8c96e9117 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 14:25:41 -0400
Subject: [PATCH 238/347] Draft ASL validation file.

---
 src/schema/rules/sidecars/asl_validation.yaml | 178 ++++++++++++++++++
 1 file changed, 178 insertions(+)
 create mode 100644 src/schema/rules/sidecars/asl_validation.yaml

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
new file mode 100644
index 0000000000..3319d3041d
--- /dev/null
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -0,0 +1,178 @@
+# Rules for ASL data that are not defined in tables.
+---
+ASLPostLabelingDelayASLContextLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order.
+        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+    selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+
+ASLLabelingDurationASLContextLength:
+    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+        a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+        `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes
+        specified in `*_aslcontext.tsv`.
+        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+
+ASLRepetitionTimePreparationASLContextLength:
+    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field.
+        The data type array provides a value for each volume in a 4D dataset and should only be used when the
+        volume timing is critical for interpretation of the data, such as in ASL.
+    level: error
+    selectors:
+    - sidecar contains "RepetitionTimePreparation"
+    - type(sidecar.RepetitionTimePreparation) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+
+ASLTotalAcquiredVolumesASLContextLength:
+    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+    description: |
+        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+    level: error
+    selectors:
+    - sidecar contains "TotalAcquiredVolumes"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+
+ASLFlipAngleASLContextLength:
+    code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+       The number of values for 'FlipAngle' for this file does not match the number of volumes in the
+       'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+       'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+       Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+       The data type number may apply to files from any MRI modality concerned with a single value for this field,
+       or to the files in a file collection where the value of this field is iterated using the flip entity.
+       The data type array provides a value for each volume in a 4D dataset and should only be used when the volume
+       timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+    level: error
+    selectors:
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
+
+ASLFlipAngleNiftiLength:
+    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+        'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+        Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field,
+        or to the files in a file collection where the value of this field is iterated using the flip entity.
+        The data type array provides a value for each volume in a 4D dataset and should only be used when the
+        volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+    level: error
+    selectors:
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.FlipAngle.size
+
+ASLPostLabelingDelayNiftiLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI header.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
+        labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
+        (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+    selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.PostLabelingDelay.size
+
+ASLContextConsistent:
+    code: ASLCONTEXT_TSV_NOT_CONSISTENT
+    description: |
+        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+        values in the NIfTI header.
+    level: error
+    selectors:
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == associated["aslcontext"].shape[0]
+
+ASLBackgroundSuppressionNumberPulses:
+    code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
+    description: |
+        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of 'BackgroundSuppressionPulseTime'.
+        'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
+        Note that this excludes any effect of background suppression pulses applied before the labeling.
+    level: warning
+    selectors:
+    - sidecar contains "BackgroundSuppressionNumberPulses"
+    - sidecar contains "BackgroundSuppressionPulseTime"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+    - suffix == "asl"
+    checks:
+    - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
+
+ASLLabelingDurationNiftiLength:
+    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.LabelingDuration.size

From c57135839c4887021e488b6076ee303e8dabaf2b Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 14:27:17 -0400
Subject: [PATCH 239/347] Fix level.

---
 src/schema/rules/sidecars/asl_validation.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 3319d3041d..dcd0764bda 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -69,7 +69,7 @@ ASLTotalAcquiredVolumesASLContextLength:
         volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
         'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
         'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-    level: error
+    level: warning
     selectors:
     - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"

From a6b22c492fdefd53dd7d43634961e9e1f30fcadb Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:25:19 -0400
Subject: [PATCH 240/347] Reorder based on code.

---
 src/schema/rules/sidecars/asl_validation.yaml | 191 +++++++++---------
 1 file changed, 101 insertions(+), 90 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index dcd0764bda..437a4d959f 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -1,81 +1,58 @@
 # Rules for ASL data that are not defined in tables.
 ---
-ASLPostLabelingDelayASLContextLength:
-    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
-        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
-        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
-        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order.
-        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
-        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-    level: error
-    selectors:
-    - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
-    checks:
-    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
 
-ASLLabelingDurationASLContextLength:
-    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+# 157
+ASLLabelingDurationNiftiLength:
+    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'LabelingDuration' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
         'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
         corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
-        a scalar must be specified.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
         In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
-        `LabelingDuration` of zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes
-        specified in `*_aslcontext.tsv`.
-        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+    - data.shape[3] == sidecar.LabelingDuration.size
 
-ASLRepetitionTimePreparationASLContextLength:
-    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+# 165
+ASLContextConsistent:
+    code: ASLCONTEXT_TSV_NOT_CONSISTENT
     description: |
-        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
-        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
-        The data type number may apply to files from any MRI modality concerned with a single value for this field.
-        The data type array provides a value for each volume in a 4D dataset and should only be used when the
-        volume timing is critical for interpretation of the data, such as in ASL.
+        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+        values in the NIfTI header.
     level: error
     selectors:
-    - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+    - data.shape[3] == associated["aslcontext"].shape[0]
 
-ASLTotalAcquiredVolumesASLContextLength:
-    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+# 168
+ASLFlipAngleNiftiLength:
+    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
-        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-    level: warning
+        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+        'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+        Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field,
+        or to the files in a file collection where the value of this field is iterated using the flip entity.
+        The data type array provides a value for each volume in a 4D dataset and should only be used when the
+        volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+    level: error
     selectors:
-    - sidecar contains "TotalAcquiredVolumes"
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+    - data.shape[3] == sidecar.FlipAngle.size
 
+# 172
 ASLFlipAngleASLContextLength:
     code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
     description: |
@@ -95,24 +72,7 @@ ASLFlipAngleASLContextLength:
     checks:
     - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
 
-ASLFlipAngleNiftiLength:
-    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
-    description: |
-        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
-        'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
-        Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
-        The data type number may apply to files from any MRI modality concerned with a single value for this field,
-        or to the files in a file collection where the value of this field is iterated using the flip entity.
-        The data type array provides a value for each volume in a 4D dataset and should only be used when the
-        volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
-    level: error
-    selectors:
-    - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
-    checks:
-    - data.shape[3] == sidecar.FlipAngle.size
-
+# 173
 ASLPostLabelingDelayNiftiLength:
     code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
     description: |
@@ -132,17 +92,72 @@ ASLPostLabelingDelayNiftiLength:
     checks:
     - data.shape[3] == sidecar.PostLabelingDelay.size
 
-ASLContextConsistent:
-    code: ASLCONTEXT_TSV_NOT_CONSISTENT
+# 174
+ASLPostLabelingDelayASLContextLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
     description: |
-        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
-        values in the NIfTI header.
+        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order.
+        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
     - suffix == "asl"
     checks:
-    - data.shape[3] == associated["aslcontext"].shape[0]
+    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+
+# 175
+ASLLabelingDurationASLContextLength:
+    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+        a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+        `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes
+        specified in `*_aslcontext.tsv`.
+        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
 
+# 177
+ASLRepetitionTimePreparationASLContextLength:
+    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field.
+        The data type array provides a value for each volume in a 4D dataset and should only be used when the
+        volume timing is critical for interpretation of the data, such as in ASL.
+    level: error
+    selectors:
+    - sidecar contains "RepetitionTimePreparation"
+    - type(sidecar.RepetitionTimePreparation) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+
+# 180
 ASLBackgroundSuppressionNumberPulses:
     code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
     description: |
@@ -158,21 +173,17 @@ ASLBackgroundSuppressionNumberPulses:
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
-ASLLabelingDurationNiftiLength:
-    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+# 181
+ASLTotalAcquiredVolumesASLContextLength:
+    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
     description: |
-        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
-        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
-        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
-        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-    level: error
+        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+    level: warning
     selectors:
-    - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"
     checks:
-    - data.shape[3] == sidecar.LabelingDuration.size
+    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes

From 60d1572c5a9dad1922665ab9b744b934416aa5ca Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:34:06 -0400
Subject: [PATCH 241/347] Add 196 and reorder selectors.

---
 src/schema/rules/sidecars/asl_validation.yaml | 40 ++++++++++++++-----
 1 file changed, 31 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 437a4d959f..fe340bc6d2 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -15,9 +15,9 @@ ASLLabelingDurationNiftiLength:
         `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.LabelingDuration.size
 
@@ -30,6 +30,7 @@ ASLContextConsistent:
     level: error
     selectors:
     - suffix == "asl"
+    - associated contains "aslcontext"
     checks:
     - data.shape[3] == associated["aslcontext"].shape[0]
 
@@ -46,9 +47,9 @@ ASLFlipAngleNiftiLength:
         volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.FlipAngle.size
 
@@ -66,9 +67,10 @@ ASLFlipAngleASLContextLength:
        timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
 
@@ -86,9 +88,9 @@ ASLPostLabelingDelayNiftiLength:
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.PostLabelingDelay.size
 
@@ -108,9 +110,10 @@ ASLPostLabelingDelayASLContextLength:
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
 
@@ -132,9 +135,10 @@ ASLLabelingDurationASLContextLength:
         Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
 
@@ -151,9 +155,10 @@ ASLRepetitionTimePreparationASLContextLength:
         volume timing is critical for interpretation of the data, such as in ASL.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
 
@@ -166,10 +171,10 @@ ASLBackgroundSuppressionNumberPulses:
         Note that this excludes any effect of background suppression pulses applied before the labeling.
     level: warning
     selectors:
+    - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
     - type(sidecar.BackgroundSuppressionPulseTime) == "array"
-    - suffix == "asl"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -183,7 +188,24 @@ ASLTotalAcquiredVolumesASLContextLength:
         'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
     level: warning
     selectors:
-    - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar contains "TotalAcquiredVolumes"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+
+# 196
+ASLEchoTimeASLContextLength:
+    code: ECHO_TIME_NOT_CONSISTENT
+    description: |
+        The number of values for 'EchoTime' for this file does not match number of volumes in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
+    level: warning
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar contains "EchoTime"
+    - type(sidecar.EchoTime) == "array"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.EchoTime.size

From f8214ba066b782506596430ca835258d5a7276fb Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:47:29 -0400
Subject: [PATCH 242/347] Add a few DWI and events rules.

---
 src/schema/rules/sidecars/dwi_validation.yaml | 39 +++++++++++++++++++
 .../rules/sidecars/events_validation.yaml     | 16 ++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 src/schema/rules/sidecars/dwi_validation.yaml
 create mode 100644 src/schema/rules/sidecars/events_validation.yaml

diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
new file mode 100644
index 0000000000..73f51ea883
--- /dev/null
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -0,0 +1,39 @@
+# Rules for DWI data that are not defined in tables.
+---
+
+# 29
+DWIVolumeCount:
+    code: VOLUME_COUNT_MISMATCH
+    description: |
+        The number of volumes in this scan does not match the number of volumes in the
+        corresponding .bvec and .bval files.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    - associated contains "bval"
+    - associated contains "bvec"
+    checks:
+    - associated["bval"].shape[0] == data.shape[3]
+    - associated["bvec"].shape[0] == data.shape[3]
+
+# 32
+DWIMissingBvec:
+    code: DWI_MISSING_BVEC
+    description: |
+        DWI scans must have a corresponding .bvec file.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    checks:
+    - associated contains "bvec"
+
+# 33
+DWIMissingBval:
+    code: DWI_MISSING_BVAL
+    description: |
+        DWI scans must have a corresponding .bval file.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    checks:
+    - associated contains "bval"
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
new file mode 100644
index 0000000000..ff445ec4c0
--- /dev/null
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -0,0 +1,16 @@
+# Rules for events data that are not defined in tables.
+---
+
+# 25
+EventsMissing:
+    code: EVENTS_TSV_MISSING
+    description: |
+        Task scans should have a corresponding events.tsv file.
+        If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
+    level: warning  # could be an error with the proper selectors, I think
+    selectors:
+    - entities contains "task"
+    - entities.task != "rest"
+    - "rest" not in entities.task  # Alternative for including the word "rest"
+    checks:
+    - associated contains "events"

From b5dc39fb120ccb6a80a11d0d9b7d1fc1c836db66 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 12 Apr 2022 16:05:48 -0400
Subject: [PATCH 243/347] started adding special_errors corresponding to
 columne 'Reason' Validator Issues google sheet

---
 src/schema/rules/sidecars/asl.yaml | 49 ++++++++++++++++++++++++++++++
 src/schema/rules/sidecars/eeg.yaml |  8 ++---
 2 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 4a81ecbfbb..abaad115ac 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -19,10 +19,40 @@ MRIASLTextOnly:
         SliceTiming:
             level: RECOMMENDED
             level_addendum: REQUIRED if `MRAcquisitionType` is defined as `2D`
+            special_error: 
+                SlICE_TIMING_NOT_DEFINED_2D_ASL: |
+                'You should define SliceTiming', in case 'SequenceType' 
+                is set to a 2D sequence. 'SliceTiming' is the time at 
+                which each slice was acquired within each volume (frame) 
+                of the acquisition. Slice timing is not slice order -- rather, 
+                it is a list of times containing the time (in seconds) of 
+                each slice acquisition in relation to the beginning of 
+                volume acquisition. The list goes through the slices along 
+                the slice axis in the slice encoding dimension (see below). 
+                Note that to ensure the proper interpretation of the 
+                `SliceTiming` field, it is important to check if the 
+                OPTIONAL `SliceEncodingDirection` exists. In particular, 
+                if `SliceEncodingDirection` is negative, the entries in 
+                `SliceTiming` are defined in reverse order with respect 
+                to the slice axis, such that the final entry in the 
+                `SliceTiming` list is the time of acquisition of slice 0. 
+                Without this parameter slice time correction will not be possible.
         RepetitionTimePreparation: REQUIRED
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if `LookLocker` is `true`
+            special_error:
+                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                You should define 'FlipAngle' for this file, in case of a LookLocker 
+                acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, 
+                specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. 
+                The data type number may apply to files from any MRI modality 
+                concerned with a single value for this field, or to the files in a file 
+                collection where the value of this field is iterated using the flip 
+                entity. The data type array provides a value for each volume in a 4D 
+                dataset and should only be used when the volume timing is critical for 
+                interpretation of the data, such as in ASL or variable flip angle fMRI 
+                sequences.
 
 MRIASLTextOnlySliceTiming:
     selectors:
@@ -59,6 +89,13 @@ MRIASLCommonMetadataFields:
         M0Estimate:
             level: OPTIONAL
             level_addendum: REQUIRED if `M0Type` is `Estimate`
+            special_error:
+                MOESTIMATE_NOT_DEFINED: |
+                You must define 'M0Estimate' for this file, in case 'M0Type' 
+                is defined as 'Estimate'. 'M0Estimate' is a single numerical 
+                whole-brain M0 value (referring to the M0 of blood), only if 
+                obtained externally (for example retrieved from CSF in a 
+                separate measurement).
         BackgroundSuppressionNumberPulses:
             level: OPTIONAL
             level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
@@ -175,6 +212,18 @@ MRIASLM0ScanTextOnly:
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if `LookLocker` is `true`
+            special_error:
+                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                You should define 'FlipAngle' for this file, in case of a LookLocker 
+                acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, 
+                specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. 
+                The data type number may apply to files from any MRI modality concerned 
+                with a single value for this field, or to the files in a file collection 
+                where the value of this field is iterated using the flip entity. The 
+                data type array provides a value for each volume in a 4D dataset and 
+                should only be used when the volume timing is critical for interpretation 
+                of the data, such as in ASL or variable flip angle fMRI sequences.
+
 
 MRIASLM0ScanTextOnlyFlipAngle:
     selectors:
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 4b1902bd23..6b86262d82 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -15,7 +15,7 @@ EEGGeneric:
     fields:
         TaskName:
             level: REQUIRED
-            addendum: |
+            level_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -34,7 +34,7 @@ EEGRecommended:
         TaskDescription: RECOMMENDED
         Instructions:
             level: RECOMMENDED
-            addendum: |
+            level_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
         CogAtlasID: RECOMMENDED
@@ -50,7 +50,7 @@ EEGRequired:
         EEGReference: REQUIRED
         SamplingFrequency:
             level: REQUIRED
-            addendum: |
+            level_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
         PowerLineFrequency: REQUIRED
@@ -88,7 +88,7 @@ EEGCoordsystemGeneral:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            level_addendum: |
                 This identifies the MRI or CT scan associated with the electrodes,
                 landmarks, and fiducials.
 

From a295fc270abb271e1a9e37f206784894b24c03b9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 16:09:52 -0400
Subject: [PATCH 244/347] Fix linter issues.

---
 src/schema/rules/sidecars/asl_validation.yaml    | 15 ++++++++++-----
 src/schema/rules/sidecars/events_validation.yaml |  2 +-
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index fe340bc6d2..e34f9b8ebd 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -8,9 +8,11 @@ ASLLabelingDurationNiftiLength:
         The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
         'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
         corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
+        specified.
         In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
+        zero.
         In case an array of numbers is provided, its length should be equal to the number of volumes specified in
         `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
@@ -78,13 +80,15 @@ ASLFlipAngleASLContextLength:
 ASLPostLabelingDelayNiftiLength:
     code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI header.
+        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
+        header.
         'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
         labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
         (for 3D acquisition) or first slice (for 2D acquisition).
         Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
         In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a
+        zero.
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
@@ -166,7 +170,8 @@ ASLRepetitionTimePreparationASLContextLength:
 ASLBackgroundSuppressionNumberPulses:
     code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
     description: |
-        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of 'BackgroundSuppressionPulseTime'.
+        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
+        'BackgroundSuppressionPulseTime'.
         'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
         Note that this excludes any effect of background suppression pulses applied before the labeling.
     level: warning
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
index ff445ec4c0..e4e74e9adc 100644
--- a/src/schema/rules/sidecars/events_validation.yaml
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -11,6 +11,6 @@ EventsMissing:
     selectors:
     - entities contains "task"
     - entities.task != "rest"
-    - "rest" not in entities.task  # Alternative for including the word "rest"
+    - entities.task not contains "rest"  # Alternative for including the word "rest"
     checks:
     - associated contains "events"

From 5d6f7cd66d6fc711c81b9c5614ea99f43480dd1f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 16:29:24 -0400
Subject: [PATCH 245/347] Add a few more rules.

---
 src/schema/rules/sidecars/asl_validation.yaml | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index e34f9b8ebd..4e02f30f2e 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -214,3 +214,46 @@ ASLEchoTimeASLContextLength:
     - type(sidecar.EchoTime) == "array"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.EchoTime.size
+
+# 198
+ASLM0TypeAbsentScan:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT
+    description: |
+        You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
+        '*_m0scan.json', or defining the 'M0Estimate' field.
+        This is not allowed, please check that this field are filled correctly.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - associated contains "m0scan"
+    checks:
+    - sidecar.M0Type != "absent"
+
+# 199
+ASLM0TypeAbsentASLContext:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
+    description: |
+        You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
+        This is not allowed, please check that this field are filled correctly.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - associated["aslcontext"]["volume_type"] contains "m0scan"
+    checks:
+    - sidecar.M0Type != "absent"
+
+# 202
+ASLM0TypeIncorrect:
+    code: M0Type_SET_INCORRECTLY
+    description: |
+        M0Type was not defined correctly.
+        If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar.M0Type == "separate"
+    checks:
+    - associated contains "m0scan"

From f541ca0f0ee5d11233b6dec787ae70adf798b7e6 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Tue, 12 Apr 2022 17:03:13 -0400
Subject: [PATCH 246/347] moved codes to sub-entities

---
 src/schema/rules/sidecars/asl.yaml | 108 ++++++++++++++++-------------
 1 file changed, 60 insertions(+), 48 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index abaad115ac..6d8e607d06 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -19,40 +19,10 @@ MRIASLTextOnly:
         SliceTiming:
             level: RECOMMENDED
             level_addendum: REQUIRED if `MRAcquisitionType` is defined as `2D`
-            special_error: 
-                SlICE_TIMING_NOT_DEFINED_2D_ASL: |
-                'You should define SliceTiming', in case 'SequenceType' 
-                is set to a 2D sequence. 'SliceTiming' is the time at 
-                which each slice was acquired within each volume (frame) 
-                of the acquisition. Slice timing is not slice order -- rather, 
-                it is a list of times containing the time (in seconds) of 
-                each slice acquisition in relation to the beginning of 
-                volume acquisition. The list goes through the slices along 
-                the slice axis in the slice encoding dimension (see below). 
-                Note that to ensure the proper interpretation of the 
-                `SliceTiming` field, it is important to check if the 
-                OPTIONAL `SliceEncodingDirection` exists. In particular, 
-                if `SliceEncodingDirection` is negative, the entries in 
-                `SliceTiming` are defined in reverse order with respect 
-                to the slice axis, such that the final entry in the 
-                `SliceTiming` list is the time of acquisition of slice 0. 
-                Without this parameter slice time correction will not be possible.
         RepetitionTimePreparation: REQUIRED
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if `LookLocker` is `true`
-            special_error:
-                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
-                You should define 'FlipAngle' for this file, in case of a LookLocker 
-                acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, 
-                specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. 
-                The data type number may apply to files from any MRI modality 
-                concerned with a single value for this field, or to the files in a file 
-                collection where the value of this field is iterated using the flip 
-                entity. The data type array provides a value for each volume in a 4D 
-                dataset and should only be used when the volume timing is critical for 
-                interpretation of the data, such as in ASL or variable flip angle fMRI 
-                sequences.
 
 MRIASLTextOnlySliceTiming:
     selectors:
@@ -62,6 +32,21 @@ MRIASLTextOnlySliceTiming:
     - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming: REQUIRED
+            code:
+                SLICE_TIMING_NOT_DEFINED_2D_ASL: |
+                "You should define SliceTiming', in case 'SequenceType' is set to a 
+                2D sequence. 'SliceTiming' is the time at which each slice was 
+                acquired within each volume (frame) of the acquisition. Slice timing 
+                is not slice order -- rather, it is a list of times containing the 
+                time (in seconds) of each slice acquisition in relation to the beginning 
+                of volume acquisition. The list goes through the slices along the slice 
+                axis in the slice encoding dimension (see below). Note that to ensure the 
+                proper interpretation of the `SliceTiming` field, it is important to check 
+                if the OPTIONAL `SliceEncodingDirection` exists. In particular, if 
+                `SliceEncodingDirection` is negative, the entries in `SliceTiming` are 
+                defined in reverse order with respect to the slice axis, such that the 
+                final entry in the `SliceTiming` list is the time of acquisition of slice 0. 
+                Without this parameter slice time correction will not be possible."
 
 MRIASLTextOnlyFlipAngle:
     selectors:
@@ -71,6 +56,19 @@ MRIASLTextOnlyFlipAngle:
     - sidecar.LookLocker == true
     fields:
         FlipAngle: REQUIRED
+            code: 
+                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                "You should define 'FlipAngle' for this file, in case of a 
+                LookLocker acquisition. 'FlipAngle' is the flip angle (FA) 
+                for the acquisition, specified in degrees. Corresponds to: 
+                DICOM Tag 0018, 1314 `Flip Angle`. The data type number may 
+                apply to files from any MRI modality concerned with a single 
+                value for this field, or to the files in a file collection 
+                where the value of this field is iterated using the flip entity. 
+                The data type array provides a value for each volume in a 4D 
+                dataset and should only be used when the volume timing is critical 
+                for interpretation of the data, such as in ASL or variable flip 
+                angle fMRI sequences."
 
 # Common metadata fields applicable to both (P)CASL and PASL
 MRIASLCommonMetadataFields:
@@ -89,13 +87,6 @@ MRIASLCommonMetadataFields:
         M0Estimate:
             level: OPTIONAL
             level_addendum: REQUIRED if `M0Type` is `Estimate`
-            special_error:
-                MOESTIMATE_NOT_DEFINED: |
-                You must define 'M0Estimate' for this file, in case 'M0Type' 
-                is defined as 'Estimate'. 'M0Estimate' is a single numerical 
-                whole-brain M0 value (referring to the M0 of blood), only if 
-                obtained externally (for example retrieved from CSF in a 
-                separate measurement).
         BackgroundSuppressionNumberPulses:
             level: OPTIONAL
             level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
@@ -119,6 +110,11 @@ MRIASLCommonMetadataFieldsM0Type:
     - sidecar.M0Type == "Estimate"
     fields:
         M0Estimate: REQUIRED
+            code:
+                M0ESTIMATE_NOT_DEFINED: |
+                You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'. 
+                'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood), 
+                only if obtained externally (for example retrieved from CSF in a separate measurement).
 
 MRIASLCommonMetadataFieldsBackgroundSuppression:
     selectors:
@@ -198,7 +194,24 @@ MRIASLPASLSpecificBolusCutOffFlag:
     - sidecar.BolusCutOffFlag == true
     fields:
         BolusCutOffDelayTime: REQUIRED
+            code: 
+                PASL_BOLUS_CUT_OFF_DELAY_TIME: |
+                It is required to define 'BolusCutOffDelayTime' for this file, 
+                when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is 
+                the duration between the end of the labeling and the start of the 
+                bolus cut-off saturation pulse(s), in seconds. This can be a number 
+                or array of numbers, of which the values must be non-negative and 
+                monotonically increasing, depending on the number of bolus cut-off 
+                saturation pulses. For Q2TIPS, only the values for the first and last 
+                bolus cut-off saturation pulses are provided. Based on DICOM Tag 
+                0018,925F ASL Bolus Cut-off Delay Time.
         BolusCutOffTechnique: REQUIRED
+            code:
+                PASL_BOLUS_CUT_OFF_TECHINIQUE: |
+                It is required to define 'BolusCutOffTechnique' for this file, 
+                when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique' 
+                is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII). 
+                Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.
 
 # m0scan metadata fields
 MRIASLM0ScanTextOnly:
@@ -212,7 +225,16 @@ MRIASLM0ScanTextOnly:
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if `LookLocker` is `true`
-            special_error:
+
+MRIASLM0ScanTextOnlyFlipAngle:
+    selectors:
+    - modality == "MRI"
+    - datatype == "perf"
+    - suffix == "m0scan"
+    - sidecar.LookLocker == true
+    fields:
+        FlipAngle: REQUIRED
+            code:
                 LOOK_LOCKER_FLIP_ANGLE_MISSING: |
                 You should define 'FlipAngle' for this file, in case of a LookLocker 
                 acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, 
@@ -224,16 +246,6 @@ MRIASLM0ScanTextOnly:
                 should only be used when the volume timing is critical for interpretation 
                 of the data, such as in ASL or variable flip angle fMRI sequences.
 
-
-MRIASLM0ScanTextOnlyFlipAngle:
-    selectors:
-    - modality == "MRI"
-    - datatype == "perf"
-    - suffix == "m0scan"
-    - sidecar.LookLocker == true
-    fields:
-        FlipAngle: REQUIRED
-
 MRIASLM0Scan:
     selectors:
     - modality == "MRI"

From 1379ab0c51ffb0bc06a333be4939b79791bd6734 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed, 13 Apr 2022 02:26:47 -0400
Subject: [PATCH 247/347] ENH: introduce versioning of the schema itself
 (#1013)

* ENH: introduce versioning of the schema itself

Note -- it is not a version of the content of the schema, it is
a version over organization of the schema (e.g. we could add some
schema to describe how schema is organized).

The 'desire' for having a version over the BIDS schema's version
is somewhat described in README.md in added section.  Just to facilitate
tools to know what versions of bids schema they can read without explicitly
whitelisting BIDS versions themselves.

* Adding versioning for after 1.0.0

I thought we had it but managed to screw it up during rebase. Thanks @sappelhoff

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* line breaks

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 src/schema/README.md      | 19 +++++++++++++++++++
 src/schema/SCHEMA_VERSION |  1 +
 2 files changed, 20 insertions(+)
 create mode 100644 src/schema/SCHEMA_VERSION

diff --git a/src/schema/README.md b/src/schema/README.md
index 04bdca0a7c..15218a1720 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -498,3 +498,22 @@ In cases where there is a data file and a metadata file, the `.json` extension f
 
 This file contains a dictionary in which each key is a directory and the value is a dictionary with one key: `required`.
 The `required` entry contains a boolean value to indicate if that directory is required for BIDS datasets or not.
+
+## Version of the schema
+
+File `SCHEMA_VERSION` in the top of the directory contains a semantic
+version (`MAJOR.MINOR.PATCH`) for the schema (how it is organized).
+Note that while in `0.` series, breaking changes are
+permitted without changing the `MAJOR` (leading) component of the version.
+Going forward, the 2nd, `MINOR` indicator should be
+incremented whenever schema organization introduces "breaking changes":
+changes which would cause existing tools reading schema to
+adjust their code to be able to read it again.
+Additions of new components to the schema should increment the last,
+`PATCH`, component of the version so that tools could selectively
+enable/disable loading specific components of the schema.
+With the release of `1.0.0` version of the schema,
+we expect that the `MAJOR` component
+will be incremented whenever schema organization introduces "breaking changes",
+`MINOR` - when adding new components to the schema,
+and `PATCH` - when fixing errors in existing components.
diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
new file mode 100644
index 0000000000..6e8bf73aa5
--- /dev/null
+++ b/src/schema/SCHEMA_VERSION
@@ -0,0 +1 @@
+0.1.0

From 66ffd5d64c91c609311f355a5890038fd63164dc Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 13 Apr 2022 12:27:29 -0400
Subject: [PATCH 248/347] added existing validator issues/codes to required
 if's where relevant

---
 src/schema/rules/sidecars/eeg.yaml  |  2 +-
 src/schema/rules/sidecars/fmap.yaml |  4 ++--
 src/schema/rules/sidecars/func.yaml |  5 ++++-
 src/schema/rules/sidecars/mri.yaml  | 34 +++++++++++++++++++++++++++++
 4 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 6b86262d82..2d7f3e291b 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -54,7 +54,7 @@ EEGRequired:
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
         PowerLineFrequency: REQUIRED
-        SoftwareFilters": REQUIRED
+        SoftwareFilters: REQUIRED
 
 EEGMoreRecommended:
     selectors:
diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
index 8eaec2707a..af0fa9ba88 100644
--- a/src/schema/rules/sidecars/fmap.yaml
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -21,7 +21,7 @@ MRIFieldmapIntendedFor:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            level_addendum: |
                 This field is OPTIONAL, and in case the fieldmaps do not correspond
                 to any particular scans, it does not have to be filled.
 
@@ -72,7 +72,7 @@ MRIFieldmapDirectFieldMapping:
     fields:
         Units:
             level: REQUIRED
-            addendum: |
+            level_addendum: |
                 Fieldmaps must be in units of Hertz (`"Hz"`),
                 radians per second (`"rad/s"`), or Tesla (`"T"`).
 
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 03714fc44e..f41e310391 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -18,7 +18,7 @@ MRIFuncRequired:
         VolumeTiming: REQUIRED
         TaskName:
             level: REQUIRED
-            addendum: |
+            level_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -37,6 +37,9 @@ MRIFuncTimingParameters:
                 REQUIRED for sequences that are described with the `VolumeTiming`
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
+            code: 
+                VOLUME_TIMING_MISSING_ACQUISITION_DURATION: |
+                The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
         DelayAfterTrigger: RECOMMENDED
 
 # The mutual exclusion table, spread across 5 definitions
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 3cbbebfacd..6b9e6134aa 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -119,11 +119,18 @@ MRISpatialEncoding:
                 This parameter is REQUIRED if corresponding fieldmap data is present
                 or when using multiple runs with different phase encoding directions
                 (which can be later used for field inhomogeneity correction).
+            code:
+                PHASE_ENCODING_DIRECTION_MUST_DEFINE: |
+                You have to define 'PhaseEncodingDirection' for this file.
         EffectiveEchoSpacing:
             level: RECOMMENDED
             level_addendum: |
                 <sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data
                 is present.
+            code:
+                EFFECTIVE_ECHO_SPACING_NOT_DEFINED: |
+                You should define 'EffectiveEchoSpacing' for this file. If you don't
+                provide this information field map correction will not be possible.
         TotalReadoutTime:
             level: RECOMMENDED
             level_addendum: |
@@ -131,6 +138,9 @@ MRISpatialEncoding:
                 acquired with opposing phase encoding directions are present
                 (see [Case 4: Multiple phase encoded
                 directions](#case-4-multiple-phase-encoded-directions-pepolar)).
+            code:
+                TOTAL_READOUT_TIME_MUST_DEFINE: |
+                You have to define 'TotalReadoutTime' for this file.
         MixingTime: RECOMMENDED
 
 MRITimingParameters:
@@ -142,6 +152,17 @@ MRITimingParameters:
             level_addendum: |
                 REQUIRED if corresponding fieldmap data is present,
                 or the data comes from a multi-echo sequence or Arterial Spin Labeling.
+            code:
+                ECHO_TIME_NOT_DEFINED: |
+                You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE) 
+                for the acquisition, specified in seconds. Corresponds to DICOM Tag 
+                0018, 0081 Echo Time (please note that the DICOM term is in milliseconds 
+                not seconds). The data type number may apply to files from any MRI modality 
+                concerned with a single value for this field, or to the files in a file 
+                collection where the value of this field is iterated using the echo entity. 
+                The data type array provides a value for each volume in a 4D dataset and 
+                should only be used when the volume timing is critical for interpretation 
+                of the data, such as in ASL or variable echo time fMRI sequences.
         InversionTime: RECOMMENDED
         SliceTiming:
             level: RECOMMENDED
@@ -175,6 +196,19 @@ MRIRFandContrast:
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if LookLocker is set to `true`.
+            code:
+                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                You should define 'FlipAngle' for this file, in 
+                case of a LookLocker acquisition. 'FlipAngle' is the 
+                flip angle (FA) for the acquisition, specified in degrees. 
+                Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data 
+                type number may apply to files from any MRI modality concerned 
+                with a single value for this field, or to the files in a file 
+                collection where the value of this field is iterated using the 
+                flip entity. The data type array provides a value for each volume 
+                in a 4D dataset and should only be used when the volume timing is 
+                critical for interpretation of the data, such as in ASL or 
+                variable flip angle fMRI sequences.
         NegativeContrast: OPTIONAL
 
 MRIFlipAngleLookLocker:

From ab3b818d55252039d290bdddac40cf76f470cedf Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 13 Apr 2022 09:49:53 -0700
Subject: [PATCH 249/347] SCHEMA: Bump SCHEMA_VERSION to indicate
 incompatibility with 0.1.0

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index 6e8bf73aa5..0ea3a944b3 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.1.0
+0.2.0

From 2abd5cba3b7104bbf0c0a89338588ff988d91c89 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 13 Apr 2022 12:50:03 -0400
Subject: [PATCH 250/347] fixed formatting issues

---
 src/schema/rules/sidecars/asl.yaml  | 120 +++++++++++++++-------------
 src/schema/rules/sidecars/func.yaml |   4 +-
 src/schema/rules/sidecars/mri.yaml  |  48 +++++------
 3 files changed, 89 insertions(+), 83 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 6d8e607d06..42db35f024 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -31,22 +31,23 @@ MRIASLTextOnlySliceTiming:
     - suffix == "asl"
     - sidecar.MRAcquisitionType == "2D"
     fields:
-        SliceTiming: REQUIRED
+        SliceTiming:
+            level: REQUIRED
             code:
                 SLICE_TIMING_NOT_DEFINED_2D_ASL: |
-                "You should define SliceTiming', in case 'SequenceType' is set to a 
-                2D sequence. 'SliceTiming' is the time at which each slice was 
-                acquired within each volume (frame) of the acquisition. Slice timing 
-                is not slice order -- rather, it is a list of times containing the 
-                time (in seconds) of each slice acquisition in relation to the beginning 
-                of volume acquisition. The list goes through the slices along the slice 
-                axis in the slice encoding dimension (see below). Note that to ensure the 
-                proper interpretation of the `SliceTiming` field, it is important to check 
-                if the OPTIONAL `SliceEncodingDirection` exists. In particular, if 
-                `SliceEncodingDirection` is negative, the entries in `SliceTiming` are 
-                defined in reverse order with respect to the slice axis, such that the 
-                final entry in the `SliceTiming` list is the time of acquisition of slice 0. 
-                Without this parameter slice time correction will not be possible."
+                    "You should define SliceTiming', in case 'SequenceType' is set to a
+                    2D sequence. 'SliceTiming' is the time at which each slice was
+                    acquired within each volume (frame) of the acquisition. Slice timing
+                    is not slice order -- rather, it is a list of times containing the
+                    time (in seconds) of each slice acquisition in relation to the beginning
+                    of volume acquisition. The list goes through the slices along the slice
+                    axis in the slice encoding dimension (see below). Note that to ensure the
+                    proper interpretation of the `SliceTiming` field, it is important to check
+                    if the OPTIONAL `SliceEncodingDirection` exists. In particular, if
+                    `SliceEncodingDirection` is negative, the entries in `SliceTiming` are
+                    defined in reverse order with respect to the slice axis, such that the
+                    final entry in the `SliceTiming` list is the time of acquisition of slice 0.
+                    Without this parameter slice time correction will not be possible."
 
 MRIASLTextOnlyFlipAngle:
     selectors:
@@ -55,20 +56,21 @@ MRIASLTextOnlyFlipAngle:
     - suffix == "asl"
     - sidecar.LookLocker == true
     fields:
-        FlipAngle: REQUIRED
-            code: 
+        FlipAngle:
+            level: REQUIRED
+            code:
                 LOOK_LOCKER_FLIP_ANGLE_MISSING: |
-                "You should define 'FlipAngle' for this file, in case of a 
-                LookLocker acquisition. 'FlipAngle' is the flip angle (FA) 
-                for the acquisition, specified in degrees. Corresponds to: 
-                DICOM Tag 0018, 1314 `Flip Angle`. The data type number may 
-                apply to files from any MRI modality concerned with a single 
-                value for this field, or to the files in a file collection 
-                where the value of this field is iterated using the flip entity. 
-                The data type array provides a value for each volume in a 4D 
-                dataset and should only be used when the volume timing is critical 
-                for interpretation of the data, such as in ASL or variable flip 
-                angle fMRI sequences."
+                    "You should define 'FlipAngle' for this file, in case of a
+                    LookLocker acquisition. 'FlipAngle' is the flip angle (FA)
+                    for the acquisition, specified in degrees. Corresponds to
+                    DICOM Tag 0018, 1314 `Flip Angle`. The data type number may
+                    apply to files from any MRI modality concerned with a single
+                    value for this field, or to the files in a file collection
+                    where the value of this field is iterated using the flip entity.
+                    The data type array provides a value for each volume in a 4D
+                    dataset and should only be used when the volume timing is critical
+                    for interpretation of the data, such as in ASL or variable flip
+                    angle fMRI sequences."
 
 # Common metadata fields applicable to both (P)CASL and PASL
 MRIASLCommonMetadataFields:
@@ -109,12 +111,13 @@ MRIASLCommonMetadataFieldsM0Type:
     - suffix == "asl"
     - sidecar.M0Type == "Estimate"
     fields:
-        M0Estimate: REQUIRED
+        M0Estimate:
+            level: REQUIRED
             code:
                 M0ESTIMATE_NOT_DEFINED: |
-                You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'. 
-                'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood), 
-                only if obtained externally (for example retrieved from CSF in a separate measurement).
+                    You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'.
+                    'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood),
+                    only if obtained externally (for example retrieved from CSF in a separate measurement).
 
 MRIASLCommonMetadataFieldsBackgroundSuppression:
     selectors:
@@ -193,25 +196,27 @@ MRIASLPASLSpecificBolusCutOffFlag:
     - sidecar.ArterialSpinLabelingType == "PASL"
     - sidecar.BolusCutOffFlag == true
     fields:
-        BolusCutOffDelayTime: REQUIRED
-            code: 
+        BolusCutOffDelayTime:
+            level: REQUIRED
+            code:
                 PASL_BOLUS_CUT_OFF_DELAY_TIME: |
-                It is required to define 'BolusCutOffDelayTime' for this file, 
-                when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is 
-                the duration between the end of the labeling and the start of the 
-                bolus cut-off saturation pulse(s), in seconds. This can be a number 
-                or array of numbers, of which the values must be non-negative and 
-                monotonically increasing, depending on the number of bolus cut-off 
-                saturation pulses. For Q2TIPS, only the values for the first and last 
-                bolus cut-off saturation pulses are provided. Based on DICOM Tag 
-                0018,925F ASL Bolus Cut-off Delay Time.
-        BolusCutOffTechnique: REQUIRED
+                    It is required to define 'BolusCutOffDelayTime' for this file,
+                    when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is
+                    the duration between the end of the labeling and the start of the
+                    bolus cut-off saturation pulse(s), in seconds. This can be a number
+                    or array of numbers, of which the values must be non-negative and
+                    monotonically increasing, depending on the number of bolus cut-off
+                    saturation pulses. For Q2TIPS, only the values for the first and last
+                    bolus cut-off saturation pulses are provided. Based on DICOM Tag
+                    0018,925F ASL Bolus Cut-off Delay Time.
+        BolusCutOffTechnique:
+            level: REQUIRED
             code:
                 PASL_BOLUS_CUT_OFF_TECHINIQUE: |
-                It is required to define 'BolusCutOffTechnique' for this file, 
-                when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique' 
-                is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII). 
-                Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.
+                    It is required to define 'BolusCutOffTechnique' for this file,
+                    when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique',
+                    is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII).
+                    Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.
 
 # m0scan metadata fields
 MRIASLM0ScanTextOnly:
@@ -233,18 +238,19 @@ MRIASLM0ScanTextOnlyFlipAngle:
     - suffix == "m0scan"
     - sidecar.LookLocker == true
     fields:
-        FlipAngle: REQUIRED
+        FlipAngle:
+            level: REQUIRED
             code:
                 LOOK_LOCKER_FLIP_ANGLE_MISSING: |
-                You should define 'FlipAngle' for this file, in case of a LookLocker 
-                acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, 
-                specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. 
-                The data type number may apply to files from any MRI modality concerned 
-                with a single value for this field, or to the files in a file collection 
-                where the value of this field is iterated using the flip entity. The 
-                data type array provides a value for each volume in a 4D dataset and 
-                should only be used when the volume timing is critical for interpretation 
-                of the data, such as in ASL or variable flip angle fMRI sequences.
+                    You should define 'FlipAngle' for this file, in case of a LookLocker
+                    acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition,
+                    specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+                    The data type number may apply to files from any MRI modality concerned
+                    with a single value for this field, or to the files in a file collection
+                    where the value of this field is iterated using the flip entity. The
+                    data type array provides a value for each volume in a 4D dataset and
+                    should only be used when the volume timing is critical for interpretation
+                    of the data, such as in ASL or variable flip angle fMRI sequences.
 
 MRIASLM0Scan:
     selectors:
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index f41e310391..fd40707a90 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -37,9 +37,9 @@ MRIFuncTimingParameters:
                 REQUIRED for sequences that are described with the `VolumeTiming`
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
-            code: 
+            code:
                 VOLUME_TIMING_MISSING_ACQUISITION_DURATION: |
-                The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
+                    The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
         DelayAfterTrigger: RECOMMENDED
 
 # The mutual exclusion table, spread across 5 definitions
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 6b9e6134aa..febc734dc7 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -121,7 +121,7 @@ MRISpatialEncoding:
                 (which can be later used for field inhomogeneity correction).
             code:
                 PHASE_ENCODING_DIRECTION_MUST_DEFINE: |
-                You have to define 'PhaseEncodingDirection' for this file.
+                    You have to define 'PhaseEncodingDirection' for this file.
         EffectiveEchoSpacing:
             level: RECOMMENDED
             level_addendum: |
@@ -129,8 +129,8 @@ MRISpatialEncoding:
                 is present.
             code:
                 EFFECTIVE_ECHO_SPACING_NOT_DEFINED: |
-                You should define 'EffectiveEchoSpacing' for this file. If you don't
-                provide this information field map correction will not be possible.
+                    You should define 'EffectiveEchoSpacing' for this file. If you don't
+                    provide this information field map correction will not be possible.
         TotalReadoutTime:
             level: RECOMMENDED
             level_addendum: |
@@ -140,7 +140,7 @@ MRISpatialEncoding:
                 directions](#case-4-multiple-phase-encoded-directions-pepolar)).
             code:
                 TOTAL_READOUT_TIME_MUST_DEFINE: |
-                You have to define 'TotalReadoutTime' for this file.
+                    You have to define 'TotalReadoutTime' for this file.
         MixingTime: RECOMMENDED
 
 MRITimingParameters:
@@ -154,15 +154,15 @@ MRITimingParameters:
                 or the data comes from a multi-echo sequence or Arterial Spin Labeling.
             code:
                 ECHO_TIME_NOT_DEFINED: |
-                You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE) 
-                for the acquisition, specified in seconds. Corresponds to DICOM Tag 
-                0018, 0081 Echo Time (please note that the DICOM term is in milliseconds 
-                not seconds). The data type number may apply to files from any MRI modality 
-                concerned with a single value for this field, or to the files in a file 
-                collection where the value of this field is iterated using the echo entity. 
-                The data type array provides a value for each volume in a 4D dataset and 
-                should only be used when the volume timing is critical for interpretation 
-                of the data, such as in ASL or variable echo time fMRI sequences.
+                    You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE)
+                    for the acquisition, specified in seconds. Corresponds to DICOM Tag
+                    0018, 0081 Echo Time (please note that the DICOM term is in milliseconds
+                    not seconds). The data type number may apply to files from any MRI modality
+                    concerned with a single value for this field, or to the files in a file
+                    collection where the value of this field is iterated using the echo entity.
+                    The data type array provides a value for each volume in a 4D dataset and
+                    should only be used when the volume timing is critical for interpretation
+                    of the data, such as in ASL or variable echo time fMRI sequences.
         InversionTime: RECOMMENDED
         SliceTiming:
             level: RECOMMENDED
@@ -198,17 +198,17 @@ MRIRFandContrast:
             level_addendum: REQUIRED if LookLocker is set to `true`.
             code:
                 LOOK_LOCKER_FLIP_ANGLE_MISSING: |
-                You should define 'FlipAngle' for this file, in 
-                case of a LookLocker acquisition. 'FlipAngle' is the 
-                flip angle (FA) for the acquisition, specified in degrees. 
-                Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data 
-                type number may apply to files from any MRI modality concerned 
-                with a single value for this field, or to the files in a file 
-                collection where the value of this field is iterated using the 
-                flip entity. The data type array provides a value for each volume 
-                in a 4D dataset and should only be used when the volume timing is 
-                critical for interpretation of the data, such as in ASL or 
-                variable flip angle fMRI sequences.
+                    You should define 'FlipAngle' for this file, in
+                    case of a LookLocker acquisition. 'FlipAngle' is the
+                    flip angle (FA) for the acquisition, specified in degrees.
+                    Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data
+                    type number may apply to files from any MRI modality concerned
+                    with a single value for this field, or to the files in a file
+                    collection where the value of this field is iterated using the
+                    flip entity. The data type array provides a value for each volume
+                    in a 4D dataset and should only be used when the volume timing is
+                    critical for interpretation of the data, such as in ASL or
+                    variable flip angle fMRI sequences.
         NegativeContrast: OPTIONAL
 
 MRIFlipAngleLookLocker:

From d2d262bf6d388b65aac665ce8524e4d569b0cb00 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 13 Apr 2022 13:31:25 -0400
Subject: [PATCH 251/347] add message and name field to code key

---
 src/schema/rules/sidecars/asl.yaml  | 18 ++++++++++++------
 src/schema/rules/sidecars/func.yaml |  3 ++-
 src/schema/rules/sidecars/mri.yaml  |  6 ++++--
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 42db35f024..6339456f09 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -34,7 +34,8 @@ MRIASLTextOnlySliceTiming:
         SliceTiming:
             level: REQUIRED
             code:
-                SLICE_TIMING_NOT_DEFINED_2D_ASL: |
+                name: SLICE_TIMING_NOT_DEFINED_2D_ASL
+                message: |
                     "You should define SliceTiming', in case 'SequenceType' is set to a
                     2D sequence. 'SliceTiming' is the time at which each slice was
                     acquired within each volume (frame) of the acquisition. Slice timing
@@ -59,7 +60,8 @@ MRIASLTextOnlyFlipAngle:
         FlipAngle:
             level: REQUIRED
             code:
-                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+                message: |
                     "You should define 'FlipAngle' for this file, in case of a
                     LookLocker acquisition. 'FlipAngle' is the flip angle (FA)
                     for the acquisition, specified in degrees. Corresponds to
@@ -114,7 +116,8 @@ MRIASLCommonMetadataFieldsM0Type:
         M0Estimate:
             level: REQUIRED
             code:
-                M0ESTIMATE_NOT_DEFINED: |
+                name: M0ESTIMATE_NOT_DEFINED
+                message: |
                     You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'.
                     'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood),
                     only if obtained externally (for example retrieved from CSF in a separate measurement).
@@ -199,7 +202,8 @@ MRIASLPASLSpecificBolusCutOffFlag:
         BolusCutOffDelayTime:
             level: REQUIRED
             code:
-                PASL_BOLUS_CUT_OFF_DELAY_TIME: |
+                name: PASL_BOLUS_CUT_OFF_DELAY_TIME
+                message: |
                     It is required to define 'BolusCutOffDelayTime' for this file,
                     when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is
                     the duration between the end of the labeling and the start of the
@@ -212,7 +216,8 @@ MRIASLPASLSpecificBolusCutOffFlag:
         BolusCutOffTechnique:
             level: REQUIRED
             code:
-                PASL_BOLUS_CUT_OFF_TECHINIQUE: |
+                name: PASL_BOLUS_CUT_OFF_TECHINIQUE
+                message: |
                     It is required to define 'BolusCutOffTechnique' for this file,
                     when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique',
                     is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII).
@@ -241,7 +246,8 @@ MRIASLM0ScanTextOnlyFlipAngle:
         FlipAngle:
             level: REQUIRED
             code:
-                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+                message: |
                     You should define 'FlipAngle' for this file, in case of a LookLocker
                     acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition,
                     specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index fd40707a90..16d17d71be 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -38,7 +38,8 @@ MRIFuncTimingParameters:
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
             code:
-                VOLUME_TIMING_MISSING_ACQUISITION_DURATION: |
+                name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
+                message: |
                     The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
         DelayAfterTrigger: RECOMMENDED
 
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index febc734dc7..3f24cd5f8a 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -153,7 +153,8 @@ MRITimingParameters:
                 REQUIRED if corresponding fieldmap data is present,
                 or the data comes from a multi-echo sequence or Arterial Spin Labeling.
             code:
-                ECHO_TIME_NOT_DEFINED: |
+                name: ECHO_TIME_NOT_DEFINED
+                message: |
                     You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE)
                     for the acquisition, specified in seconds. Corresponds to DICOM Tag
                     0018, 0081 Echo Time (please note that the DICOM term is in milliseconds
@@ -197,7 +198,8 @@ MRIRFandContrast:
             level: RECOMMENDED
             level_addendum: REQUIRED if LookLocker is set to `true`.
             code:
-                LOOK_LOCKER_FLIP_ANGLE_MISSING: |
+                name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+                message: |
                     You should define 'FlipAngle' for this file, in
                     case of a LookLocker acquisition. 'FlipAngle' is the
                     flip angle (FA) for the acquisition, specified in degrees.

From a3e55bacecb52e26fccad6799aa4be07e363e7dc Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 13 Apr 2022 13:34:27 -0400
Subject: [PATCH 252/347] missed 3 of em

---
 src/schema/rules/sidecars/mri.yaml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 3f24cd5f8a..5831d5438a 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -120,7 +120,8 @@ MRISpatialEncoding:
                 or when using multiple runs with different phase encoding directions
                 (which can be later used for field inhomogeneity correction).
             code:
-                PHASE_ENCODING_DIRECTION_MUST_DEFINE: |
+                name: PHASE_ENCODING_DIRECTION_MUST_DEFINE
+                code: |
                     You have to define 'PhaseEncodingDirection' for this file.
         EffectiveEchoSpacing:
             level: RECOMMENDED
@@ -128,7 +129,8 @@ MRISpatialEncoding:
                 <sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data
                 is present.
             code:
-                EFFECTIVE_ECHO_SPACING_NOT_DEFINED: |
+                name: EFFECTIVE_ECHO_SPACING_NOT_DEFINED
+                message: |
                     You should define 'EffectiveEchoSpacing' for this file. If you don't
                     provide this information field map correction will not be possible.
         TotalReadoutTime:
@@ -139,7 +141,8 @@ MRISpatialEncoding:
                 (see [Case 4: Multiple phase encoded
                 directions](#case-4-multiple-phase-encoded-directions-pepolar)).
             code:
-                TOTAL_READOUT_TIME_MUST_DEFINE: |
+                name: TOTAL_READOUT_TIME_MUST_DEFINE
+                message: |
                     You have to define 'TotalReadoutTime' for this file.
         MixingTime: RECOMMENDED
 

From d171b9973c24f34d17b742735f9493a2b34f2f7b Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 13 Apr 2022 13:46:05 -0400
Subject: [PATCH 253/347] Replace addendum with description_addendum.

---
 src/schema/rules/sidecars/asl.yaml  |  2 +-
 src/schema/rules/sidecars/eeg.yaml  | 10 +++++-----
 src/schema/rules/sidecars/fmap.yaml |  4 ++--
 src/schema/rules/sidecars/func.yaml |  4 ++--
 src/schema/rules/sidecars/ieeg.yaml | 10 +++++-----
 src/schema/rules/sidecars/meg.yaml  | 18 +++++++++---------
 src/schema/rules/sidecars/micr.yaml |  2 +-
 src/schema/rules/sidecars/mri.yaml  | 16 ++++++++--------
 src/schema/rules/sidecars/pet.yaml  | 14 +++++++-------
 9 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 4a81ecbfbb..98a1239985 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -193,5 +193,5 @@ MRIASLM0Scan:
     fields:
         IntendedFor:
             level: REQUIRED
-            addendum: This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
+            description_addendum: This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
         AcquisitionVoxelSize: RECOMMENDED
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 4b1902bd23..af63fb5861 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -15,7 +15,7 @@ EEGGeneric:
     fields:
         TaskName:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -34,7 +34,7 @@ EEGRecommended:
         TaskDescription: RECOMMENDED
         Instructions:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
         CogAtlasID: RECOMMENDED
@@ -50,7 +50,7 @@ EEGRequired:
         EEGReference: REQUIRED
         SamplingFrequency:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
         PowerLineFrequency: REQUIRED
@@ -88,7 +88,7 @@ EEGCoordsystemGeneral:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 This identifies the MRI or CT scan associated with the electrodes,
                 landmarks, and fiducials.
 
@@ -148,7 +148,7 @@ EEGCoordsystemLandmark:
         AnatomicalLandmarkCoordinates: RECOMMENDED
         AnatomicalLandmarkCoordinateSystem:
             level: RECOMMENDED
-            addendum: Preferably the same as the `EEGCoordinateSystem`.
+            description_addendum: Preferably the same as the `EEGCoordinateSystem`.
         AnatomicalLandmarkCoordinateUnits: RECOMMENDED
         AnatomicalLandmarkCoordinateSystemDescription:
             level: RECOMMENDED
diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
index 8eaec2707a..48291235be 100644
--- a/src/schema/rules/sidecars/fmap.yaml
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -21,7 +21,7 @@ MRIFieldmapIntendedFor:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 This field is OPTIONAL, and in case the fieldmaps do not correspond
                 to any particular scans, it does not have to be filled.
 
@@ -72,7 +72,7 @@ MRIFieldmapDirectFieldMapping:
     fields:
         Units:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 Fieldmaps must be in units of Hertz (`"Hz"`),
                 radians per second (`"rad/s"`), or Tesla (`"T"`).
 
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 03714fc44e..f9fb9251d7 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -18,7 +18,7 @@ MRIFuncRequired:
         VolumeTiming: REQUIRED
         TaskName:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -98,7 +98,7 @@ MRIFuncTaskInformation:
     fields:
         Instructions:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
         TaskDescription: RECOMMENDED
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index 90b43db4ca..8cc9290d72 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -15,7 +15,7 @@ iEEGGeneric:
     fields:
         TaskName:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -30,13 +30,13 @@ iEEGRecommended:
         InstitutionalDepartmentName: RECOMMENDED
         Manufacturer:
             level: RECOMMENDED
-            addendum: For example, `"TDT"`, `"Blackrock"`.
+            description_addendum: For example, `"TDT"`, `"Blackrock"`.
         ManufacturersModelName: RECOMMENDED
         SoftwareVersions: RECOMMENDED
         TaskDescription: RECOMMENDED
         Instructions:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
         CogAtlasID: RECOMMENDED
@@ -53,7 +53,7 @@ iEEGRequired:
         iEEGReference: REQUIRED
         SamplingFrequency:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
         PowerLineFrequency: REQUIRED
@@ -105,7 +105,7 @@ iEEGCoordsystemGeneral:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 If only a surface reconstruction is available, this should point to
                 the surface reconstruction file.
                 Note that this file should have the same coordinate system
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index 804d9e11e3..aa822ab4cc 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -17,7 +17,7 @@ MEGGeneric:
     fields:
         TaskName:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 A RECOMMENDED convention is to name resting state task using labels
                 beginning with `rest`.
 
@@ -32,7 +32,7 @@ MEGRecommended:
         InstitutionalDepartmentName: RECOMMENDED
         Manufacturer:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 For MEG scanners, this must be one of:
                 `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
                 `"ITAB"`, `"KRISS"`, `"Other"`.
@@ -40,14 +40,14 @@ MEGRecommended:
                 preferred names.
         ManufacturersModelName:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 See [Appendix VII](/99-appendices/07-meg-systems.html) for
                 preferred names.
         SoftwareVersions: RECOMMENDED
         TaskDescription: RECOMMENDED
         Instructions:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
         CogAtlasID: RECOMMENDED
@@ -63,7 +63,7 @@ MEGRequired:
     fields:
         SamplingFrequency:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
         PowerLineFrequency: REQUIRED
@@ -127,7 +127,7 @@ MEGCoordsystemWithEEG:
             level_addendum: REQUIRED if `MEGCoordinateSystem` is `Other`
         EEGCoordinateSystem:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 See [Recording EEG simultaneously with MEG]
                 (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
                 Preferably the same as the `MEGCoordinateSystem`.
@@ -135,7 +135,7 @@ MEGCoordsystemWithEEG:
         EEGCoordinateSystemDescription:
             level: OPTIONAL
             level_addendum: REQUIRED if `EEGCoordinateSystem` is `Other`
-            addendum: |
+            description_addendum: |
                 See [Recording EEG simultaneously with MEG]
                 (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
 
@@ -215,7 +215,7 @@ MEGCoordsystemAnatomicalMRI:
     fields:
         IntendedFor:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 This is used to identify the structural MRI(s),
                 possibly of different types if a list is specified,
                 to be used with the MEG recording.
@@ -230,7 +230,7 @@ MEGCoordsystemAnatomicalLandmarks:
         AnatomicalLandmarkCoordinates: OPTIONAL
         AnatomicalLandmarkCoordinateSystem:
             level: OPTIONAL
-            addendum: |
+            description_addendum: |
                 Preferably the same as the `MEGCoordinateSystem`.
         AnatomicalLandmarkCoordinateUnits: OPTIONAL
         AnatomicalLandmarkCoordinateSystemDescription:
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
index c4fd7d41ed..a8b3d66ad1 100644
--- a/src/schema/rules/sidecars/micr.yaml
+++ b/src/schema/rules/sidecars/micr.yaml
@@ -43,7 +43,7 @@ MicroscopySample:
     fields:
         BodyPart:
             level: RECOMMENDED
-            addendum: |
+            description_addendum: |
                 From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/
                 output/chtml/part16/chapter_L.html#chapter_L)
                 (for example `"BRAIN"`).
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 3cbbebfacd..4eba44adf3 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -13,19 +13,19 @@ MRIScannerHardware:
     fields:
         Manufacturer:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
         ManufacturersModelName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
+            description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
         DeviceSerialNumber:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`.
+            description_addendum: Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`.
         StationName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 1010 `Station Name`.
+            description_addendum: Corresponds to DICOM Tag 0008, 1010 `Station Name`.
         SoftwareVersions:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`.
+            description_addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`.
         HardcopyDeviceSoftwareVersion: DEPRECATED
         MagneticFieldStrength:
             level: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
@@ -209,10 +209,10 @@ MRIInstitutionInformation:
     fields:
         InstitutionName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
         InstitutionAddress:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
         InstitutionalDepartmentName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
+            description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index 0a8a509450..5ee41b1f23 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -6,27 +6,27 @@ PETScannerHardware:
     fields:
         Manufacturer:
             level: REQUIRED
-            addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
         ManufacturersModelName:
             level: REQUIRED
-            addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
+            description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
         Units:
             level: REQUIRED
-            addendum: |
+            description_addendum: |
                 SI unit for radioactivity (Becquerel) should be used (for example, "Bq/mL").
                 Corresponds to DICOM Tag 0054, 1001 `Units`.
         InstitutionName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
         InstitutionAddress:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
+            description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
         InstitutionalDepartmentName:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
+            description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
         BodyPart:
             level: RECOMMENDED
-            addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
+            description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
 
 PETRadioChemistry:
     selectors:

From 43f6b58b94cce19d3f42832c122be5aac26aaa53 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 13 Apr 2022 13:49:42 -0400
Subject: [PATCH 254/347] Fix line length.

---
 src/schema/rules/sidecars/asl.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 98a1239985..38bbf1b87a 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -193,5 +193,6 @@ MRIASLM0Scan:
     fields:
         IntendedFor:
             level: REQUIRED
-            description_addendum: This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
+            description_addendum: |
+                This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
         AcquisitionVoxelSize: RECOMMENDED

From 47a645787c237a3c01ab35bf979ab2cd074c0cf4 Mon Sep 17 00:00:00 2001
From: anthony galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 13 Apr 2022 13:50:24 -0400
Subject: [PATCH 255/347] replaced code: with issue:

---
 src/schema/rules/sidecars/asl.yaml  | 12 ++++++------
 src/schema/rules/sidecars/func.yaml |  2 +-
 src/schema/rules/sidecars/mri.yaml  | 12 ++++++------
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 6339456f09..c47a584952 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -33,7 +33,7 @@ MRIASLTextOnlySliceTiming:
     fields:
         SliceTiming:
             level: REQUIRED
-            code:
+            issue::
                 name: SLICE_TIMING_NOT_DEFINED_2D_ASL
                 message: |
                     "You should define SliceTiming', in case 'SequenceType' is set to a
@@ -59,7 +59,7 @@ MRIASLTextOnlyFlipAngle:
     fields:
         FlipAngle:
             level: REQUIRED
-            code:
+            issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
                     "You should define 'FlipAngle' for this file, in case of a
@@ -115,7 +115,7 @@ MRIASLCommonMetadataFieldsM0Type:
     fields:
         M0Estimate:
             level: REQUIRED
-            code:
+            issue:
                 name: M0ESTIMATE_NOT_DEFINED
                 message: |
                     You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'.
@@ -201,7 +201,7 @@ MRIASLPASLSpecificBolusCutOffFlag:
     fields:
         BolusCutOffDelayTime:
             level: REQUIRED
-            code:
+            issue:
                 name: PASL_BOLUS_CUT_OFF_DELAY_TIME
                 message: |
                     It is required to define 'BolusCutOffDelayTime' for this file,
@@ -215,7 +215,7 @@ MRIASLPASLSpecificBolusCutOffFlag:
                     0018,925F ASL Bolus Cut-off Delay Time.
         BolusCutOffTechnique:
             level: REQUIRED
-            code:
+            issue:
                 name: PASL_BOLUS_CUT_OFF_TECHINIQUE
                 message: |
                     It is required to define 'BolusCutOffTechnique' for this file,
@@ -245,7 +245,7 @@ MRIASLM0ScanTextOnlyFlipAngle:
     fields:
         FlipAngle:
             level: REQUIRED
-            code:
+            issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
                     You should define 'FlipAngle' for this file, in case of a LookLocker
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 16d17d71be..fc6f262932 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -37,7 +37,7 @@ MRIFuncTimingParameters:
                 REQUIRED for sequences that are described with the `VolumeTiming`
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
-            code:
+            issue::
                 name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
                 message: |
                     The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 5831d5438a..469e55db3d 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -119,16 +119,16 @@ MRISpatialEncoding:
                 This parameter is REQUIRED if corresponding fieldmap data is present
                 or when using multiple runs with different phase encoding directions
                 (which can be later used for field inhomogeneity correction).
-            code:
+            issue::
                 name: PHASE_ENCODING_DIRECTION_MUST_DEFINE
-                code: |
+                issue: |
                     You have to define 'PhaseEncodingDirection' for this file.
         EffectiveEchoSpacing:
             level: RECOMMENDED
             level_addendum: |
                 <sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data
                 is present.
-            code:
+            issue:
                 name: EFFECTIVE_ECHO_SPACING_NOT_DEFINED
                 message: |
                     You should define 'EffectiveEchoSpacing' for this file. If you don't
@@ -140,7 +140,7 @@ MRISpatialEncoding:
                 acquired with opposing phase encoding directions are present
                 (see [Case 4: Multiple phase encoded
                 directions](#case-4-multiple-phase-encoded-directions-pepolar)).
-            code:
+            issue:
                 name: TOTAL_READOUT_TIME_MUST_DEFINE
                 message: |
                     You have to define 'TotalReadoutTime' for this file.
@@ -155,7 +155,7 @@ MRITimingParameters:
             level_addendum: |
                 REQUIRED if corresponding fieldmap data is present,
                 or the data comes from a multi-echo sequence or Arterial Spin Labeling.
-            code:
+            issue:
                 name: ECHO_TIME_NOT_DEFINED
                 message: |
                     You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE)
@@ -200,7 +200,7 @@ MRIRFandContrast:
         FlipAngle:
             level: RECOMMENDED
             level_addendum: REQUIRED if LookLocker is set to `true`.
-            code:
+            issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
                     You should define 'FlipAngle' for this file, in

From 41f44ca5e69d51c3da74102bcd6ab80b9a648f9c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 11:18:25 -0700
Subject: [PATCH 256/347] SCHEMA: Initial shot at EEG channels and electrodes

---
 src/schema/rules/tabular_data/eeg.yaml | 55 ++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/eeg.yaml

diff --git a/src/schema/rules/tabular_data/eeg.yaml b/src/schema/rules/tabular_data/eeg.yaml
new file mode 100644
index 0000000000..21d086f644
--- /dev/null
+++ b/src/schema/rules/tabular_data/eeg.yaml
@@ -0,0 +1,55 @@
+---
+EEGChannels:
+    selectors:
+    - datatype == "eeg"
+    - suffix == "channels"
+    - extension == ".tsv"
+    initial_columns: [name__channels, type, units]
+    columns:
+        name__channels: REQUIRED
+        type__channels:
+            level: REQUIRED
+            enum:
+            - AUDIO
+            - EEG
+            - EOG
+            - ECG
+            - EMG
+            - EYEGAZE
+            - GSR
+            - HEOG
+            - MISC
+            - PPG
+            - PUPIL
+            - REF
+            - RESP
+            - SYSCLOCK
+            - TEMP
+            - TRIG
+            - VEOG
+        units: REQUIRED
+        description: OPTIONAL
+        sampling_frequency: OPTIONAL
+        reference: OPTIONAL
+        low_cutoff: OPTIONAL
+        high_cutoff: OPTIONAL
+        notch: OPTIONAL
+        status: OPTIONAL
+        status_descriptions: OPTIONAL
+    unknown_column_metadata: REQUIRED
+
+EEGElectrodes:
+    selectors:
+    - datatype == "eeg"
+    - suffix == "electrodes"
+    - extension == ".tsv"
+    initial_columns: [name__electrodes, x, y, z]
+    columns:
+        name__electrodes: REQUIRED
+        x: REQUIRED
+        y: REQUIRED
+        z: REQUIRED
+        type__electrodes: RECOMMENDED
+        material: RECOMMENDED
+        impedance: RECOMMENDED
+    unknown_column_metadata: REQUIRED

From fe1cf9700d809b424b694ec0882f110a877fb733 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 16:00:25 -0700
Subject: [PATCH 257/347] SCHEMA: Add aslcontext column validation

---
 src/schema/rules/tabular_data/perf.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/perf.yaml

diff --git a/src/schema/rules/tabular_data/perf.yaml b/src/schema/rules/tabular_data/perf.yaml
new file mode 100644
index 0000000000..4ced4b5e7d
--- /dev/null
+++ b/src/schema/rules/tabular_data/perf.yaml
@@ -0,0 +1,8 @@
+---
+ASLContext:
+    selectors:
+    - datatype == "perf"
+    - suffix == "aslcontext"
+    columns:
+        volume_type: REQUIRED
+    additional_columns: not_allowed

From 2e833321e07ed3390d4db2f10012bc5e0ef849a3 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 16:10:23 -0700
Subject: [PATCH 258/347] SCHEMA add MEG channels.tsv

---
 src/schema/rules/tabular_data/meg.yaml | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/meg.yaml

diff --git a/src/schema/rules/tabular_data/meg.yaml b/src/schema/rules/tabular_data/meg.yaml
new file mode 100644
index 0000000000..68078a3a37
--- /dev/null
+++ b/src/schema/rules/tabular_data/meg.yaml
@@ -0,0 +1,20 @@
+---
+MEGChannels:
+    selectors:
+    - datatype == "eeg"
+    - suffix == "channels"
+    - extension == ".tsv"
+    initial_columns: [name__channels, type, units]
+    columns:
+        name__channels: REQUIRED
+        type__channels: REQUIRED
+        units: REQUIRED
+        description: OPTIONAL
+        sampling_frequency: OPTIONAL
+        low_cutoff: OPTIONAL
+        high_cutoff: OPTIONAL
+        notch: OPTIONAL
+        software_filters: OPTIONAL
+        status: OPTIONAL
+        status_descriptions: OPTIONAL
+    additional_columns: allowed_if_defined

From 0955ed4ceb453a69d47be4be1416e68a9990ebfc Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 16:10:56 -0700
Subject: [PATCH 259/347] SCHEMA: eeg addtional_columnns

---
 src/schema/rules/tabular_data/eeg.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/rules/tabular_data/eeg.yaml b/src/schema/rules/tabular_data/eeg.yaml
index 21d086f644..8bb47541aa 100644
--- a/src/schema/rules/tabular_data/eeg.yaml
+++ b/src/schema/rules/tabular_data/eeg.yaml
@@ -36,7 +36,7 @@ EEGChannels:
         notch: OPTIONAL
         status: OPTIONAL
         status_descriptions: OPTIONAL
-    unknown_column_metadata: REQUIRED
+    additional_columns: allowed_if_defined
 
 EEGElectrodes:
     selectors:
@@ -52,4 +52,4 @@ EEGElectrodes:
         type__electrodes: RECOMMENDED
         material: RECOMMENDED
         impedance: RECOMMENDED
-    unknown_column_metadata: REQUIRED
+    additional_columns: allowed_if_defined

From 7f779528858261169314120762f4dd4a322ea8c8 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 16:33:01 -0700
Subject: [PATCH 260/347] SCHEMA: Add iEEG channels/electrodes TSV

---
 src/schema/rules/tabular_data/ieeg.yaml | 64 +++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/ieeg.yaml

diff --git a/src/schema/rules/tabular_data/ieeg.yaml b/src/schema/rules/tabular_data/ieeg.yaml
new file mode 100644
index 0000000000..6b17731b1a
--- /dev/null
+++ b/src/schema/rules/tabular_data/ieeg.yaml
@@ -0,0 +1,64 @@
+---
+iEEGChannels:
+    selectors:
+    - datatype == "ieeg"
+    - suffix == "channels"
+    - extension == ".tsv"
+    initial_columns: [name__channels, type, units]
+    columns:
+        name__channels: REQUIRED
+        type__channels:
+            level: REQUIRED
+            enum:
+            - EEG
+            - ECOG
+            - SEEG
+            - DBS
+            - VEOG
+            - HEOG
+            - EOG
+            - ECG
+            - EMG
+            - TRIG
+            - AUDIO
+            - PD
+            - EYEGAZE
+            - PUPIL
+            - MISC
+            - SYSCLOCK
+            - ADC
+            - DAC
+            - REF
+            - OTHER
+        units: REQUIRED
+        low_cutoff: REQUIRED
+        high_cutoff: REQUIRED
+        reference: OPTIONAL
+        group: OPTIONAL
+        sampling_frequency: OPTIONAL
+        description: OPTIONAL
+        notch: OPTIONAL
+        status: OPTIONAL
+        status_descriptions: OPTIONAL
+    additional_columns: allowed_if_defined
+
+iEEGElectrodes:
+    selectors:
+    - datatype == "ieeg"
+    - suffix == "electrodes"
+    - extension == ".tsv"
+    initial_columns: [name__electrodes, x, y, z]
+    columns:
+        name__electrodes: REQUIRED
+        x: REQUIRED
+        y: REQUIRED
+        z: REQUIRED
+        size: REQUIRED
+        material: RECOMMENDED
+        manufacturer: RECOMMENDED
+        group: RECOMMENDED
+        hemisphere: RECOMMENDED
+        type__electrodes: OPTIONAL
+        impedance: OPTIONAL
+        dimension: OPTIONAL
+    additional_columns: allowed_if_defined

From 042ed90bb2b424b5ad67adc640b86559f3f201c6 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 17:36:16 -0700
Subject: [PATCH 261/347] Define task columns

---
 src/schema/rules/tabular_data/task.yaml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/task.yaml

diff --git a/src/schema/rules/tabular_data/task.yaml b/src/schema/rules/tabular_data/task.yaml
new file mode 100644
index 0000000000..a370adc739
--- /dev/null
+++ b/src/schema/rules/tabular_data/task.yaml
@@ -0,0 +1,15 @@
+---
+TaskEvents:
+    selectors:
+    - entities contains "task"
+    - suffix == "events"
+    columns:
+        onset: REQUIRED
+        duration: REQUIRED
+        sample: OPTIONAL
+        trial_type: OPTIONAL
+        response_time: OPTIONAL
+        value: OPTIONAL
+        HED: OPTIONAL
+        stim_file: OPTIONAL
+    additional_columns: allowed

From 885b509becbe038e90000b60f17890748281c478 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 17:38:47 -0700
Subject: [PATCH 262/347] SCHEMA: Define physio columns

---
 src/schema/rules/tabular_data/physio.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/physio.yaml

diff --git a/src/schema/rules/tabular_data/physio.yaml b/src/schema/rules/tabular_data/physio.yaml
new file mode 100644
index 0000000000..e8d122f6ea
--- /dev/null
+++ b/src/schema/rules/tabular_data/physio.yaml
@@ -0,0 +1,9 @@
+---
+PhysioColumns:
+    selectors:
+    - suffix == "physio"
+    columns:
+        cardiac: OPTIONAL
+        respiratory: OPTIONAL
+        trigger: OPTIONAL
+    additional_columns: allowed

From 232f41d9aa5e692b828b5ac0b21b65d1f3a56249 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 13 Apr 2022 13:50:53 -0400
Subject: [PATCH 263/347] Update src/schema/rules/tabular_data/eeg.yaml

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 src/schema/rules/tabular_data/eeg.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/tabular_data/eeg.yaml b/src/schema/rules/tabular_data/eeg.yaml
index 8bb47541aa..d153304a0c 100644
--- a/src/schema/rules/tabular_data/eeg.yaml
+++ b/src/schema/rules/tabular_data/eeg.yaml
@@ -4,7 +4,7 @@ EEGChannels:
     - datatype == "eeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type, units]
+    initial_columns: [name__channels, type__channels, units]
     columns:
         name__channels: REQUIRED
         type__channels:

From 3bec3f8b56f65f4176c91f52d9df00528ac33958 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 13 Apr 2022 14:29:36 -0400
Subject: [PATCH 264/347] Add a few more rules.

---
 src/schema/rules/sidecars/dwi_validation.yaml | 22 +++++++++++++++++
 .../rules/sidecars/fmap_validation.yaml       | 24 +++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 src/schema/rules/sidecars/fmap_validation.yaml

diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 73f51ea883..2ed5401f6d 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -16,6 +16,28 @@ DWIVolumeCount:
     - associated["bval"].shape[0] == data.shape[3]
     - associated["bvec"].shape[0] == data.shape[3]
 
+# 30
+DWIBvalRows:
+    code: BVAL_MULTIPLE_ROWS
+    description: |
+        '.bval' files should contain exactly one row of volumes.
+    level: error
+    selectors:
+    - extension == "bval"
+    checks:
+    - data.n_rows == 1
+
+# 31
+DWIBvecRows:
+    code: BVEC_NUMBER_ROWS
+    description: |
+        '.bvec' files should contain exactly three rows of volumes.
+    level: error
+    selectors:
+    - extension == "bvec"
+    checks:
+    - data.n_rows == 3
+
 # 32
 DWIMissingBvec:
     code: DWI_MISSING_BVEC
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/sidecars/fmap_validation.yaml
new file mode 100644
index 0000000000..b88bce11ef
--- /dev/null
+++ b/src/schema/rules/sidecars/fmap_validation.yaml
@@ -0,0 +1,24 @@
+# Rules for fieldmap data that are not defined in tables.
+---
+
+# 91
+FmapFieldmapWithoutMagnitude:
+    code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
+    description: |
+        '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
+    level: error
+    selectors:
+    - suffix == "fieldmap"
+    checks:
+    - associated contains "magnitude"
+
+# 92
+FmapPhasediffWithoutMagnitude:
+    code: MISSING_MAGNITUDE1_FILE
+    description: |
+        Each '_phasediff.nii[.gz]' file should be associated with a '_magnitude1.nii[.gz]' file.
+    level: warning
+    selectors:
+    - suffix == "phasediff"
+    checks:
+    - associated contains "magnitude1"

From 069abd6d7beaa2bbd3a3821491cb35fd0490c44e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 13 Apr 2022 11:19:36 -0700
Subject: [PATCH 265/347] SCHEMA: Separate out channel types for *EG

---
 .../02-magnetoencephalography.md              |  2 +-
 .../03-electroencephalography.md              |  2 +-
 .../04-intracranial-electroencephalography.md |  2 +-
 src/schema/objects/columns.yaml               | 53 ++++++++++++++++++-
 src/schema/rules/tabular_data/eeg.yaml        | 23 +-------
 src/schema/rules/tabular_data/ieeg.yaml       | 26 +--------
 src/schema/rules/tabular_data/meg.yaml        |  4 +-
 7 files changed, 61 insertions(+), 51 deletions(-)

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index b49c9ae556..80aa26abad 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -284,7 +284,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
-      "type__channels": "REQUIRED",
+      "type__meg_channels": "REQUIRED",
       "units": "REQUIRED",
    }
 ) }}
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 95bdeb7850..52c5cd0b8a 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -252,7 +252,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_columns_table(
    {
       "name__channels": "REQUIRED",
-      "type__channels": "REQUIRED",
+      "type__eeg_channels": "REQUIRED",
       "units": "REQUIRED",
    }
 ) }}
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index a79387f0e2..0f4551c651 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -276,7 +276,7 @@ and a guide for using macros can be found at
       "name__channels": ("REQUIRED", "When a corresponding electrode is specified in `_electrodes.tsv`, "
                          "the name of that electrode MAY be specified here and the reference electrode "
                          "name MAY be provided in the `reference` column."),
-      "type__channels": "REQUIRED",
+      "type__ieeg_channels": "REQUIRED",
       "units": "REQUIRED",
       "low_cutoff": "REQUIRED",
       "high_cutoff": "REQUIRED",
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 36e93fe308..b9547f176f 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -466,7 +466,31 @@ trigger:
     continuous measurement of the scanner trigger signal
   type: number
 # type column in channels.tsv files
-type__channels:
+type__eeg_channels:
+  name: type
+  description: |
+    Type of channel; MUST use the channel types listed below.
+    Note that the type MUST be in upper-case.
+  type: string
+  enum:
+  - AUDIO
+  - EEG
+  - EOG
+  - ECG
+  - EMG
+  - EYEGAZE
+  - GSR
+  - HEOG
+  - MISC
+  - PPG
+  - PUPIL
+  - REF
+  - RESP
+  - SYSCLOCK
+  - TEMP
+  - TRIG
+  - VEOG
+type__meg_channels:
   name: type
   description: |
     Type of channel; MUST use the channel types listed below.
@@ -501,6 +525,33 @@ type__channels:
   - HLU
   - FITERR
   - OTHER
+type__ieg_channels:
+  name: type
+  description: |
+    Type of channel; MUST use the channel types listed below.
+    Note that the type MUST be in upper-case.
+  type: string
+  enum:
+  - EEG
+  - ECOG
+  - SEEG
+  - DBS
+  - VEOG
+  - HEOG
+  - EOG
+  - ECG
+  - EMG
+  - TRIG
+  - AUDIO
+  - PD
+  - EYEGAZE
+  - PUPIL
+  - MISC
+  - SYSCLOCK
+  - ADC
+  - DAC
+  - REF
+  - OTHER
 # type column for electrodes.tsv files
 type__electrodes:
   name: type
diff --git a/src/schema/rules/tabular_data/eeg.yaml b/src/schema/rules/tabular_data/eeg.yaml
index d153304a0c..ee987de4f7 100644
--- a/src/schema/rules/tabular_data/eeg.yaml
+++ b/src/schema/rules/tabular_data/eeg.yaml
@@ -4,29 +4,10 @@ EEGChannels:
     - datatype == "eeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type__channels, units]
+    initial_columns: [name__channels, type__eeg_channels, units]
     columns:
         name__channels: REQUIRED
-        type__channels:
-            level: REQUIRED
-            enum:
-            - AUDIO
-            - EEG
-            - EOG
-            - ECG
-            - EMG
-            - EYEGAZE
-            - GSR
-            - HEOG
-            - MISC
-            - PPG
-            - PUPIL
-            - REF
-            - RESP
-            - SYSCLOCK
-            - TEMP
-            - TRIG
-            - VEOG
+        type__eeg_channels: REQUIRED
         units: REQUIRED
         description: OPTIONAL
         sampling_frequency: OPTIONAL
diff --git a/src/schema/rules/tabular_data/ieeg.yaml b/src/schema/rules/tabular_data/ieeg.yaml
index 6b17731b1a..faa968f160 100644
--- a/src/schema/rules/tabular_data/ieeg.yaml
+++ b/src/schema/rules/tabular_data/ieeg.yaml
@@ -4,32 +4,10 @@ iEEGChannels:
     - datatype == "ieeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type, units]
+    initial_columns: [name__channels, type__ieeg_channels, units]
     columns:
         name__channels: REQUIRED
-        type__channels:
-            level: REQUIRED
-            enum:
-            - EEG
-            - ECOG
-            - SEEG
-            - DBS
-            - VEOG
-            - HEOG
-            - EOG
-            - ECG
-            - EMG
-            - TRIG
-            - AUDIO
-            - PD
-            - EYEGAZE
-            - PUPIL
-            - MISC
-            - SYSCLOCK
-            - ADC
-            - DAC
-            - REF
-            - OTHER
+        type__ieeg_channels: REQUIRED
         units: REQUIRED
         low_cutoff: REQUIRED
         high_cutoff: REQUIRED
diff --git a/src/schema/rules/tabular_data/meg.yaml b/src/schema/rules/tabular_data/meg.yaml
index 68078a3a37..f5bc01862a 100644
--- a/src/schema/rules/tabular_data/meg.yaml
+++ b/src/schema/rules/tabular_data/meg.yaml
@@ -4,10 +4,10 @@ MEGChannels:
     - datatype == "eeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type, units]
+    initial_columns: [name__channels, type__meg_channels, units]
     columns:
         name__channels: REQUIRED
-        type__channels: REQUIRED
+        type__meg_channels: REQUIRED
         units: REQUIRED
         description: OPTIONAL
         sampling_frequency: OPTIONAL

From d6b137514d40d17262f385783bb83e6f2295b0f9 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 12 Apr 2022 16:37:26 -0700
Subject: [PATCH 266/347] first pass at blodd tsv for pet

---
 src/schema/rules/tabular_data/pet.yaml | 50 ++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 src/schema/rules/tabular_data/pet.yaml

diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
new file mode 100644
index 0000000000..d3b0c18bab
--- /dev/null
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -0,0 +1,50 @@
+---
+Blood:
+  anyOf:
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    columns:
+      time:
+        level: REQUIRED
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    - sidecar.PlasmaAvail == true
+    columns:
+      plasma_radioactivity:
+        level: REQUIRED
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    - sidecar.MetaboliteAvail == true
+    columns:
+      metabolite_parent_fraction:
+        level: REQUIRED
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    - sidecar.MetaboliteAvail == true
+    columns:
+      metabolite_polar_fraction:
+        level: REQUIRED
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    - sidecar.MetaboliteRecoveryCorrectionApplied == true
+    columns:
+      hplc_recovery_fractions:
+        level: REQUIRED
+  - selectors:
+    - modality == "pet"
+    - suffix == "blood"
+    - extension == ".tsv"
+    - sidecar.WholeBloodAvail == true
+    columns:
+      whole_blood_radioactivity:
+        level: REQUIRED

From 1517379a077d66b0b0f28c825fd988d5c7292dbb Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 12 Apr 2022 19:45:17 -0400
Subject: [PATCH 267/347] RF: Break blood TSV rules into conditioned rules

---
 src/schema/rules/tabular_data/pet.yaml | 52 +++++++++++++-------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index d3b0c18bab..6eab38633d 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -1,50 +1,50 @@
 ---
 Blood:
-  anyOf:
-  - selectors:
+    selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
     columns:
-      time:
-        level: REQUIRED
-  - selectors:
+      time: REQUIRED
+      plasma_radioactivity: OPTIONAL
+      metabolite_parent_fraction: OPTIONAL
+      metabolite_polar_fraction: OPTIONAL
+      hplc_recovery_fractions: OPTIONAL
+      whole_blood_radioactivity: OPTIONAL
+
+BloodPlasma:
+    selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar.PlasmaAvail == true
+    - sidecar.PlasmaAvail
     columns:
-      plasma_radioactivity:
-        level: REQUIRED
-  - selectors:
+      plasma_radioactivity: REQUIRED
+
+BloodMetabolite:
+    selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar.MetaboliteAvail == true
+    - sidecar.MetaboliteAvail
     columns:
-      metabolite_parent_fraction:
-        level: REQUIRED
-  - selectors:
-    - modality == "pet"
-    - suffix == "blood"
-    - extension == ".tsv"
-    - sidecar.MetaboliteAvail == true
-    columns:
-      metabolite_polar_fraction:
-        level: REQUIRED
-  - selectors:
+      metabolite_parent_fraction: REQUIRED
+      metabolite_polar_fraction: RECOMMENDED
+ 
+ BloodMetaboliteCorrection:
+    selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
     columns:
-      hplc_recovery_fractions:
-        level: REQUIRED
-  - selectors:
+      hplc_recovery_fractions: REQUIRED
+ 
+ BloodWholeBlood:
+    selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
     - sidecar.WholeBloodAvail == true
     columns:
-      whole_blood_radioactivity:
-        level: REQUIRED
+      whole_blood_radioactivity: REQUIRED

From 269dc003c5a220c00e260efc53ca04c36d249f41 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 13 Apr 2022 07:44:56 -0700
Subject: [PATCH 268/347] lint fixes for pet.yaml

---
 src/schema/rules/tabular_data/pet.yaml | 30 +++++++++++++-------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index 6eab38633d..1960b34fd7 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -5,12 +5,12 @@ Blood:
     - suffix == "blood"
     - extension == ".tsv"
     columns:
-      time: REQUIRED
-      plasma_radioactivity: OPTIONAL
-      metabolite_parent_fraction: OPTIONAL
-      metabolite_polar_fraction: OPTIONAL
-      hplc_recovery_fractions: OPTIONAL
-      whole_blood_radioactivity: OPTIONAL
+        time: REQUIRED
+        plasma_radioactivity: OPTIONAL
+        metabolite_parent_fraction: OPTIONAL
+        metabolite_polar_fraction: OPTIONAL
+        hplc_recovery_fractions: OPTIONAL
+        whole_blood_radioactivity: OPTIONAL
 
 BloodPlasma:
     selectors:
@@ -19,7 +19,7 @@ BloodPlasma:
     - extension == ".tsv"
     - sidecar.PlasmaAvail
     columns:
-      plasma_radioactivity: REQUIRED
+        plasma_radioactivity: REQUIRED
 
 BloodMetabolite:
     selectors:
@@ -28,23 +28,23 @@ BloodMetabolite:
     - extension == ".tsv"
     - sidecar.MetaboliteAvail
     columns:
-      metabolite_parent_fraction: REQUIRED
-      metabolite_polar_fraction: RECOMMENDED
- 
- BloodMetaboliteCorrection:
+        metabolite_parent_fraction: REQUIRED
+        metabolite_polar_fraction: RECOMMENDED
+
+BloodMetaboliteCorrection:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
     columns:
-      hplc_recovery_fractions: REQUIRED
- 
- BloodWholeBlood:
+        hplc_recovery_fractions: REQUIRED
+
+BloodWholeBlood:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
     - sidecar.WholeBloodAvail == true
     columns:
-      whole_blood_radioactivity: REQUIRED
+        whole_blood_radioactivity: REQUIRED

From df339be6dd5704904a198569262fc6ac5a7f22d9 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 13 Apr 2022 10:14:06 -0700
Subject: [PATCH 269/347] common derivatives schema start with no good very bad
 yaml formatting

---
 .../rules/sidecars/common_derivative.yaml     | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 src/schema/rules/sidecars/common_derivative.yaml

diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
new file mode 100644
index 0000000000..75ae60053d
--- /dev/null
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -0,0 +1,60 @@
+---
+CommonDerivativeFields:
+    selectors:
+        - isDerivative
+    fields:
+        - Description: RECOMMENDED
+        - Sources: OPTIONAL
+        - RawSources: OPTIONAL
+
+# should this apply to *eg space entities
+SpatialReference:
+    selectors:
+        - isDerivative
+        # - this file can use space entity
+    allOf:
+        - SpatialReferenceEntity:
+            selectors:
+                - entities contains "space"
+            fields:
+                - SpatialReference: RECOMMENDED
+        - SpatialReferenceNonStandard:
+            selectors:
+                - entities.space not in _StandardTemplateCoordSys
+            fields:
+                - SpatialReference: REQUIRED
+        - SpatialReferenceNoEntity:
+            selectors:
+                - enties does not contain "space"
+            fields:
+                - SpatialReference: REQUIRED
+
+# rules for invalidating fields on derived data
+
+ImageDerivatives:
+    selectors:
+        - isDerivative
+        - isImaging
+    fields:
+        - SkullStripped: REQUIRED
+    allOf:
+        - ImageDerivativeResEntity:
+            selectors:
+                - entities contains "res"
+            fields:
+                - Resolution: REQUIRED
+        - ImageDerivativeDenEntity:
+            selectors:
+                - entities contains "den"
+            fields:
+                - Density: REQUIRED
+        - ResInSidecar
+            selectors:
+                - type(sidecars.Resolution) == "object"
+            checks:
+                - sidecar.resolution contains entities.res
+        - DenInSidecar
+            selectors:
+                - type(sidecars.density) == "object"
+            checks:
+                - sidecar.density contains entities.den

From e2ba28c066cfedf2bb65c2298797b499da90e032 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 14 Apr 2022 07:59:30 -0700
Subject: [PATCH 270/347] update common derivatives sidecar yaml to look more
 like other sidecar files

---
 src/schema/meta/nifti_header.yaml             |  68 ++++++++++++
 .../rules/sidecars/common_derivative.yaml     | 102 ++++++++++--------
 2 files changed, 125 insertions(+), 45 deletions(-)
 create mode 100644 src/schema/meta/nifti_header.yaml

diff --git a/src/schema/meta/nifti_header.yaml b/src/schema/meta/nifti_header.yaml
new file mode 100644
index 0000000000..b3e7fa5536
--- /dev/null
+++ b/src/schema/meta/nifti_header.yaml
@@ -0,0 +1,68 @@
+---
+nifti_header:
+    name: "NiFTI Header"
+    description: "Parsed contents of NifTI header referenced elsewhere in schema." 
+    type: object
+    properties:
+        dim_info:
+            name: "Dimension Information"
+            description:
+            type: object
+            properties:
+                freq:
+                    name: "Frequency"
+                    description: "These fields encode which spatial dimension (1,2, or 3)"
+                    type: int
+                phase:
+                    name: "Phase"
+                    description: "Corresponds to which acquisition dimension for MRI data"
+                    type: int
+                slice:
+                    name: "Slice"
+                    description: "Slice dimensions"
+                    type: int
+        dim:
+            name: "Data Dimensions"
+            description: "Data array dimensions."
+            type: array
+            minItems: 8
+            maxItems: 8
+            items:
+            type: int
+        pixdim:
+            name: "Pixel Dimension"
+            description: "Grid spacings (unit per dimension)."
+            type: array
+            minItems: 8
+            maxItems: 8
+            items:
+            type: float
+        xyzt_units:
+            name: "XYZT Units"
+            description: "Units of pixdim[1..4]"
+            xyz:
+                name: "XYZ Units"
+                description: "String representing the unit used by all 3 spatial dimensions data"
+                type: string
+            enum:
+                - "unknown"
+                - "meter"
+                - "mm"
+                - "um"
+            t:
+                name: "Time Unit"
+                description: "String representing the unit used by temporal dimension data"
+                type: string
+                enum:
+                    - "unknown"
+                    - "sec"
+                    - "msec"
+                    - "usec"
+        qform_code:
+            name: "qform code"
+            description: "Use of the quaternion fields."
+            type: int
+        sform_code:
+            name: "sform code"
+            description: "Use of the affine fields."
+            type: int
diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index 75ae60053d..75091f0b29 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -1,60 +1,72 @@
 ---
 CommonDerivativeFields:
     selectors:
-        - isDerivative
+        - dataset.DatasetType == "derivative"
     fields:
         - Description: RECOMMENDED
         - Sources: OPTIONAL
         - RawSources: OPTIONAL
 
-# should this apply to *eg space entities
 SpatialReference:
     selectors:
-        - isDerivative
+        - dataset.DatasetType == "derivative"
         # - this file can use space entity
-    allOf:
-        - SpatialReferenceEntity:
-            selectors:
-                - entities contains "space"
-            fields:
-                - SpatialReference: RECOMMENDED
-        - SpatialReferenceNonStandard:
-            selectors:
-                - entities.space not in _StandardTemplateCoordSys
-            fields:
-                - SpatialReference: REQUIRED
-        - SpatialReferenceNoEntity:
-            selectors:
-                - enties does not contain "space"
-            fields:
-                - SpatialReference: REQUIRED
-
-# rules for invalidating fields on derived data
+SpatialReferenceEntity:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - entities contains "space"
+    fields:
+        SpatialReference: RECOMMENDED
+SpatialReferenceNonStandard:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - not(entities.space in _StandardTemplateCoordSys)
+    fields:
+        SpatialReference: REQUIRED
+SpatialReferenceNoEntity:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - not(entities contains "space")
+    fields:
+        SpatialReference: REQUIRED
 
+# Derivatives -> Imaging data types
 ImageDerivatives:
     selectors:
-        - isDerivative
-        - isImaging
+        - dataset.DatasetType == "derivative"
+        - modality in ["mri", "pet"]
+        - extension in [".nii", ".nii.gz"]
     fields:
-        - SkullStripped: REQUIRED
-    allOf:
-        - ImageDerivativeResEntity:
-            selectors:
-                - entities contains "res"
-            fields:
-                - Resolution: REQUIRED
-        - ImageDerivativeDenEntity:
-            selectors:
-                - entities contains "den"
-            fields:
-                - Density: REQUIRED
-        - ResInSidecar
-            selectors:
-                - type(sidecars.Resolution) == "object"
-            checks:
-                - sidecar.resolution contains entities.res
-        - DenInSidecar
-            selectors:
-                - type(sidecars.density) == "object"
-            checks:
-                - sidecar.density contains entities.den
+        SkullStripped: REQUIRED
+ImageDerivativeResEntity:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - modality in ["mri", "pet"]
+        - extension in [".nii", ".nii.gz"]
+        - entities contains "res"
+    fields:
+        Resolution: REQUIRED
+ImageDerivativeDenEntity:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - modality in ["mri", "pet"]
+        - extension in [".nii", ".nii.gz"]
+        - entities contains "den"
+    fields:
+        Density: REQUIRED
+ResInSidecar:
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - modality in ["mri", "pet"]
+        - extension in ["nii", " nii.gz"]
+        - type(sidecars.Resolution) == "object"
+    checks:
+        - sidecar.resolution contains entities.res
+DenInSidecar
+    selectors:
+        - dataset.DatasetType == "derivative"
+        - modality in ["mri", "pet"]
+        - extension in [".nii", ".nii.gz"]
+        - type(sidecars.density) == "object"
+    checks:
+        - sidecar.density contains entities.den

From 4cc1c378c4ae273adb0ab1db8d822c80b92d15ca Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 14 Apr 2022 09:20:07 -0700
Subject: [PATCH 271/347] split derivative checks into own files outside
 sidecars

---
 .../rules/common_derivatives_validation.yaml  | 17 +++++
 .../rules/sidecars/common_derivative.yaml     | 62 +++++++------------
 2 files changed, 40 insertions(+), 39 deletions(-)
 create mode 100644 src/schema/rules/common_derivatives_validation.yaml

diff --git a/src/schema/rules/common_derivatives_validation.yaml b/src/schema/rules/common_derivatives_validation.yaml
new file mode 100644
index 0000000000..0a91b931e8
--- /dev/null
+++ b/src/schema/rules/common_derivatives_validation.yaml
@@ -0,0 +1,17 @@
+---
+ResInSidecar:
+    selectors:
+    - dataset.DatasetType == "derivative"
+    - modality in ["mri", "pet"]
+    - extension in ["nii", " nii.gz"]
+    - type(sidecars.Resolution) == "object"
+    checks:
+    - sidecar.resolution contains entities.res
+DenInSidecar:
+    selectors:
+    - dataset.DatasetType == "derivative"
+    - modality in ["mri", "pet"]
+    - extension in [".nii", ".nii.gz"]
+    - type(sidecars.density) == "object"
+    checks:
+    - sidecar.density contains entities.den
diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index 75091f0b29..1c69a0c937 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -1,72 +1,56 @@
 ---
 CommonDerivativeFields:
     selectors:
-        - dataset.DatasetType == "derivative"
+    - dataset.DatasetType == "derivative"
     fields:
-        - Description: RECOMMENDED
-        - Sources: OPTIONAL
-        - RawSources: OPTIONAL
+    - Description: RECOMMENDED
+    - Sources: OPTIONAL
+    - RawSources: OPTIONAL
 
 SpatialReference:
     selectors:
-        - dataset.DatasetType == "derivative"
-        # - this file can use space entity
+    - dataset.DatasetType == "derivative"
+    # - this file can use space entity
 SpatialReferenceEntity:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - entities contains "space"
+    - dataset.DatasetType == "derivative"
+    - entities contains "space"
     fields:
         SpatialReference: RECOMMENDED
 SpatialReferenceNonStandard:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - not(entities.space in _StandardTemplateCoordSys)
+    - dataset.DatasetType == "derivative"
+    - not(entities.space in _StandardTemplateCoordSys)
     fields:
         SpatialReference: REQUIRED
 SpatialReferenceNoEntity:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - not(entities contains "space")
+    - dataset.DatasetType == "derivative"
+    - not(entities contains "space")
     fields:
         SpatialReference: REQUIRED
 
 # Derivatives -> Imaging data types
 ImageDerivatives:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - modality in ["mri", "pet"]
-        - extension in [".nii", ".nii.gz"]
+    - dataset.DatasetType == "derivative"
+    - modality in ["mri", "pet"]
+    - extension in [".nii", ".nii.gz"]
     fields:
         SkullStripped: REQUIRED
 ImageDerivativeResEntity:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - modality in ["mri", "pet"]
-        - extension in [".nii", ".nii.gz"]
-        - entities contains "res"
+    - dataset.DatasetType == "derivative"
+    - modality in ["mri", "pet"]
+    - extension in [".nii", ".nii.gz"]
+    - entities contains "res"
     fields:
         Resolution: REQUIRED
 ImageDerivativeDenEntity:
     selectors:
-        - dataset.DatasetType == "derivative"
-        - modality in ["mri", "pet"]
-        - extension in [".nii", ".nii.gz"]
-        - entities contains "den"
+    - dataset.DatasetType == "derivative"
+    - modality in ["mri", "pet"]
+    - extension in [".nii", ".nii.gz"]
+    - entities contains "den"
     fields:
         Density: REQUIRED
-ResInSidecar:
-    selectors:
-        - dataset.DatasetType == "derivative"
-        - modality in ["mri", "pet"]
-        - extension in ["nii", " nii.gz"]
-        - type(sidecars.Resolution) == "object"
-    checks:
-        - sidecar.resolution contains entities.res
-DenInSidecar
-    selectors:
-        - dataset.DatasetType == "derivative"
-        - modality in ["mri", "pet"]
-        - extension in [".nii", ".nii.gz"]
-        - type(sidecars.density) == "object"
-    checks:
-        - sidecar.density contains entities.den

From acb2d92f22eb7aff2ee22f81fb3b8f9db9a3d41a Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 14 Apr 2022 09:23:06 -0700
Subject: [PATCH 272/347] remove nifti_header schemam

---
 src/schema/meta/nifti_header.yaml | 68 -------------------------------
 1 file changed, 68 deletions(-)
 delete mode 100644 src/schema/meta/nifti_header.yaml

diff --git a/src/schema/meta/nifti_header.yaml b/src/schema/meta/nifti_header.yaml
deleted file mode 100644
index b3e7fa5536..0000000000
--- a/src/schema/meta/nifti_header.yaml
+++ /dev/null
@@ -1,68 +0,0 @@
----
-nifti_header:
-    name: "NiFTI Header"
-    description: "Parsed contents of NifTI header referenced elsewhere in schema." 
-    type: object
-    properties:
-        dim_info:
-            name: "Dimension Information"
-            description:
-            type: object
-            properties:
-                freq:
-                    name: "Frequency"
-                    description: "These fields encode which spatial dimension (1,2, or 3)"
-                    type: int
-                phase:
-                    name: "Phase"
-                    description: "Corresponds to which acquisition dimension for MRI data"
-                    type: int
-                slice:
-                    name: "Slice"
-                    description: "Slice dimensions"
-                    type: int
-        dim:
-            name: "Data Dimensions"
-            description: "Data array dimensions."
-            type: array
-            minItems: 8
-            maxItems: 8
-            items:
-            type: int
-        pixdim:
-            name: "Pixel Dimension"
-            description: "Grid spacings (unit per dimension)."
-            type: array
-            minItems: 8
-            maxItems: 8
-            items:
-            type: float
-        xyzt_units:
-            name: "XYZT Units"
-            description: "Units of pixdim[1..4]"
-            xyz:
-                name: "XYZ Units"
-                description: "String representing the unit used by all 3 spatial dimensions data"
-                type: string
-            enum:
-                - "unknown"
-                - "meter"
-                - "mm"
-                - "um"
-            t:
-                name: "Time Unit"
-                description: "String representing the unit used by temporal dimension data"
-                type: string
-                enum:
-                    - "unknown"
-                    - "sec"
-                    - "msec"
-                    - "usec"
-        qform_code:
-            name: "qform code"
-            description: "Use of the quaternion fields."
-            type: int
-        sform_code:
-            name: "sform code"
-            description: "Use of the affine fields."
-            type: int

From c900deab94679b3db5793b9beef40afd63aaac84 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 14 Apr 2022 10:41:21 -0700
Subject: [PATCH 273/347] create derivatives datatypes for use in sidecar rule
 application

---
 src/schema/rules/datatypes/derivatives.yaml   | 36 +++++++++++++++++++
 .../rules/sidecars/common_derivative.yaml     | 35 ++++++++++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 src/schema/rules/datatypes/derivatives.yaml

diff --git a/src/schema/rules/datatypes/derivatives.yaml b/src/schema/rules/datatypes/derivatives.yaml
new file mode 100644
index 0000000000..a79ce0468e
--- /dev/null
+++ b/src/schema/rules/datatypes/derivatives.yaml
@@ -0,0 +1,36 @@
+---
+- name: "derivatives_common"
+  # all datatypes
+  additional_entities:
+    space: OPTIONAL
+    desc: OPTIONAL
+
+- name: "volumetric_preproc"
+  # nii, niigz in pet and mri
+  additional_entities:
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    desc: OPTIONAL
+
+- name: "mask"
+  # anat, func, dwi
+  suffixes:
+  - desg
+  extensions:
+  additional_entities:
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+- name: "discreate_segmentation"
+  # anat, func, dwi
+  suffixes:
+  - desg
+  extensions:
+  - .nii.gz
+  additional_entities:
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index 1c69a0c937..4f75b8e46b 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -11,6 +11,7 @@ SpatialReference:
     selectors:
     - dataset.DatasetType == "derivative"
     # - this file can use space entity
+    - datatype_rules_match.entities contains "space"
 SpatialReferenceEntity:
     selectors:
     - dataset.DatasetType == "derivative"
@@ -30,6 +31,38 @@ SpatialReferenceNoEntity:
     fields:
         SpatialReference: REQUIRED
 
+# this needs to come before density and resolution overrides selected in a
+# different way
+MaskDerivatives:
+    selectors:
+    - dataset.DatasetType == "derivative"
+    - datatype_rules_match.name is "mask"
+    fields:
+        RawSources: REQUIRED
+        Type: RECOMMENDED
+        Atlas: OPTIONAL 
+        Resolution: OPTIONAL
+        Density: OPTIONAL
+
+MaskDerivativesAtlas:
+    selectors:
+    - dataset.DatasetType == "derivative"
+    - datatype_rules_match.name is "mask"
+    - entities contains "label"
+    fields:
+        atlas: RECOMMENDED
+
+SegmentationCommon
+    selectors:
+    - dataset.DatasetType == "derivative"
+    # isSegmentation?
+    fields: 
+        Type: RECOMMENDED
+        Atlas: OPTIONAL 
+        Resolution: OPTIONAL
+        Density: OPTIONAL
+
+
 # Derivatives -> Imaging data types
 ImageDerivatives:
     selectors:
@@ -54,3 +87,5 @@ ImageDerivativeDenEntity:
     - entities contains "den"
     fields:
         Density: REQUIRED
+
+       

From a5ecdc87bab1164396f36625f28509f21af1b831 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 14 Apr 2022 11:10:36 -0700
Subject: [PATCH 274/347] Update
 src/schema/rules/sidecars/common_derivative.yaml

---
 src/schema/rules/sidecars/common_derivative.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index 4f75b8e46b..c219ec85e3 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -21,7 +21,7 @@ SpatialReferenceEntity:
 SpatialReferenceNonStandard:
     selectors:
     - dataset.DatasetType == "derivative"
-    - not(entities.space in _StandardTemplateCoordSys)
+    - not(entities.space in schema.objects.metadata._StandardTemplateCoordSys)
     fields:
         SpatialReference: REQUIRED
 SpatialReferenceNoEntity:

From 8f4eec7c5eebef177ee9b26ba7e06671a39bae94 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:14:05 -0400
Subject: [PATCH 275/347] Update src/schema/rules/sidecars/asl_validation.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/sidecars/asl_validation.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 4e02f30f2e..02a824e10e 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -34,7 +34,7 @@ ASLContextConsistent:
     - suffix == "asl"
     - associated contains "aslcontext"
     checks:
-    - data.shape[3] == associated["aslcontext"].shape[0]
+    - nifti_header.pixdim[4] == aslcontext.n_rows
 
 # 168
 ASLFlipAngleNiftiLength:

From c040e0942a1fe95e10631c7207f6afc4398bdf95 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:16:43 -0400
Subject: [PATCH 276/347] Switch to new context terms.

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 02a824e10e..903cc81f50 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -21,7 +21,7 @@ ASLLabelingDurationNiftiLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - data.shape[3] == sidecar.LabelingDuration.size
+    - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
 # 165
 ASLContextConsistent:
@@ -53,7 +53,7 @@ ASLFlipAngleNiftiLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - data.shape[3] == sidecar.FlipAngle.size
+    - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
 # 172
 ASLFlipAngleASLContextLength:
@@ -74,7 +74,7 @@ ASLFlipAngleASLContextLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
+    - associated["aslcontext"].n_rows == sidecar.FlipAngle.size
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -96,7 +96,7 @@ ASLPostLabelingDelayNiftiLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - data.shape[3] == sidecar.PostLabelingDelay.size
+    - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
 # 174
 ASLPostLabelingDelayASLContextLength:
@@ -119,7 +119,7 @@ ASLPostLabelingDelayASLContextLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+    - associated["aslcontext"].n_rows == sidecar.PostLabelingDelay.size
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -144,7 +144,7 @@ ASLLabelingDurationASLContextLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+    - associated["aslcontext"].n_rows == sidecar.LabelingDuration.size
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -164,7 +164,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+    - associated["aslcontext"].n_rows == sidecar.RepetitionTimePreparation.size
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -197,7 +197,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     - associated contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+    - associated["aslcontext"].n_rows == sidecar.TotalAcquiredVolumes
 
 # 196
 ASLEchoTimeASLContextLength:
@@ -213,7 +213,7 @@ ASLEchoTimeASLContextLength:
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.EchoTime.size
+    - associated["aslcontext"].n_rows == sidecar.EchoTime.size
 
 # 198
 ASLM0TypeAbsentScan:
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 2ed5401f6d..0bc0970609 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - associated["bval"].shape[0] == data.shape[3]
-    - associated["bvec"].shape[0] == data.shape[3]
+    - associated["bval"].n_rows == nifti_header.pixdim[4]
+    - associated["bvec"].n_rows == nifti_header.pixdim[4]
 
 # 30
 DWIBvalRows:

From 3b40559695dd271378827d216d05fd64587eada9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:19:18 -0400
Subject: [PATCH 277/347] More.

---
 src/schema/rules/sidecars/asl_validation.yaml | 14 +++++++-------
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 903cc81f50..6546891a41 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -74,7 +74,7 @@ ASLFlipAngleASLContextLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.FlipAngle.size
+    - aslcontext.n_rows == sidecar.FlipAngle.size
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -119,7 +119,7 @@ ASLPostLabelingDelayASLContextLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.PostLabelingDelay.size
+    - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -144,7 +144,7 @@ ASLLabelingDurationASLContextLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.LabelingDuration.size
+    - aslcontext.n_rows == sidecar.LabelingDuration.size
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -164,7 +164,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.RepetitionTimePreparation.size
+    - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -197,7 +197,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     - associated contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.TotalAcquiredVolumes
+    - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
 
 # 196
 ASLEchoTimeASLContextLength:
@@ -213,7 +213,7 @@ ASLEchoTimeASLContextLength:
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.EchoTime.size
+    - aslcontext.n_rows == sidecar.EchoTime.size
 
 # 198
 ASLM0TypeAbsentScan:
@@ -240,7 +240,7 @@ ASLM0TypeAbsentASLContext:
     selectors:
     - suffix == "asl"
     - associated contains "aslcontext"
-    - associated["aslcontext"]["volume_type"] contains "m0scan"
+    - aslcontext.volume_type contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
 
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 0bc0970609..f8b3a31140 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - associated["bval"].n_rows == nifti_header.pixdim[4]
-    - associated["bvec"].n_rows == nifti_header.pixdim[4]
+    - bval.n_rows == nifti_header.pixdim[4]
+    - bvec.n_rows == nifti_header.pixdim[4]
 
 # 30
 DWIBvalRows:

From b3dbb443fc84f8f963d5e2cd6934e7b7731c562c Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:21:15 -0400
Subject: [PATCH 278/347] [SCHEMA] Add datatypes field to datatype rule files
 (#1012)

* Add datatypes field to datatype rule files.

* Update src/schema/rules/datatypes/meg.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/datatypes/anat.yaml | 18 ++++++++++++++++++
 src/schema/rules/datatypes/beh.yaml  |  4 ++++
 src/schema/rules/datatypes/dwi.yaml  |  6 ++++++
 src/schema/rules/datatypes/eeg.yaml  | 14 ++++++++++++++
 src/schema/rules/datatypes/fmap.yaml | 14 ++++++++++++++
 src/schema/rules/datatypes/func.yaml |  8 ++++++++
 src/schema/rules/datatypes/ieeg.yaml | 12 ++++++++++++
 src/schema/rules/datatypes/meg.yaml  | 20 ++++++++++++++++++++
 src/schema/rules/datatypes/micr.yaml |  4 ++++
 src/schema/rules/datatypes/perf.yaml |  8 ++++++++
 src/schema/rules/datatypes/pet.yaml  |  8 ++++++++
 11 files changed, 116 insertions(+)

diff --git a/src/schema/rules/datatypes/anat.yaml b/src/schema/rules/datatypes/anat.yaml
index b1a470c2ef..04cd0539bc 100644
--- a/src/schema/rules/datatypes/anat.yaml
+++ b/src/schema/rules/datatypes/anat.yaml
@@ -17,6 +17,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -49,6 +51,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -64,6 +68,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -81,6 +87,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -98,6 +106,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -116,6 +126,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -133,6 +145,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -153,6 +167,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
@@ -172,6 +188,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - anat
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/beh.yaml b/src/schema/rules/datatypes/beh.yaml
index 59358b59ba..539f50d095 100644
--- a/src/schema/rules/datatypes/beh.yaml
+++ b/src/schema/rules/datatypes/beh.yaml
@@ -6,6 +6,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - beh
   entities:
     subject: required
     session: optional
@@ -21,6 +23,8 @@
   extensions:
   - .tsv
   - .json
+  datatypes:
+  - beh
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/dwi.yaml b/src/schema/rules/datatypes/dwi.yaml
index dfb178760b..2df4d8cc08 100644
--- a/src/schema/rules/datatypes/dwi.yaml
+++ b/src/schema/rules/datatypes/dwi.yaml
@@ -8,6 +8,8 @@
   - .json
   - .bvec
   - .bval
+  datatypes:
+  - dwi
   entities:
     subject: required
     session: optional
@@ -23,6 +25,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - dwi
   entities:
     subject: required
     session: optional
@@ -38,6 +42,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - dwi
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/eeg.yaml b/src/schema/rules/datatypes/eeg.yaml
index 6b112e343d..112470d0b8 100644
--- a/src/schema/rules/datatypes/eeg.yaml
+++ b/src/schema/rules/datatypes/eeg.yaml
@@ -10,6 +10,8 @@
   - .set
   - .fdt
   - .bdf
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -22,6 +24,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -33,6 +37,8 @@
   - coordsystem
   extensions:
   - .json
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -44,6 +50,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -55,6 +63,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -66,6 +76,8 @@
   - photo
   extensions:
   - .jpg
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
@@ -78,6 +90,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - eeg
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/fmap.yaml b/src/schema/rules/datatypes/fmap.yaml
index 2c445196d6..f5c44c6e1e 100644
--- a/src/schema/rules/datatypes/fmap.yaml
+++ b/src/schema/rules/datatypes/fmap.yaml
@@ -12,6 +12,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -26,6 +28,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -41,6 +45,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -59,6 +65,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -81,6 +89,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -100,6 +110,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
@@ -120,6 +132,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - fmap
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/func.yaml b/src/schema/rules/datatypes/func.yaml
index 1fbdca7b53..a8e9269bc0 100644
--- a/src/schema/rules/datatypes/func.yaml
+++ b/src/schema/rules/datatypes/func.yaml
@@ -8,6 +8,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - func
   entities:
     subject: required
     session: optional
@@ -27,6 +29,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - func
   entities:
     subject: required
     session: optional
@@ -44,6 +48,8 @@
   extensions:
   - .tsv
   - .json
+  datatypes:
+  - func
   entities:
     subject: required
     session: optional
@@ -61,6 +67,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - func
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/ieeg.yaml b/src/schema/rules/datatypes/ieeg.yaml
index 37c02963f5..44c0ea4630 100644
--- a/src/schema/rules/datatypes/ieeg.yaml
+++ b/src/schema/rules/datatypes/ieeg.yaml
@@ -11,6 +11,8 @@
   - .set
   - .fdt
   - .nwb
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
@@ -23,6 +25,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
@@ -34,6 +38,8 @@
   - coordsystem
   extensions:
   - .json
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
@@ -45,6 +51,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
@@ -56,6 +64,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
@@ -79,6 +89,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - ieeg
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/meg.yaml b/src/schema/rules/datatypes/meg.yaml
index 6231204d51..1377a7dc70 100644
--- a/src/schema/rules/datatypes/meg.yaml
+++ b/src/schema/rules/datatypes/meg.yaml
@@ -17,6 +17,8 @@
   - .mhd
   - .trg
   - .chn
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -32,6 +34,8 @@
   - meg
   extensions:
   - .dat
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -47,6 +51,8 @@
   - meg
   extensions:
   - .fif
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -62,6 +68,8 @@
   extensions:
   - .*
   - .pos
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -73,6 +81,8 @@
   extensions:
   - .sqd
   - .mrk
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -85,6 +95,8 @@
   - coordsystem
   extensions:
   - .json
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -96,6 +108,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -110,6 +124,8 @@
   extensions:
   - .json
   - .tsv
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -122,6 +138,8 @@
   - photo
   extensions:
   - .jpg
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
@@ -134,6 +152,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - meg
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/micr.yaml b/src/schema/rules/datatypes/micr.yaml
index 3af2fb86d3..25911888c4 100644
--- a/src/schema/rules/datatypes/micr.yaml
+++ b/src/schema/rules/datatypes/micr.yaml
@@ -24,6 +24,8 @@
   - .png
   - .tif
   - .json
+  datatypes:
+  - micr
   entities:
     subject: required
     session: optional
@@ -39,6 +41,8 @@
   - .jpg
   - .png
   - .tif
+  datatypes:
+  - micr
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/perf.yaml b/src/schema/rules/datatypes/perf.yaml
index 14b4ffe407..7872378cd1 100644
--- a/src/schema/rules/datatypes/perf.yaml
+++ b/src/schema/rules/datatypes/perf.yaml
@@ -7,6 +7,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - perf
   entities:
     subject: required
     session: optional
@@ -21,6 +23,8 @@
   extensions:
   - .tsv
   - .json
+  datatypes:
+  - perf
   entities:
     subject: required
     session: optional
@@ -34,6 +38,8 @@
   - asllabeling
   extensions:
   - .jpg
+  datatypes:
+  - perf
   entities:
     subject: required
     session: optional
@@ -48,6 +54,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - perf
   entities:
     subject: required
     session: optional
diff --git a/src/schema/rules/datatypes/pet.yaml b/src/schema/rules/datatypes/pet.yaml
index 33f1a9f3e3..38508aa94b 100644
--- a/src/schema/rules/datatypes/pet.yaml
+++ b/src/schema/rules/datatypes/pet.yaml
@@ -6,6 +6,8 @@
   - .nii.gz
   - .nii
   - .json
+  datatypes:
+  - pet
   entities:
     subject: required
     session: optional
@@ -20,6 +22,8 @@
   extensions:
   - .tsv
   - .json
+  datatypes:
+  - pet
   entities:
     subject: required
     session: optional
@@ -35,6 +39,8 @@
   extensions:
   - .tsv
   - .json
+  datatypes:
+  - pet
   entities:
     subject: required
     session: optional
@@ -50,6 +56,8 @@
   extensions:
   - .tsv.gz
   - .json
+  datatypes:
+  - pet
   entities:
     subject: required
     session: optional

From 6530002fcfab843e89092331bf18713c8ca5d9f2 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:21:29 -0400
Subject: [PATCH 279/347] Use YAML schema types.

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 6546891a41..9a629e9028 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,7 +19,7 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - type(sidecar.LabelingDuration) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
@@ -51,7 +51,7 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
+    - type(sidecar.FlipAngle) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
@@ -72,7 +72,7 @@ ASLFlipAngleASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
+    - type(sidecar.FlipAngle) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.FlipAngle.size
 
@@ -94,7 +94,7 @@ ASLPostLabelingDelayNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
+    - type(sidecar.PostLabelingDelay) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
@@ -117,7 +117,7 @@ ASLPostLabelingDelayASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
+    - type(sidecar.PostLabelingDelay) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
@@ -142,7 +142,7 @@ ASLLabelingDurationASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - type(sidecar.LabelingDuration) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.LabelingDuration.size
 
@@ -162,7 +162,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "array"
+    - type(sidecar.RepetitionTimePreparation) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
@@ -179,7 +179,7 @@ ASLBackgroundSuppressionNumberPulses:
     - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
-    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "seq"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -211,7 +211,7 @@ ASLEchoTimeASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "EchoTime"
-    - type(sidecar.EchoTime) == "array"
+    - type(sidecar.EchoTime) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.EchoTime.size
 

From 14f389e88524d094f69d7b2ea824e9bedcb110b2 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 14 Apr 2022 16:19:05 -0400
Subject: [PATCH 280/347] Update mri.yaml

removed ::
---
 src/schema/rules/sidecars/mri.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index c58f4ad3cd..67bec335f5 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -119,7 +119,7 @@ MRISpatialEncoding:
                 This parameter is REQUIRED if corresponding fieldmap data is present
                 or when using multiple runs with different phase encoding directions
                 (which can be later used for field inhomogeneity correction).
-            issue::
+            issue:
                 name: PHASE_ENCODING_DIRECTION_MUST_DEFINE
                 issue: |
                     You have to define 'PhaseEncodingDirection' for this file.

From 900194517a18e4c03f50d8dabe10cc3f805ebcac Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 14 Apr 2022 16:20:06 -0400
Subject: [PATCH 281/347] Update func.yaml

removed ::
---
 src/schema/rules/sidecars/func.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 2371b70f6b..43bd5f286f 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -37,7 +37,7 @@ MRIFuncTimingParameters:
                 REQUIRED for sequences that are described with the `VolumeTiming`
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
-            issue::
+            issue:
                 name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
                 message: |
                     The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.

From c054ae550c95321a9b406a01172d604b48a4b76f Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 14 Apr 2022 16:20:44 -0400
Subject: [PATCH 282/347] Update asl.yaml

---
 src/schema/rules/sidecars/asl.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 358d9c5f3d..3ab54df391 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -33,7 +33,7 @@ MRIASLTextOnlySliceTiming:
     fields:
         SliceTiming:
             level: REQUIRED
-            issue::
+            issue:
                 name: SLICE_TIMING_NOT_DEFINED_2D_ASL
                 message: |
                     "You should define SliceTiming', in case 'SequenceType' is set to a

From f04b47ff5e90373dd6574f4dff27c84dda0941f4 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 12:27:35 -0700
Subject: [PATCH 283/347] SCHEMA: Convert datatype lists to objects

---
 src/schema/rules/datatypes/anat.yaml | 36 +++++++++++------------
 src/schema/rules/datatypes/beh.yaml  |  7 +++--
 src/schema/rules/datatypes/dwi.yaml  | 12 ++++----
 src/schema/rules/datatypes/eeg.yaml  | 22 ++++++++------
 src/schema/rules/datatypes/fmap.yaml | 28 +++++++++---------
 src/schema/rules/datatypes/func.yaml | 16 +++++------
 src/schema/rules/datatypes/ieeg.yaml | 22 ++++++++------
 src/schema/rules/datatypes/meg.yaml  | 43 +++++++++++++---------------
 src/schema/rules/datatypes/micr.yaml |  7 +++--
 src/schema/rules/datatypes/perf.yaml | 16 +++++------
 src/schema/rules/datatypes/pet.yaml  | 16 +++++------
 11 files changed, 118 insertions(+), 107 deletions(-)

diff --git a/src/schema/rules/datatypes/anat.yaml b/src/schema/rules/datatypes/anat.yaml
index 04cd0539bc..7e0f04d6c3 100644
--- a/src/schema/rules/datatypes/anat.yaml
+++ b/src/schema/rules/datatypes/anat.yaml
@@ -1,6 +1,6 @@
 ---
-# Nonparametric
-- suffixes:
+nonparametric:
+  suffixes:
   - T1w
   - T2w
   - PDw
@@ -28,8 +28,8 @@
     reconstruction: optional
     part: optional
 
-# Parametric
-- suffixes:
+parametric:
+  suffixes:
   - T1map
   - T2map
   - T2starmap
@@ -61,8 +61,8 @@
     ceagent: optional
     reconstruction: optional
 
-# Defacemask
-- suffixes:
+defacemask:
+  suffixes:
   - defacemask
   extensions:
   - .nii.gz
@@ -79,8 +79,8 @@
     reconstruction: optional
     modality: optional
 
-# Multi-echo
-- suffixes:
+multiecho:
+  suffixes:
   - MESE
   - MEGRE
   extensions:
@@ -99,8 +99,8 @@
     echo: required
     part: optional
 
-# Multi-flip
-- suffixes:
+multiflip:
+  suffixes:
   - VFA
   extensions:
   - .nii.gz
@@ -119,8 +119,8 @@
     flip: required
     part: optional
 
-# Multi-inv
-- suffixes:
+multiinversion:
+  suffixes:
   - IRT1
   extensions:
   - .nii.gz
@@ -138,8 +138,8 @@
     inversion: required
     part: optional
 
-# MP2RAGE
-- suffixes:
+mp2rage:
+  suffixes:
   - MP2RAGE
   extensions:
   - .nii.gz
@@ -159,8 +159,8 @@
     inversion: required
     part: optional
 
-# VFA+MT
-- suffixes:
+vfamt:
+  suffixes:
   - MPM
   - MTS
   extensions:
@@ -181,8 +181,8 @@
     mtransfer: required
     part: optional
 
-# MTR
-- suffixes:
+mtr:
+  suffixes:
   - MTR
   extensions:
   - .nii.gz
diff --git a/src/schema/rules/datatypes/beh.yaml b/src/schema/rules/datatypes/beh.yaml
index 539f50d095..1f3111799c 100644
--- a/src/schema/rules/datatypes/beh.yaml
+++ b/src/schema/rules/datatypes/beh.yaml
@@ -1,6 +1,6 @@
 ---
-# Continuous data
-- suffixes:
+timeseries:
+  suffixes:
   - stim
   - physio
   extensions:
@@ -17,7 +17,8 @@
     recording: optional
 
 # Non-continuous data
-- suffixes:
+noncontinuous:
+  suffixes:
   - events
   - beh
   extensions:
diff --git a/src/schema/rules/datatypes/dwi.yaml b/src/schema/rules/datatypes/dwi.yaml
index 2df4d8cc08..3853ee703c 100644
--- a/src/schema/rules/datatypes/dwi.yaml
+++ b/src/schema/rules/datatypes/dwi.yaml
@@ -1,6 +1,6 @@
 ---
-# DWI
-- suffixes:
+dwi:
+  suffixes:
   - dwi
   extensions:
   - .nii.gz
@@ -18,8 +18,8 @@
     run: optional
     part: optional
 
-# Single-band reference images
-- suffixes:
+sbref:
+  suffixes:
   - sbref
   extensions:
   - .nii.gz
@@ -35,8 +35,8 @@
     run: optional
     part: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/eeg.yaml b/src/schema/rules/datatypes/eeg.yaml
index 112470d0b8..7516cc2ff1 100644
--- a/src/schema/rules/datatypes/eeg.yaml
+++ b/src/schema/rules/datatypes/eeg.yaml
@@ -1,5 +1,6 @@
 ---
-- suffixes:
+eeg:
+  suffixes:
   - eeg
   extensions:
   - .json
@@ -19,7 +20,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+channels:
+  suffixes:
   - channels
   extensions:
   - .json
@@ -33,7 +35,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+coordsystem:
+  suffixes:
   - coordsystem
   extensions:
   - .json
@@ -45,7 +48,8 @@
     acquisition: optional
     space: optional
 
-- suffixes:
+electrodes:
+  suffixes:
   - electrodes
   extensions:
   - .json
@@ -58,7 +62,8 @@
     acquisition: optional
     space: optional
 
-- suffixes:
+events:
+  suffixes:
   - events
   extensions:
   - .json
@@ -72,7 +77,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+photo:
+  suffixes:
   - photo
   extensions:
   - .jpg
@@ -83,8 +89,8 @@
     session: optional
     acquisition: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/fmap.yaml b/src/schema/rules/datatypes/fmap.yaml
index f5c44c6e1e..cda02c410a 100644
--- a/src/schema/rules/datatypes/fmap.yaml
+++ b/src/schema/rules/datatypes/fmap.yaml
@@ -1,6 +1,6 @@
 ---
-# Fieldmaps
-- suffixes:
+fieldmaps:
+  suffixes:
   - phasediff
   - phase1
   - phase2
@@ -20,8 +20,8 @@
     acquisition: optional
     run: optional
 
-# PEPolar
-- suffixes:
+pepolar:
+  suffixes:
   - epi
   - m0scan
   extensions:
@@ -38,8 +38,8 @@
     direction: required
     run: optional
 
-# TB1DAM
-- suffixes:
+TB1DAM:
+  suffixes:
   - TB1DAM
   extensions:
   - .nii.gz
@@ -58,8 +58,8 @@
     inversion: optional
     part: optional
 
-# TB1EPI
-- suffixes:
+TB1EPI:
+  suffixes:
   - TB1EPI
   extensions:
   - .nii.gz
@@ -79,8 +79,8 @@
     inversion: optional
     part: optional
 
-# RFFieldMaps
-- suffixes:
+RFFieldMaps:
+  suffixes:
   - TB1AFI
   - TB1TFL
   - TB1RFM
@@ -103,8 +103,8 @@
     inversion: optional
     part: optional
 
-# TB1SRGE
-- suffixes:
+TB1SRGE:
+  suffixes:
   - TB1SRGE
   extensions:
   - .nii.gz
@@ -124,8 +124,8 @@
     inversion: required
     part: optional
 
-# Parametric
-- suffixes:
+parametric:
+  suffixes:
   - TB1map
   - RB1map
   extensions:
diff --git a/src/schema/rules/datatypes/func.yaml b/src/schema/rules/datatypes/func.yaml
index a8e9269bc0..77c3b3acc8 100644
--- a/src/schema/rules/datatypes/func.yaml
+++ b/src/schema/rules/datatypes/func.yaml
@@ -1,6 +1,6 @@
 ---
-# Func
-- suffixes:
+func:
+  suffixes:
   - bold
   - cbv
   - sbref
@@ -22,8 +22,8 @@
     echo: optional
     part: optional
 
-# Phase (deprecated)
-- suffixes:
+phase:
+  suffixes:
   - phase  # deprecated
   extensions:
   - .nii.gz
@@ -42,8 +42,8 @@
     run: optional
     echo: optional
 
-# Events
-- suffixes:
+events:
+  suffixes:
   - events
   extensions:
   - .tsv
@@ -60,8 +60,8 @@
     direction: optional
     run: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/ieeg.yaml b/src/schema/rules/datatypes/ieeg.yaml
index 44c0ea4630..8cb687a1f1 100644
--- a/src/schema/rules/datatypes/ieeg.yaml
+++ b/src/schema/rules/datatypes/ieeg.yaml
@@ -1,5 +1,6 @@
 ---
-- suffixes:
+ieeg:
+  suffixes:
   - ieeg
   extensions:
   - .mefd/
@@ -20,7 +21,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+channels:
+  suffixes:
   - channels
   extensions:
   - .json
@@ -34,7 +36,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+coordsystem:
+  suffixes:
   - coordsystem
   extensions:
   - .json
@@ -46,7 +49,8 @@
     acquisition: optional
     space: optional
 
-- suffixes:
+electrodes:
+  suffixes:
   - electrodes
   extensions:
   - .json
@@ -59,7 +63,8 @@
     acquisition: optional
     space: optional
 
-- suffixes:
+events:
+  suffixes:
   - events
   extensions:
   - .json
@@ -73,7 +78,8 @@
     acquisition: optional
     run: optional
 
-- suffixes:
+photo:
+  suffixes:
   - photo
   extensions:
   - .jpg
@@ -82,8 +88,8 @@
     session: optional
     acquisition: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/meg.yaml b/src/schema/rules/datatypes/meg.yaml
index 1377a7dc70..596af66c62 100644
--- a/src/schema/rules/datatypes/meg.yaml
+++ b/src/schema/rules/datatypes/meg.yaml
@@ -1,7 +1,6 @@
 ---
-# MEG data files
-# First group
-- suffixes:
+meg:
+  suffixes:
   - meg
   extensions:
   - /  # corresponds to BTi/4D data
@@ -28,9 +27,8 @@
     processing: optional
     split: optional
 
-# Second group
-# Specifically, it's dat files with "acq-calibration"
-- suffixes:
+calibration:
+  suffixes:
   - meg
   extensions:
   - .dat
@@ -45,9 +43,8 @@
       enum:
       - calibration
 
-# Third group
-# fif files with "acq-crosstalk"
-- suffixes:
+crosstalk:
+  suffixes:
   - meg
   extensions:
   - .fif
@@ -62,8 +59,8 @@
       enum:
       - crosstalk
 
-# Headshape files
-- suffixes:
+headshape:
+  suffixes:
   - headshape
   extensions:
   - .*
@@ -75,8 +72,8 @@
     session: optional
     acquisition: optional
 
-# Marker files
-- suffixes:
+markers:
+  suffixes:
   - markers
   extensions:
   - .sqd
@@ -90,8 +87,8 @@
     acquisition: optional
     space: optional
 
-# Coordinate systems
-- suffixes:
+coordsystem:
+  suffixes:
   - coordsystem
   extensions:
   - .json
@@ -102,8 +99,8 @@
     session: optional
     acquisition: optional
 
-# Channel files
-- suffixes:
+channels:
+  suffixes:
   - channels
   extensions:
   - .json
@@ -118,8 +115,8 @@
     run: optional
     processing: optional
 
-# Events files
-- suffixes:
+events:
+  suffixes:
   - events
   extensions:
   - .json
@@ -133,8 +130,8 @@
     acquisition: optional
     run: optional
 
-# Head photos
-- suffixes:
+photo:
+  suffixes:
   - photo
   extensions:
   - .jpg
@@ -145,8 +142,8 @@
     session: optional
     acquisition: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/micr.yaml b/src/schema/rules/datatypes/micr.yaml
index 25911888c4..b5caf97b21 100644
--- a/src/schema/rules/datatypes/micr.yaml
+++ b/src/schema/rules/datatypes/micr.yaml
@@ -1,6 +1,6 @@
 ---
-# Microscopy
-- suffixes:
+microscopy:
+  suffixes:
   - TEM
   - SEM
   - uCT
@@ -35,7 +35,8 @@
     run: optional
     chunk: optional
 
-- suffixes:
+photo:
+  suffixes:
   - photo
   extensions:
   - .jpg
diff --git a/src/schema/rules/datatypes/perf.yaml b/src/schema/rules/datatypes/perf.yaml
index 7872378cd1..ef97ffb549 100644
--- a/src/schema/rules/datatypes/perf.yaml
+++ b/src/schema/rules/datatypes/perf.yaml
@@ -1,6 +1,6 @@
 ---
-# First group
-- suffixes:
+asl:
+  suffixes:
   - asl
   - m0scan
   extensions:
@@ -17,8 +17,8 @@
     direction: optional
     run: optional
 
-# Second group
-- suffixes:
+aslcontext:
+  suffixes:
   - aslcontext
   extensions:
   - .tsv
@@ -33,8 +33,8 @@
     direction: optional
     run: optional
 
-# Third group
-- suffixes:
+asllabeling:
+  suffixes:
   - asllabeling
   extensions:
   - .jpg
@@ -47,8 +47,8 @@
     reconstruction: optional
     run: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:
diff --git a/src/schema/rules/datatypes/pet.yaml b/src/schema/rules/datatypes/pet.yaml
index 38508aa94b..36d8cd3ced 100644
--- a/src/schema/rules/datatypes/pet.yaml
+++ b/src/schema/rules/datatypes/pet.yaml
@@ -1,6 +1,6 @@
 ---
-# PET recordings
-- suffixes:
+pet:
+  suffixes:
   - pet
   extensions:
   - .nii.gz
@@ -16,8 +16,8 @@
     reconstruction: optional
     run: optional
 
-# Blood recordings
-- suffixes:
+blood:
+  suffixes:
   - blood
   extensions:
   - .tsv
@@ -33,8 +33,8 @@
     run: optional
     recording: required
 
-# Events
-- suffixes:
+events:
+  suffixes:
   - events
   extensions:
   - .tsv
@@ -49,8 +49,8 @@
     reconstruction: optional
     run: optional
 
-# Timeseries
-- suffixes:
+timeseries:
+  suffixes:
   - physio
   - stim
   extensions:

From 24c0aa443143394d8608953acc13a8de1424e16c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 12:55:49 -0700
Subject: [PATCH 284/347] SCHEMACODE: Update loop logic to use dict instead of
 list

---
 tools/schemacode/schemacode/render.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index c1b8872142..3ccc3b4854 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -188,7 +188,7 @@ def make_filename_template(schema, n_dupes_to_combine=6, **kwargs):
         paragraph += "\t\t{}/\n".format(datatype)
 
         # Unique filename patterns
-        for group in schema["rules"]["datatypes"][datatype]:
+        for group in schema["rules"]["datatypes"][datatype].values():
             string = "\t\t\t"
             for ent in entity_order:
                 if "enum" in schema["objects"]["entities"][ent].keys():
@@ -302,7 +302,7 @@ def make_entity_table(schema, tablefmt="github", **kwargs):
         duplicate_row_counter = 0
 
         # each dtype could have multiple specs
-        for i_dtype_spec, dtype_spec in enumerate(dtype_specs):
+        for dtype_spec in dtype_specs.values():
             suffixes = dtype_spec.get("suffixes")
 
             # Skip this part of the schema if no suffixes are found.

From 6a32925e6a8d60f1d89a537cdac8ca41e0d051b5 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 14 Apr 2022 18:07:34 -0400
Subject: [PATCH 285/347] Hostile takeover

---
 .../rules/common_derivatives_validation.yaml  | 13 ++++++------
 .../rules/sidecars/common_derivative.yaml     | 21 +++++++------------
 2 files changed, 15 insertions(+), 19 deletions(-)

diff --git a/src/schema/rules/common_derivatives_validation.yaml b/src/schema/rules/common_derivatives_validation.yaml
index 0a91b931e8..8991a240ec 100644
--- a/src/schema/rules/common_derivatives_validation.yaml
+++ b/src/schema/rules/common_derivatives_validation.yaml
@@ -1,17 +1,18 @@
 ---
 ResInSidecar:
     selectors:
-    - dataset.DatasetType == "derivative"
+    - dataset.dataset_description.DatasetType == "derivative"
     - modality in ["mri", "pet"]
     - extension in ["nii", " nii.gz"]
-    - type(sidecars.Resolution) == "object"
+    - type(sidecar.Resolution) == "object"
     checks:
-    - sidecar.resolution contains entities.res
+    - sidecar.Resolution contains entities.resolution
+
 DenInSidecar:
     selectors:
-    - dataset.DatasetType == "derivative"
+    - dataset.dataset_description.DatasetType == "derivative"
     - modality in ["mri", "pet"]
     - extension in [".nii", ".nii.gz"]
-    - type(sidecars.density) == "object"
+    - type(sidecar.Density) == "object"
     checks:
-    - sidecar.density contains entities.den
+    - sidecar.Density contains entities.density
diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index c219ec85e3..503662ad2c 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -7,23 +7,20 @@ CommonDerivativeFields:
     - Sources: OPTIONAL
     - RawSources: OPTIONAL
 
-SpatialReference:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    # - this file can use space entity
-    - datatype_rules_match.entities contains "space"
 SpatialReferenceEntity:
     selectors:
     - dataset.DatasetType == "derivative"
     - entities contains "space"
     fields:
         SpatialReference: RECOMMENDED
+
 SpatialReferenceNonStandard:
     selectors:
     - dataset.DatasetType == "derivative"
     - not(entities.space in schema.objects.metadata._StandardTemplateCoordSys)
     fields:
         SpatialReference: REQUIRED
+
 SpatialReferenceNoEntity:
     selectors:
     - dataset.DatasetType == "derivative"
@@ -36,7 +33,7 @@ SpatialReferenceNoEntity:
 MaskDerivatives:
     selectors:
     - dataset.DatasetType == "derivative"
-    - datatype_rules_match.name is "mask"
+    - suffix == "mask"
     fields:
         RawSources: REQUIRED
         Type: RECOMMENDED
@@ -47,22 +44,21 @@ MaskDerivatives:
 MaskDerivativesAtlas:
     selectors:
     - dataset.DatasetType == "derivative"
-    - datatype_rules_match.name is "mask"
+    - suffix == "mask"
     - entities contains "label"
     fields:
         atlas: RECOMMENDED
 
-SegmentationCommon
+SegmentationCommon:
     selectors:
     - dataset.DatasetType == "derivative"
-    # isSegmentation?
+    - suffix in ["dseg", "probseg"]
     fields: 
         Type: RECOMMENDED
         Atlas: OPTIONAL 
         Resolution: OPTIONAL
         Density: OPTIONAL
 
-
 # Derivatives -> Imaging data types
 ImageDerivatives:
     selectors:
@@ -71,21 +67,20 @@ ImageDerivatives:
     - extension in [".nii", ".nii.gz"]
     fields:
         SkullStripped: REQUIRED
+
 ImageDerivativeResEntity:
     selectors:
     - dataset.DatasetType == "derivative"
     - modality in ["mri", "pet"]
-    - extension in [".nii", ".nii.gz"]
     - entities contains "res"
     fields:
         Resolution: REQUIRED
+
 ImageDerivativeDenEntity:
     selectors:
     - dataset.DatasetType == "derivative"
     - modality in ["mri", "pet"]
-    - extension in [".nii", ".nii.gz"]
     - entities contains "den"
     fields:
         Density: REQUIRED
 
-       

From 5a191a87e5545a70142078dd3340e71476fa5a98 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Fri, 15 Apr 2022 13:36:04 +0000
Subject: [PATCH 286/347] [DOC] Auto-generate changelog entry for PR #1049

---
 src/CHANGES.md | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index bffffb8630..12d2f9b7f5 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,12 +2,26 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[DOC] Preface each macro call with comment [#1052](https://github.com/bids-standard/bids-specification/pull/1052) ([Remi-Gau](https://github.com/Remi-Gau))
+-   ENH: allow for .png and .tif in eeg/ieeg/meg as allowed for micr [#1049](https://github.com/bids-standard/bids-specification/pull/1049) ([yarikoptic](https://github.com/yarikoptic))
+-   \[SCHEMA] Add a new `file\_relative` format [#1046](https://github.com/bids-standard/bids-specification/pull/1046) ([tsalo](https://github.com/tsalo))
+-   \[FIX] typo in "rawdata" example [#1045](https://github.com/bids-standard/bids-specification/pull/1045) ([sappelhoff](https://github.com/sappelhoff))
+-   \[MISC] consistently use "directory" instead of "folder" as a term [#1044](https://github.com/bids-standard/bids-specification/pull/1044) ([sappelhoff](https://github.com/sappelhoff))
+-   \[MISC] Update CODEOWNERS [#1040](https://github.com/bids-standard/bids-specification/pull/1040) ([erdalkaraca](https://github.com/erdalkaraca))
+-   \[SCHEMA] Add extensions to schema [#1036](https://github.com/bids-standard/bids-specification/pull/1036) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Allow README file extensions. [#1033](https://github.com/bids-standard/bids-specification/pull/1033) ([mateuszpawlik](https://github.com/mateuszpawlik))
+-   \[MISC] Rewrite and update html build instructions [#1032](https://github.com/bids-standard/bids-specification/pull/1032) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Add coordsystem-specific definition of DigitizedHeadPoints [#1023](https://github.com/bids-standard/bids-specification/pull/1023) ([tsalo](https://github.com/tsalo))
+-   \[FIX] PET Spec; added known DICOM tags, fixed tag error, updated citation, clarified scale factor. [#1021](https://github.com/bids-standard/bids-specification/pull/1021) ([bendhouseart](https://github.com/bendhouseart))
 -   \[MISC] clarify copyright for logo [#1019](https://github.com/bids-standard/bids-specification/pull/1019) ([sappelhoff](https://github.com/sappelhoff))
 -   \[SCHEMA] Tests for render listings [#1018](https://github.com/bids-standard/bids-specification/pull/1018) ([TheChymera](https://github.com/TheChymera))
+-   \[INFRA] introduce versioning of the schema itself [#1013](https://github.com/bids-standard/bids-specification/pull/1013) ([yarikoptic](https://github.com/yarikoptic))
 -   \[SCHEMA] Tabular metadata rules for both top and second-level tabular files [#1006](https://github.com/bids-standard/bids-specification/pull/1006) ([TheChymera](https://github.com/TheChymera))
+-   \[FIX] Change recording entity to REQUIRED for pet/blood modality [#1005](https://github.com/bids-standard/bids-specification/pull/1005) ([ghisvail](https://github.com/ghisvail))
 -   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
 -   \[DOC] add documentation for macros [#963](https://github.com/bids-standard/bids-specification/pull/963) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[SCHEMA] Add patterns for format validation [#885](https://github.com/bids-standard/bids-specification/pull/885) ([tsalo](https://github.com/tsalo))
+-   \[FIX] run entity - "scans" -> "data acquisitions" [#760](https://github.com/bids-standard/bids-specification/pull/760) ([yarikoptic](https://github.com/yarikoptic))
 
 ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
 
@@ -302,7 +316,7 @@
 -   \[FIX] Clarify channels.tsv is RECOMMENDED consistently across ephys [#347](https://github.com/bids-standard/bids-specification/pull/347) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase))
 -   \[MISC] rm TOC.md - seems no longer pertinent/used [#341](https://github.com/bids-standard/bids-specification/pull/341) ([yarikoptic](https://github.com/yarikoptic))
--   \[MISC] Move the PR template to a separate directory and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta))
+-   \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta))
 -   \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Clarify phenotypic and assessment data in new section [#331](https://github.com/bids-standard/bids-specification/pull/331) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] add information about continuous integration checks to PR template [#330](https://github.com/bids-standard/bids-specification/pull/330) ([sappelhoff](https://github.com/sappelhoff))

From 0dbfaa0028e3e4c3b79e65eb901f69aa7862349d Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 06:41:03 -0700
Subject: [PATCH 287/347] Quiet latin check, clean up some message text

---
 src/schema/rules/sidecars/asl.yaml | 34 ++++++++++++++++--------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 3ab54df391..81c10c6846 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -36,8 +36,8 @@ MRIASLTextOnlySliceTiming:
             issue:
                 name: SLICE_TIMING_NOT_DEFINED_2D_ASL
                 message: |
-                    "You should define SliceTiming', in case 'SequenceType' is set to a
-                    2D sequence. 'SliceTiming' is the time at which each slice was
+                    You should define `SliceTiming` for this file, because `SequenceType` is sets
+                    to a 2D sequence. `SliceTiming` is the time at which each slice was
                     acquired within each volume (frame) of the acquisition. Slice timing
                     is not slice order -- rather, it is a list of times containing the
                     time (in seconds) of each slice acquisition in relation to the beginning
@@ -48,7 +48,7 @@ MRIASLTextOnlySliceTiming:
                     `SliceEncodingDirection` is negative, the entries in `SliceTiming` are
                     defined in reverse order with respect to the slice axis, such that the
                     final entry in the `SliceTiming` list is the time of acquisition of slice 0.
-                    Without this parameter slice time correction will not be possible."
+                    Without this parameter slice time correction will not be possible.
 
 MRIASLTextOnlyFlipAngle:
     selectors:
@@ -62,8 +62,8 @@ MRIASLTextOnlyFlipAngle:
             issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
-                    "You should define 'FlipAngle' for this file, in case of a
-                    LookLocker acquisition. 'FlipAngle' is the flip angle (FA)
+                    You should define `FlipAngle` for this file, in case of a
+                    LookLocker acquisition. `FlipAngle` is the flip angle (FA)
                     for the acquisition, specified in degrees. Corresponds to
                     DICOM Tag 0018, 1314 `Flip Angle`. The data type number may
                     apply to files from any MRI modality concerned with a single
@@ -72,7 +72,7 @@ MRIASLTextOnlyFlipAngle:
                     The data type array provides a value for each volume in a 4D
                     dataset and should only be used when the volume timing is critical
                     for interpretation of the data, such as in ASL or variable flip
-                    angle fMRI sequences."
+                    angle fMRI sequences.
 
 # Common metadata fields applicable to both (P)CASL and PASL
 MRIASLCommonMetadataFields:
@@ -118,9 +118,10 @@ MRIASLCommonMetadataFieldsM0Type:
             issue:
                 name: M0ESTIMATE_NOT_DEFINED
                 message: |
-                    You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'.
-                    'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood),
-                    only if obtained externally (for example retrieved from CSF in a separate measurement).
+                    You must define `M0Estimate` for this file, because `M0Type` is set to
+                    'Estimate'. `M0Estimate` is a single numerical whole-brain M0 value
+                    (referring to the M0 of blood), only if obtained externally (for example
+                    retrieved from CSF in a separate measurement).
 
 MRIASLCommonMetadataFieldsBackgroundSuppression:
     selectors:
@@ -218,10 +219,11 @@ MRIASLPASLSpecificBolusCutOffFlag:
             issue:
                 name: PASL_BOLUS_CUT_OFF_TECHINIQUE
                 message: |
-                    It is required to define 'BolusCutOffTechnique' for this file,
-                    when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique',
-                    is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII).
-                    Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.
+                    It is required to define `BolusCutOffTechnique` for this file,
+                    when `BolusCutOffFlag` is set to `true`. `BolusCutOffTechnique`,
+                    is the name of the technique used
+                    (for example, Q2TIPS, QUIPSS or QUIPSSII).
+                    Corresponds to DICOM Tag 0018,925E `ASL Bolus Cut-off Technique`.
 
 # m0scan metadata fields
 MRIASLM0ScanTextOnly:
@@ -248,9 +250,9 @@ MRIASLM0ScanTextOnlyFlipAngle:
             issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
-                    You should define 'FlipAngle' for this file, in case of a LookLocker
-                    acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition,
-                    specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+                    You should define `FlipAngle` for this file, in case of a LookLocker
+                    acquisition. `FlipAngle` is the flip angle (FA) for the acquisition,
+                    specified in degrees. Corresponds to DICOM Tag 0018, 1314 `Flip Angle`.
                     The data type number may apply to files from any MRI modality concerned
                     with a single value for this field, or to the files in a file collection
                     where the value of this field is iterated using the flip entity. The

From e73a60c425cdf5aaf6c59f27bd23978af468bd52 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 12 Apr 2022 11:10:09 -0700
Subject: [PATCH 288/347] first pass at a description of what format nifti
 headers will be shaped as

---
 src/schema/rules/nifti_header.yaml | 39 ++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 src/schema/rules/nifti_header.yaml

diff --git a/src/schema/rules/nifti_header.yaml b/src/schema/rules/nifti_header.yaml
new file mode 100644
index 0000000000..5ce137edb8
--- /dev/null
+++ b/src/schema/rules/nifti_header.yaml
@@ -0,0 +1,39 @@
+- nifti_header:
+  dim_info:
+    freq:
+        type: int
+    phase:
+        type: int
+    slice:
+        type: int
+  dim:
+    type: array
+    minItems: 8
+    maxItems: 8
+    items:
+        type: int
+   pixdim:
+      type: array
+      minItems: 8
+      maxItems: 8
+      items:
+        type: float
+  xyzt_units:
+    xyz:
+      type: string
+      enum:
+        - "unknown"
+        - "meter"
+        - "mm"
+        - "um"
+    t:
+      type: string
+      enum:
+        - "unknown"
+        - "sec"
+        - "msec"
+        - "usec"
+  qform_code:
+    type: int
+  sform_code:
+    type: int

From 220f531c2c2c39bd1962a45ad785bb1ed0092f1c Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 12 Apr 2022 11:22:24 -0700
Subject: [PATCH 289/347] lint nifti_header.yaml

---
 src/schema/rules/nifti_header.yaml | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/schema/rules/nifti_header.yaml b/src/schema/rules/nifti_header.yaml
index 5ce137edb8..27509a7821 100644
--- a/src/schema/rules/nifti_header.yaml
+++ b/src/schema/rules/nifti_header.yaml
@@ -1,23 +1,24 @@
+---
 - nifti_header:
   dim_info:
     freq:
-        type: int
+      type: int
     phase:
-        type: int
+      type: int
     slice:
-        type: int
+      type: int
   dim:
     type: array
     minItems: 8
     maxItems: 8
     items:
-        type: int
-   pixdim:
-      type: array
-      minItems: 8
-      maxItems: 8
-      items:
-        type: float
+      type: int
+  pixdim:
+    type: array
+    minItems: 8
+    maxItems: 8
+    items:
+      type: float
   xyzt_units:
     xyz:
       type: string

From 9b8d2c79bf2a38dde3655a0ca1f0208e0aa73fec Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 13 Apr 2022 07:48:12 -0700
Subject: [PATCH 290/347] lint fixes for nifti_header.yaml

---
 src/schema/rules/nifti_header.yaml | 78 +++++++++++++++---------------
 1 file changed, 39 insertions(+), 39 deletions(-)

diff --git a/src/schema/rules/nifti_header.yaml b/src/schema/rules/nifti_header.yaml
index 27509a7821..e568c77afc 100644
--- a/src/schema/rules/nifti_header.yaml
+++ b/src/schema/rules/nifti_header.yaml
@@ -1,40 +1,40 @@
 ---
-- nifti_header:
-  dim_info:
-    freq:
-      type: int
-    phase:
-      type: int
-    slice:
-      type: int
-  dim:
-    type: array
-    minItems: 8
-    maxItems: 8
-    items:
-      type: int
-  pixdim:
-    type: array
-    minItems: 8
-    maxItems: 8
-    items:
-      type: float
-  xyzt_units:
-    xyz:
-      type: string
-      enum:
-        - "unknown"
-        - "meter"
-        - "mm"
-        - "um"
-    t:
-      type: string
-      enum:
-        - "unknown"
-        - "sec"
-        - "msec"
-        - "usec"
-  qform_code:
-    type: int
-  sform_code:
-    type: int
+nifti_header:
+    dim_info:
+        freq:
+            type: int
+        phase:
+            type: int
+        slice:
+            type: int
+    dim:
+        type: array
+        minItems: 8
+        maxItems: 8
+        items:
+        type: int
+    pixdim:
+        type: array
+        minItems: 8
+        maxItems: 8
+        items:
+        type: float
+    xyzt_units:
+        xyz:
+            type: string
+            enum:
+            - "unknown"
+            - "meter"
+            - "mm"
+            - "um"
+        t:
+            type: string
+            enum:
+            - "unknown"
+            - "sec"
+            - "msec"
+            - "usec"
+    qform_code:
+        type: int
+    sform_code:
+        type: int

From 3dec62af5843630f2dce9b31f3daa244302a2afc Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 08:25:28 -0700
Subject: [PATCH 291/347] SCHEMA: Create context schema in meta/

---
 src/schema/meta/context.yaml       | 109 +++++++++++++++++++++++++++++
 src/schema/rules/nifti_header.yaml |  40 -----------
 2 files changed, 109 insertions(+), 40 deletions(-)
 create mode 100644 src/schema/meta/context.yaml
 delete mode 100644 src/schema/rules/nifti_header.yaml

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
new file mode 100644
index 0000000000..c21aa58231
--- /dev/null
+++ b/src/schema/meta/context.yaml
@@ -0,0 +1,109 @@
+#
+# The context provides the namespaces available to rules.
+# These namespaces are used by selectors to define the scope of application
+# for a rule, as well as assertions, to determine whether the rule is satisfied.
+#
+# Not all components of the context will be defined; for example a NIfTI header
+# will only be defined when examining a NIfTI file.
+#
+# The dataset namespace is constructed once and is available when visiting all
+# files.
+#
+# The subject namespace is constructed once per subject, and is available when
+# visiting all files within that subject.
+#
+# All other (current) namespaces are defined on individual files.
+# Sidecar metadata and file associations are built according to the inheritance
+# principle.
+#
+---
+context:
+    dataset:
+        dataset_description:
+            type: object
+        files:
+            type: list
+        tree:
+            type: object
+        ignored:
+            type: set
+        subjects:
+            sub_dirs:
+                type: list
+                # source: sub-*/
+            participant_id:
+                type: list
+                # source: participants.tsv
+            phenotype:
+                type: list
+                # source: union of participant_ids in all phenotype files
+    subject:
+        sessions:
+            ses_dirs:
+                type: list
+                # source: ses-*/
+            session_id:
+                type: list
+                # source: sessions.tsv
+            phenotype:
+                type: list
+                # source: union of session_ids in all phenotype files
+
+    entities:
+        type: object
+    datatype:
+        type: str
+    modality:
+        type: str
+    path:
+        type: str
+    sidecar:
+        type: object
+    associations:
+        events:
+            type: path
+        aslcontext:
+            type: path
+    columns:
+        # TSV files generate an object that maps column headers to arrays of
+        # values in that column
+        type: object
+    nifti_header:
+        dim_info:
+            freq:
+                type: int
+            phase:
+                type: int
+            slice:
+                type: int
+        dim:
+            type: array
+            minItems: 8
+            maxItems: 8
+            items:
+            type: int
+        pixdim:
+            type: array
+            minItems: 8
+            maxItems: 8
+            items:
+            type: float
+        xyzt_units:
+            xyz:
+                type: string
+                enum:
+                - "unknown"
+                - "meter"
+                - "mm"
+                - "um"
+            t:
+                type: string
+                enum:
+                - "unknown"
+                - "sec"
+                - "msec"
+                - "usec"
+        qform_code:
+            type: int
+        sform_code:
+            type: int
diff --git a/src/schema/rules/nifti_header.yaml b/src/schema/rules/nifti_header.yaml
deleted file mode 100644
index e568c77afc..0000000000
--- a/src/schema/rules/nifti_header.yaml
+++ /dev/null
@@ -1,40 +0,0 @@
----
-nifti_header:
-    dim_info:
-        freq:
-            type: int
-        phase:
-            type: int
-        slice:
-            type: int
-    dim:
-        type: array
-        minItems: 8
-        maxItems: 8
-        items:
-        type: int
-    pixdim:
-        type: array
-        minItems: 8
-        maxItems: 8
-        items:
-        type: float
-    xyzt_units:
-        xyz:
-            type: string
-            enum:
-            - "unknown"
-            - "meter"
-            - "mm"
-            - "um"
-        t:
-            type: string
-            enum:
-            - "unknown"
-            - "sec"
-            - "msec"
-            - "usec"
-    qform_code:
-        type: int
-    sform_code:
-        type: int

From 844518a590aef250080d5794fd1d2438637af8a6 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 08:56:11 -0700
Subject: [PATCH 292/347] Update nifti_header based on more recent work from
 Ross

---
 src/schema/meta/context.yaml | 98 +++++++++++++++++++++++-------------
 1 file changed, 63 insertions(+), 35 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index c21aa58231..0bc2f97b80 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -69,41 +69,69 @@ context:
         # values in that column
         type: object
     nifti_header:
-        dim_info:
-            freq:
+        name: "NIfTI Header"
+        description: "Parsed contents of NIfTI header referenced elsewhere in schema."
+        type: object
+        properties:
+            dim_info:
+                name: "Dimension Information"
+                description: "Metadata about dimensions data."
+                type: object
+                properties:
+                    freq:
+                        name: "Frequency"
+                        description: "These fields encode which spatial dimension (1,2, or 3)."
+                        type: int
+                    phase:
+                        name: "Phase"
+                        description: "Corresponds to which acquisition dimension for MRI data."
+                        type: int
+                    slice:
+                        name: "Slice"
+                        description: "Slice dimensions."
+                        type: int
+            dim:
+                name: "Data Dimensions"
+                description: "Data array dimensions."
+                type: array
+                minItems: 8
+                maxItems: 8
+                items:
                 type: int
-            phase:
+            pixdim:
+                name: "Pixel Dimension"
+                description: "Grid spacings (unit per dimension)."
+                type: array
+                minItems: 8
+                maxItems: 8
+                items:
+                type: float
+            xyzt_units:
+                name: "XYZT Units"
+                description: "Units of pixdim[1..4]"
+                xyz:
+                    name: "XYZ Units"
+                    description: "String representing the unit used by all 3 spatial dimensions data."
+                    type: string
+                    enum:
+                        - "unknown"
+                        - "meter"
+                        - "mm"
+                        - "um"
+                t:
+                    name: "Time Unit"
+                    description: "String representing the unit used by temporal dimension data."
+                    type: string
+                    enum:
+                        - "unknown"
+                        - "sec"
+                        - "msec"
+                        - "usec"
+            qform_code:
+                name: "qform code"
+                description: "Use of the quaternion fields."
                 type: int
-            slice:
+            sform_code:
+                name: "sform code"
+                description: "Use of the affine fields."
                 type: int
-        dim:
-            type: array
-            minItems: 8
-            maxItems: 8
-            items:
-            type: int
-        pixdim:
-            type: array
-            minItems: 8
-            maxItems: 8
-            items:
-            type: float
-        xyzt_units:
-            xyz:
-                type: string
-                enum:
-                - "unknown"
-                - "meter"
-                - "mm"
-                - "um"
-            t:
-                type: string
-                enum:
-                - "unknown"
-                - "sec"
-                - "msec"
-                - "usec"
-        qform_code:
-            type: int
-        sform_code:
-            type: int

From 4798fa33bc0add16916691cfff7678cab846c479 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 09:35:52 -0700
Subject: [PATCH 293/347] Flesh out context object

---
 src/schema/meta/context.yaml | 119 +++++++++++++++++++++++------------
 1 file changed, 79 insertions(+), 40 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 0bc2f97b80..1e9017c852 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -19,54 +19,93 @@
 ---
 context:
     dataset:
-        dataset_description:
-            type: object
-        files:
-            type: list
-        tree:
-            type: object
-        ignored:
-            type: set
-        subjects:
-            sub_dirs:
-                type: list
-                # source: sub-*/
-            participant_id:
-                type: list
-                # source: participants.tsv
-            phenotype:
-                type: list
-                # source: union of participant_ids in all phenotype files
+        description: "Properties and contents of the entire dataset"
+        type: object
+        properties:
+            dataset_description:
+                description: "Contents of /dataset_description.json"
+                type: object
+            files:
+                description: "List of all files in dataset"
+                type: array
+            tree:
+                description: "Tree view of all files in dataset"
+                type: object
+            ignored:
+                description: "Set of ignored files"
+                type: array
+            subjects:
+                description: "Collections of subjects in dataset"
+                type: object
+                properties:
+                    sub_dirs:
+                        description: "Subjects as determined by sub-*/ directories"
+                        type: array
+                        items:
+                            type: string
+                    participant_id:
+                        description: "The participant_id column of participants.tsv"
+                        type: array
+                        items:
+                            type: string
+                    phenotype:
+                        description: "The union of participant_id columns in phenotype files"
+                        type: array
+                        items:
+                            type: string
     subject:
-        sessions:
-            ses_dirs:
-                type: list
-                # source: ses-*/
-            session_id:
-                type: list
-                # source: sessions.tsv
-            phenotype:
-                type: list
-                # source: union of session_ids in all phenotype files
+        description: "Properties and contents of the current subject"
+        type: object
+        properties:
+            sessions:
+                description: "Collections of sessions in subject"
+                type: object
+                properties:
+                    ses_dirs:
+                        description: "Sessions as determined by ses-*/ directories"
+                        type: array
+                        items:
+                            type: string
+                    session_id:
+                        description: "The session_id column of sessions.tsv"
+                        type: array
+                        items:
+                            type: string
+                    phenotype:
+                        description: "The union of session_id columns in phenotype files"
+                        type: array
+                        items:
+                            type: string
 
+    # Properties of the current file
+    path:
+        description: "Path of the current file"
+        type: string
     entities:
+        description: "Entities parsed from the current filename"
         type: object
     datatype:
-        type: str
+        description: "Datatype of current file, e.g., anat"
+        type: string
     modality:
-        type: str
-    path:
-        type: str
+        description: "Modality of current file, e.g., MRI"
+        type: string
     sidecar:
+        description: "Sidecar metadata constructed via the inheritance principle"
         type: object
     associations:
-        events:
-            type: path
-        aslcontext:
-            type: path
+        description: |
+            Associated files, indexed by suffix, selected according to the inheritance principle
+        type: object
+        properties:
+            events:
+                description: "Path to associated events file"
+                type: path
+            aslcontext:
+                description: "Path to associated aslcontext file"
+                type: path
     columns:
-        # TSV files generate an object that maps column headers to arrays of
-        # values in that column
+        description: "TSV columns, indexed by column header, values are arrays with data contents"
         type: object
     nifti_header:
         name: "NIfTI Header"
@@ -97,7 +136,7 @@ context:
                 minItems: 8
                 maxItems: 8
                 items:
-                type: int
+                    type: int
             pixdim:
                 name: "Pixel Dimension"
                 description: "Grid spacings (unit per dimension)."
@@ -105,7 +144,7 @@ context:
                 minItems: 8
                 maxItems: 8
                 items:
-                type: float
+                    type: float
             xyzt_units:
                 name: "XYZT Units"
                 description: "Units of pixdim[1..4]"

From c7fd45cf8969abbdfd6577aa0a0c594f26e38418 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 09:39:03 -0700
Subject: [PATCH 294/347] Specify that columns have type array

---
 src/schema/meta/context.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 1e9017c852..9f3b58a655 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -105,8 +105,10 @@ context:
                 description: "Path to associated aslcontext file"
                 type: path
     columns:
-        description: "TSV columns, indexed by column header, values are arrays with data contents"
+        description: "TSV columns, indexed by column header, values are arrays with column contents"
         type: object
+        additionalProperties:
+            type: array
     nifti_header:
         name: "NIfTI Header"
         description: "Parsed contents of NIfTI header referenced elsewhere in schema."

From e48aa036a0516fb14e60590b3598365c51ff93da Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 09:40:53 -0700
Subject: [PATCH 295/347] Add dataset.modalities

---
 src/schema/meta/context.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 9f3b58a655..7e1627faa5 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -34,6 +34,9 @@ context:
             ignored:
                 description: "Set of ignored files"
                 type: array
+            modalities:
+                description: "Modalities present in the dataset"
+                type: array
             subjects:
                 description: "Collections of subjects in dataset"
                 type: object

From 3d0be5ab9bdf8fd31d9a5bf84b2616cdc050e51e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 10:16:57 -0700
Subject: [PATCH 296/347] Add json object

---
 src/schema/meta/context.yaml | 83 +++++++++++++++++++-----------------
 1 file changed, 44 insertions(+), 39 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 7e1627faa5..76be3a41da 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -20,111 +20,116 @@
 context:
     dataset:
         description: "Properties and contents of the entire dataset"
-        type: object
+        type: map
         properties:
             dataset_description:
                 description: "Contents of /dataset_description.json"
-                type: object
+                type: map
             files:
                 description: "List of all files in dataset"
-                type: array
+                type: seq
             tree:
                 description: "Tree view of all files in dataset"
-                type: object
+                type: map
             ignored:
                 description: "Set of ignored files"
-                type: array
+                type: seq
             modalities:
                 description: "Modalities present in the dataset"
-                type: array
+                type: seq
             subjects:
                 description: "Collections of subjects in dataset"
-                type: object
+                type: map
                 properties:
                     sub_dirs:
                         description: "Subjects as determined by sub-*/ directories"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
                     participant_id:
                         description: "The participant_id column of participants.tsv"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
                     phenotype:
                         description: "The union of participant_id columns in phenotype files"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
     subject:
         description: "Properties and contents of the current subject"
-        type: object
+        type: map
         properties:
             sessions:
                 description: "Collections of sessions in subject"
-                type: object
+                type: map
                 properties:
                     ses_dirs:
                         description: "Sessions as determined by ses-*/ directories"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
                     session_id:
                         description: "The session_id column of sessions.tsv"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
                     phenotype:
                         description: "The union of session_id columns in phenotype files"
-                        type: array
+                        type: seq
                         items:
-                            type: string
+                            type: str
 
     # Properties of the current file
     path:
         description: "Path of the current file"
-        type: string
+        type: str
     entities:
         description: "Entities parsed from the current filename"
-        type: object
+        type: map
     datatype:
         description: "Datatype of current file, e.g., anat"
-        type: string
+        type: str
     modality:
         description: "Modality of current file, e.g., MRI"
-        type: string
+        type: str
     sidecar:
         description: "Sidecar metadata constructed via the inheritance principle"
-        type: object
+        type: map
     associations:
         description: |
             Associated files, indexed by suffix, selected according to the inheritance principle
-        type: object
+        type: map
         properties:
             events:
                 description: "Path to associated events file"
-                type: path
+                type: str
             aslcontext:
                 description: "Path to associated aslcontext file"
-                type: path
+                type: str
+
+    # The following properties are populated if the current file is of an appropriate type
     columns:
         description: "TSV columns, indexed by column header, values are arrays with column contents"
-        type: object
+        type: map
         additionalProperties:
-            type: array
+            type: seq
+    json:
+        description: "Contents of the current JSON file"
+        type: map
     nifti_header:
         name: "NIfTI Header"
         description: "Parsed contents of NIfTI header referenced elsewhere in schema."
-        type: object
+        type: map
         properties:
             dim_info:
                 name: "Dimension Information"
                 description: "Metadata about dimensions data."
-                type: object
+                type: map
                 properties:
                     freq:
                         name: "Frequency"
-                        description: "These fields encode which spatial dimension (1,2, or 3)."
+                        description: "These fields encode which spatial dimension (1, 2, or 3)."
                         type: int
                     phase:
                         name: "Phase"
@@ -136,8 +141,8 @@ context:
                         type: int
             dim:
                 name: "Data Dimensions"
-                description: "Data array dimensions."
-                type: array
+                description: "Data seq dimensions."
+                type: seq
                 minItems: 8
                 maxItems: 8
                 items:
@@ -145,7 +150,7 @@ context:
             pixdim:
                 name: "Pixel Dimension"
                 description: "Grid spacings (unit per dimension)."
-                type: array
+                type: seq
                 minItems: 8
                 maxItems: 8
                 items:
@@ -156,7 +161,7 @@ context:
                 xyz:
                     name: "XYZ Units"
                     description: "String representing the unit used by all 3 spatial dimensions data."
-                    type: string
+                    type: str
                     enum:
                         - "unknown"
                         - "meter"
@@ -165,7 +170,7 @@ context:
                 t:
                     name: "Time Unit"
                     description: "String representing the unit used by temporal dimension data."
-                    type: string
+                    type: str
                     enum:
                         - "unknown"
                         - "sec"

From 007af7f2126a79c06e08c32862bbd1de6c228e4c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 10:17:14 -0700
Subject: [PATCH 297/347] Define type of entire context

---
 src/schema/meta/context.yaml | 326 ++++++++++++++++++-----------------
 1 file changed, 164 insertions(+), 162 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 76be3a41da..c6c95008f8 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -18,169 +18,171 @@
 #
 ---
 context:
-    dataset:
-        description: "Properties and contents of the entire dataset"
-        type: map
-        properties:
-            dataset_description:
-                description: "Contents of /dataset_description.json"
-                type: map
-            files:
-                description: "List of all files in dataset"
-                type: seq
-            tree:
-                description: "Tree view of all files in dataset"
-                type: map
-            ignored:
-                description: "Set of ignored files"
-                type: seq
-            modalities:
-                description: "Modalities present in the dataset"
-                type: seq
-            subjects:
-                description: "Collections of subjects in dataset"
-                type: map
-                properties:
-                    sub_dirs:
-                        description: "Subjects as determined by sub-*/ directories"
-                        type: seq
-                        items:
-                            type: str
-                    participant_id:
-                        description: "The participant_id column of participants.tsv"
-                        type: seq
-                        items:
-                            type: str
-                    phenotype:
-                        description: "The union of participant_id columns in phenotype files"
-                        type: seq
-                        items:
-                            type: str
-    subject:
-        description: "Properties and contents of the current subject"
-        type: map
-        properties:
-            sessions:
-                description: "Collections of sessions in subject"
-                type: map
-                properties:
-                    ses_dirs:
-                        description: "Sessions as determined by ses-*/ directories"
-                        type: seq
-                        items:
-                            type: str
-                    session_id:
-                        description: "The session_id column of sessions.tsv"
-                        type: seq
-                        items:
-                            type: str
-                    phenotype:
-                        description: "The union of session_id columns in phenotype files"
-                        type: seq
-                        items:
-                            type: str
+    type: map
+    properties:
+        dataset:
+            description: "Properties and contents of the entire dataset"
+            type: map
+            properties:
+                dataset_description:
+                    description: "Contents of /dataset_description.json"
+                    type: map
+                files:
+                    description: "List of all files in dataset"
+                    type: seq
+                tree:
+                    description: "Tree view of all files in dataset"
+                    type: map
+                ignored:
+                    description: "Set of ignored files"
+                    type: seq
+                modalities:
+                    description: "Modalities present in the dataset"
+                    type: seq
+                subjects:
+                    description: "Collections of subjects in dataset"
+                    type: map
+                    properties:
+                        sub_dirs:
+                            description: "Subjects as determined by sub-*/ directories"
+                            type: seq
+                            items:
+                                type: str
+                        participant_id:
+                            description: "The participant_id column of participants.tsv"
+                            type: seq
+                            items:
+                                type: str
+                        phenotype:
+                            description: "The union of participant_id columns in phenotype files"
+                            type: seq
+                            items:
+                                type: str
+        subject:
+            description: "Properties and contents of the current subject"
+            type: map
+            properties:
+                sessions:
+                    description: "Collections of sessions in subject"
+                    type: map
+                    properties:
+                        ses_dirs:
+                            description: "Sessions as determined by ses-*/ directories"
+                            type: seq
+                            items:
+                                type: str
+                        session_id:
+                            description: "The session_id column of sessions.tsv"
+                            type: seq
+                            items:
+                                type: str
+                        phenotype:
+                            description: "The union of session_id columns in phenotype files"
+                            type: seq
+                            items:
+                                type: str
 
-    # Properties of the current file
-    path:
-        description: "Path of the current file"
-        type: str
-    entities:
-        description: "Entities parsed from the current filename"
-        type: map
-    datatype:
-        description: "Datatype of current file, e.g., anat"
-        type: str
-    modality:
-        description: "Modality of current file, e.g., MRI"
-        type: str
-    sidecar:
-        description: "Sidecar metadata constructed via the inheritance principle"
-        type: map
-    associations:
-        description: |
-            Associated files, indexed by suffix, selected according to the inheritance principle
-        type: map
-        properties:
-            events:
-                description: "Path to associated events file"
-                type: str
-            aslcontext:
-                description: "Path to associated aslcontext file"
-                type: str
+        # Properties of the current file
+        path:
+            description: "Path of the current file"
+            type: str
+        entities:
+            description: "Entities parsed from the current filename"
+            type: map
+        datatype:
+            description: "Datatype of current file, e.g., anat"
+            type: str
+        modality:
+            description: "Modality of current file, e.g., MRI"
+            type: str
+        sidecar:
+            description: "Sidecar metadata constructed via the inheritance principle"
+            type: map
+        associations:
+            description: |
+                Associated files, indexed by suffix, selected according to the inheritance principle
+            type: map
+            properties:
+                events:
+                    description: "Path to associated events file"
+                    type: str
+                aslcontext:
+                    description: "Path to associated aslcontext file"
+                    type: str
 
-    # The following properties are populated if the current file is of an appropriate type
-    columns:
-        description: "TSV columns, indexed by column header, values are arrays with column contents"
-        type: map
-        additionalProperties:
-            type: seq
-    json:
-        description: "Contents of the current JSON file"
-        type: map
-    nifti_header:
-        name: "NIfTI Header"
-        description: "Parsed contents of NIfTI header referenced elsewhere in schema."
-        type: map
-        properties:
-            dim_info:
-                name: "Dimension Information"
-                description: "Metadata about dimensions data."
-                type: map
-                properties:
-                    freq:
-                        name: "Frequency"
-                        description: "These fields encode which spatial dimension (1, 2, or 3)."
-                        type: int
-                    phase:
-                        name: "Phase"
-                        description: "Corresponds to which acquisition dimension for MRI data."
-                        type: int
-                    slice:
-                        name: "Slice"
-                        description: "Slice dimensions."
-                        type: int
-            dim:
-                name: "Data Dimensions"
-                description: "Data seq dimensions."
+        # The following properties are populated if the current file is of an appropriate type
+        columns:
+            description: "TSV columns, indexed by column header, values are arrays with column contents"
+            type: map
+            additionalProperties:
                 type: seq
-                minItems: 8
-                maxItems: 8
-                items:
+        json:
+            description: "Contents of the current JSON file"
+            type: map
+        nifti_header:
+            name: "NIfTI Header"
+            description: "Parsed contents of NIfTI header referenced elsewhere in schema."
+            type: map
+            properties:
+                dim_info:
+                    name: "Dimension Information"
+                    description: "Metadata about dimensions data."
+                    type: map
+                    properties:
+                        freq:
+                            name: "Frequency"
+                            description: "These fields encode which spatial dimension (1, 2, or 3)."
+                            type: int
+                        phase:
+                            name: "Phase"
+                            description: "Corresponds to which acquisition dimension for MRI data."
+                            type: int
+                        slice:
+                            name: "Slice"
+                            description: "Slice dimensions."
+                            type: int
+                dim:
+                    name: "Data Dimensions"
+                    description: "Data seq dimensions."
+                    type: seq
+                    minItems: 8
+                    maxItems: 8
+                    items:
+                        type: int
+                pixdim:
+                    name: "Pixel Dimension"
+                    description: "Grid spacings (unit per dimension)."
+                    type: seq
+                    minItems: 8
+                    maxItems: 8
+                    items:
+                        type: float
+                xyzt_units:
+                    name: "XYZT Units"
+                    description: "Units of pixdim[1..4]"
+                    xyz:
+                        name: "XYZ Units"
+                        description: "String representing the unit used by all 3 spatial dimensions data."
+                        type: str
+                        enum:
+                            - "unknown"
+                            - "meter"
+                            - "mm"
+                            - "um"
+                    t:
+                        name: "Time Unit"
+                        description: "String representing the unit used by temporal dimension data."
+                        type: str
+                        enum:
+                            - "unknown"
+                            - "sec"
+                            - "msec"
+                            - "usec"
+                qform_code:
+                    name: "qform code"
+                    description: "Use of the quaternion fields."
+                    type: int
+                sform_code:
+                    name: "sform code"
+                    description: "Use of the affine fields."
                     type: int
-            pixdim:
-                name: "Pixel Dimension"
-                description: "Grid spacings (unit per dimension)."
-                type: seq
-                minItems: 8
-                maxItems: 8
-                items:
-                    type: float
-            xyzt_units:
-                name: "XYZT Units"
-                description: "Units of pixdim[1..4]"
-                xyz:
-                    name: "XYZ Units"
-                    description: "String representing the unit used by all 3 spatial dimensions data."
-                    type: str
-                    enum:
-                        - "unknown"
-                        - "meter"
-                        - "mm"
-                        - "um"
-                t:
-                    name: "Time Unit"
-                    description: "String representing the unit used by temporal dimension data."
-                    type: str
-                    enum:
-                        - "unknown"
-                        - "sec"
-                        - "msec"
-                        - "usec"
-            qform_code:
-                name: "qform code"
-                description: "Use of the quaternion fields."
-                type: int
-            sform_code:
-                name: "sform code"
-                description: "Use of the affine fields."
-                type: int

From bc8418a1d1cc0f2b6a3b047be9943d2a00eeee49 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 15:20:25 -0700
Subject: [PATCH 298/347] Back to JSON schema

---
 src/schema/meta/context.yaml | 92 ++++++++++++++++++------------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index c6c95008f8..64b276da4b 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -18,152 +18,152 @@
 #
 ---
 context:
-    type: map
+    type: object
     properties:
         dataset:
             description: "Properties and contents of the entire dataset"
-            type: map
+            type: object
             properties:
                 dataset_description:
                     description: "Contents of /dataset_description.json"
-                    type: map
+                    type: object
                 files:
                     description: "List of all files in dataset"
-                    type: seq
+                    type: array
                 tree:
                     description: "Tree view of all files in dataset"
-                    type: map
+                    type: object
                 ignored:
                     description: "Set of ignored files"
-                    type: seq
+                    type: array
                 modalities:
                     description: "Modalities present in the dataset"
-                    type: seq
+                    type: array
                 subjects:
                     description: "Collections of subjects in dataset"
-                    type: map
+                    type: object
                     properties:
                         sub_dirs:
                             description: "Subjects as determined by sub-*/ directories"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
                         participant_id:
                             description: "The participant_id column of participants.tsv"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
                         phenotype:
                             description: "The union of participant_id columns in phenotype files"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
         subject:
             description: "Properties and contents of the current subject"
-            type: map
+            type: object
             properties:
                 sessions:
                     description: "Collections of sessions in subject"
-                    type: map
+                    type: object
                     properties:
                         ses_dirs:
                             description: "Sessions as determined by ses-*/ directories"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
                         session_id:
                             description: "The session_id column of sessions.tsv"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
                         phenotype:
                             description: "The union of session_id columns in phenotype files"
-                            type: seq
+                            type: array
                             items:
-                                type: str
+                                type: string
 
         # Properties of the current file
         path:
             description: "Path of the current file"
-            type: str
+            type: string
         entities:
             description: "Entities parsed from the current filename"
-            type: map
+            type: object
         datatype:
             description: "Datatype of current file, e.g., anat"
-            type: str
+            type: string
         modality:
             description: "Modality of current file, e.g., MRI"
-            type: str
+            type: string
         sidecar:
             description: "Sidecar metadata constructed via the inheritance principle"
-            type: map
+            type: object
         associations:
             description: |
                 Associated files, indexed by suffix, selected according to the inheritance principle
-            type: map
+            type: object
             properties:
                 events:
                     description: "Path to associated events file"
-                    type: str
+                    type: string
                 aslcontext:
                     description: "Path to associated aslcontext file"
-                    type: str
+                    type: string
 
         # The following properties are populated if the current file is of an appropriate type
         columns:
             description: "TSV columns, indexed by column header, values are arrays with column contents"
-            type: map
+            type: object
             additionalProperties:
-                type: seq
+                type: array
         json:
             description: "Contents of the current JSON file"
-            type: map
+            type: object
         nifti_header:
             name: "NIfTI Header"
             description: "Parsed contents of NIfTI header referenced elsewhere in schema."
-            type: map
+            type: object
             properties:
                 dim_info:
                     name: "Dimension Information"
                     description: "Metadata about dimensions data."
-                    type: map
+                    type: object
                     properties:
                         freq:
                             name: "Frequency"
                             description: "These fields encode which spatial dimension (1, 2, or 3)."
-                            type: int
+                            type: integer
                         phase:
                             name: "Phase"
                             description: "Corresponds to which acquisition dimension for MRI data."
-                            type: int
+                            type: integer
                         slice:
                             name: "Slice"
                             description: "Slice dimensions."
-                            type: int
+                            type: integer
                 dim:
                     name: "Data Dimensions"
                     description: "Data seq dimensions."
-                    type: seq
+                    type: array
                     minItems: 8
                     maxItems: 8
                     items:
-                        type: int
+                        type: integer
                 pixdim:
                     name: "Pixel Dimension"
                     description: "Grid spacings (unit per dimension)."
-                    type: seq
+                    type: array
                     minItems: 8
                     maxItems: 8
                     items:
-                        type: float
+                        type: number
                 xyzt_units:
                     name: "XYZT Units"
                     description: "Units of pixdim[1..4]"
                     xyz:
                         name: "XYZ Units"
                         description: "String representing the unit used by all 3 spatial dimensions data."
-                        type: str
+                        type: string
                         enum:
                             - "unknown"
                             - "meter"
@@ -172,7 +172,7 @@ context:
                     t:
                         name: "Time Unit"
                         description: "String representing the unit used by temporal dimension data."
-                        type: str
+                        type: string
                         enum:
                             - "unknown"
                             - "sec"
@@ -181,8 +181,8 @@ context:
                 qform_code:
                     name: "qform code"
                     description: "Use of the quaternion fields."
-                    type: int
+                    type: integer
                 sform_code:
                     name: "sform code"
                     description: "Use of the affine fields."
-                    type: int
+                    type: integer

From 749c6affce6e0ba9ef250a9055bf0acc1196221c Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 15:47:15 -0700
Subject: [PATCH 299/347] Add aslcontext and events

---
 src/schema/meta/context.yaml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 64b276da4b..417ac8c63f 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -186,3 +186,26 @@ context:
                     name: "sform code"
                     description: "Use of the affine fields."
                     type: integer
+
+        # Aspects of associated files that are needed to perform assertions on the
+        # "main" file
+        aslcontext:
+            description: "ASL context object"
+            properties:
+                n_rows:
+                    description: "Number of rows in aslcontext.tsv"
+                    type: integer
+                volume_type:
+                    description: "Contents of the volume_type column"
+                    type: array
+                    items:
+                        type: string
+
+        events:
+            description: "Associated events file"
+            properties:
+                onset:
+                    description: "Contents of the onset column"
+                    type: array
+                    items:
+                        type: string

From 035b67ec3e764bb888d5197483476e0776c7645b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 16:06:50 -0700
Subject: [PATCH 300/347] Add suffix and extension to context

---
 src/schema/meta/context.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 417ac8c63f..5be28ba6e4 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -92,9 +92,16 @@ context:
         datatype:
             description: "Datatype of current file, e.g., anat"
             type: string
+        suffix:
+            description: "Suffix of current file"
+            type: string
+        extension:
+            description: "Extension of current file including initial dot"
+            type: string
         modality:
             description: "Modality of current file, e.g., MRI"
             type: string
+
         sidecar:
             description: "Sidecar metadata constructed via the inheritance principle"
             type: object

From bde127b9410070daa4d7aba26f77226cf8e237f2 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 16:21:24 -0700
Subject: [PATCH 301/347] Move all association fields inside the associations
 context

---
 src/schema/meta/context.yaml | 52 +++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 5be28ba6e4..9d48ddb44e 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -111,11 +111,32 @@ context:
             type: object
             properties:
                 events:
-                    description: "Path to associated events file"
-                    type: string
+                    description: "Events file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated events file"
+                            type: string
+                        onset:
+                            description: "Contents of the onset column"
+                            type: array
+                            items:
+                                type: string
                 aslcontext:
-                    description: "Path to associated aslcontext file"
-                    type: string
+                    description: "ASL context file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated aslcontext file"
+                            type: string
+                        n_rows:
+                            description: "Number of rows in aslcontext.tsv"
+                            type: integer
+                        volume_type:
+                            description: "Contents of the volume_type column"
+                            type: array
+                            items:
+                                type: string
 
         # The following properties are populated if the current file is of an appropriate type
         columns:
@@ -193,26 +214,3 @@ context:
                     name: "sform code"
                     description: "Use of the affine fields."
                     type: integer
-
-        # Aspects of associated files that are needed to perform assertions on the
-        # "main" file
-        aslcontext:
-            description: "ASL context object"
-            properties:
-                n_rows:
-                    description: "Number of rows in aslcontext.tsv"
-                    type: integer
-                volume_type:
-                    description: "Contents of the volume_type column"
-                    type: array
-                    items:
-                        type: string
-
-        events:
-            description: "Associated events file"
-            properties:
-                onset:
-                    description: "Contents of the onset column"
-                    type: array
-                    items:
-                        type: string

From d468d7bf207b5fd91693658b2783c2aec3a14ba2 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 17:32:20 -0700
Subject: [PATCH 302/347] Add m0scan, magnitude images and bval/bvec associated
 files

---
 src/schema/meta/context.yaml | 41 ++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 9d48ddb44e..8d78a279ce 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -137,6 +137,47 @@ context:
                             type: array
                             items:
                                 type: string
+                m0scan:
+                    description: "M0 scan file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated M0 scan file"
+                            type: string
+                magnitude:
+                    description: "Magnitude image file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated magnitude file"
+                            type: string
+                magnitude1:
+                    description: "Magnitude1 image file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated magnitude1 file"
+                            type: string
+                bval:
+                    description: "B value file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated bval file"
+                            type: string
+                        n_cols:
+                            description: "Number of columns in bval file"
+                            type: integer
+                bvec:
+                    description: "B vector file"
+                    type: object
+                    properties:
+                        path:
+                            description: "Path to associated bvec file"
+                            type: string
+                        n_cols:
+                            description: "Number of columns in bvec file"
+                            type: integer
 
         # The following properties are populated if the current file is of an appropriate type
         columns:

From ae524082d8cac5b76dbb3cc1102e90ac6cf6a0e9 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 06:28:52 -0700
Subject: [PATCH 303/347] Comment context

---
 src/schema/meta/context.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 8d78a279ce..d0bf8de093 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -106,6 +106,9 @@ context:
             description: "Sidecar metadata constructed via the inheritance principle"
             type: object
         associations:
+            # Note that this is not intended to be an exhaustive list of associated files
+            # or to expose every attribute of those files. It is specifically those files
+            # and attributes for which a rule needs to be applied from an originating file.
             description: |
                 Associated files, indexed by suffix, selected according to the inheritance principle
             type: object

From 1fd48a00084264bd93eb716cdb09b2760e0b832e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 07:10:57 -0700
Subject: [PATCH 304/347] STY: Fix YAML, shorten descriptions

---
 src/schema/meta/context.yaml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index d0bf8de093..3defdfcb36 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -234,22 +234,22 @@ context:
                     description: "Units of pixdim[1..4]"
                     xyz:
                         name: "XYZ Units"
-                        description: "String representing the unit used by all 3 spatial dimensions data."
+                        description: "String representing the unit of voxel spacing."
                         type: string
                         enum:
-                            - "unknown"
-                            - "meter"
-                            - "mm"
-                            - "um"
+                        - "unknown"
+                        - "meter"
+                        - "mm"
+                        - "um"
                     t:
                         name: "Time Unit"
-                        description: "String representing the unit used by temporal dimension data."
+                        description: "String representing the unit of inter-volume intervals."
                         type: string
                         enum:
-                            - "unknown"
-                            - "sec"
-                            - "msec"
-                            - "usec"
+                        - "unknown"
+                        - "sec"
+                        - "msec"
+                        - "usec"
                 qform_code:
                     name: "qform code"
                     description: "Use of the quaternion fields."

From 9820ae752dd574a1a827e54550dd5df4b6c362e4 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:31:59 -0400
Subject: [PATCH 305/347] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/sidecars/asl_validation.yaml | 10 +++++-----
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 9a629e9028..d6f614d7a2 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,9 +19,9 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
-    - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
+    - nifti_header.dim[4] == len(sidecar.LabelingDuration)
 
 # 165
 ASLContextConsistent:
@@ -34,7 +34,7 @@ ASLContextConsistent:
     - suffix == "asl"
     - associated contains "aslcontext"
     checks:
-    - nifti_header.pixdim[4] == aslcontext.n_rows
+    - nifti_header.dim[4] == associations.aslcontext.n_rows
 
 # 168
 ASLFlipAngleNiftiLength:
@@ -51,9 +51,9 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
-    - nifti_header.pixdim[4] == sidecar.FlipAngle.size
+    - nifti_header.dim[4] == len(sidecar.FlipAngle)
 
 # 172
 ASLFlipAngleASLContextLength:
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index f8b3a31140..68b6a8a61a 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - bval.n_rows == nifti_header.pixdim[4]
-    - bvec.n_rows == nifti_header.pixdim[4]
+    - associations.bval.n_cols == nifti_header.dim[4]
+    - associations.bvec.n_cols == nifti_header.dim[4]
 
 # 30
 DWIBvalRows:

From ebf3c23920cd9d3bca94b16b6a2e42de0c013e72 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:33:30 -0400
Subject: [PATCH 306/347] associated --> associations

---
 src/schema/rules/sidecars/asl_validation.yaml | 24 +++++++++----------
 src/schema/rules/sidecars/dwi_validation.yaml |  8 +++----
 src/schema/rules/sidecars/eeg.yaml            |  2 +-
 .../rules/sidecars/events_validation.yaml     |  2 +-
 .../rules/sidecars/fmap_validation.yaml       |  6 ++---
 5 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 9a629e9028..47c4ed3fe4 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -32,7 +32,7 @@ ASLContextConsistent:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     checks:
     - nifti_header.pixdim[4] == aslcontext.n_rows
 
@@ -70,7 +70,7 @@ ASLFlipAngleASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "seq"
     checks:
@@ -115,7 +115,7 @@ ASLPostLabelingDelayASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "seq"
     checks:
@@ -140,7 +140,7 @@ ASLLabelingDurationASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "seq"
     checks:
@@ -160,7 +160,7 @@ ASLRepetitionTimePreparationASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "seq"
     checks:
@@ -194,7 +194,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     level: warning
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
     - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
@@ -209,7 +209,7 @@ ASLEchoTimeASLContextLength:
     level: warning
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "seq"
     checks:
@@ -225,8 +225,8 @@ ASLM0TypeAbsentScan:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
-    - associated contains "m0scan"
+    - associations contains "aslcontext"
+    - associations contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
 
@@ -239,7 +239,7 @@ ASLM0TypeAbsentASLContext:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - aslcontext.volume_type contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
@@ -253,7 +253,7 @@ ASLM0TypeIncorrect:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar.M0Type == "separate"
     checks:
-    - associated contains "m0scan"
+    - associations contains "m0scan"
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index f8b3a31140..9ebf597882 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -10,8 +10,8 @@ DWIVolumeCount:
     level: error
     selectors:
     - suffix == "dwi"
-    - associated contains "bval"
-    - associated contains "bvec"
+    - associations contains "bval"
+    - associations contains "bvec"
     checks:
     - bval.n_rows == nifti_header.pixdim[4]
     - bvec.n_rows == nifti_header.pixdim[4]
@@ -47,7 +47,7 @@ DWIMissingBvec:
     selectors:
     - suffix == "dwi"
     checks:
-    - associated contains "bvec"
+    - associations contains "bvec"
 
 # 33
 DWIMissingBval:
@@ -58,4 +58,4 @@ DWIMissingBval:
     selectors:
     - suffix == "dwi"
     checks:
-    - associated contains "bval"
+    - associations contains "bval"
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 4b1902bd23..224558cc06 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -89,7 +89,7 @@ EEGCoordsystemGeneral:
         IntendedFor:
             level: OPTIONAL
             addendum: |
-                This identifies the MRI or CT scan associated with the electrodes,
+                This identifies the MRI or CT scan associations with the electrodes,
                 landmarks, and fiducials.
 
 # Fields relating to the EEG electrode positions
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
index e4e74e9adc..4e735a38e0 100644
--- a/src/schema/rules/sidecars/events_validation.yaml
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -13,4 +13,4 @@ EventsMissing:
     - entities.task != "rest"
     - entities.task not contains "rest"  # Alternative for including the word "rest"
     checks:
-    - associated contains "events"
+    - associations contains "events"
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/sidecars/fmap_validation.yaml
index b88bce11ef..53c231d89e 100644
--- a/src/schema/rules/sidecars/fmap_validation.yaml
+++ b/src/schema/rules/sidecars/fmap_validation.yaml
@@ -10,15 +10,15 @@ FmapFieldmapWithoutMagnitude:
     selectors:
     - suffix == "fieldmap"
     checks:
-    - associated contains "magnitude"
+    - associations contains "magnitude"
 
 # 92
 FmapPhasediffWithoutMagnitude:
     code: MISSING_MAGNITUDE1_FILE
     description: |
-        Each '_phasediff.nii[.gz]' file should be associated with a '_magnitude1.nii[.gz]' file.
+        Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
     level: warning
     selectors:
     - suffix == "phasediff"
     checks:
-    - associated contains "magnitude1"
+    - associations contains "magnitude1"

From fd046c4e8a48ddcee253f0f4121fa40ba9a3967a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:34:28 -0400
Subject: [PATCH 307/347] seq --> array

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 47c4ed3fe4..a6f5c67734 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,7 +19,7 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
@@ -51,7 +51,7 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
@@ -72,7 +72,7 @@ ASLFlipAngleASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
     - aslcontext.n_rows == sidecar.FlipAngle.size
 
@@ -94,7 +94,7 @@ ASLPostLabelingDelayNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "seq"
+    - type(sidecar.PostLabelingDelay) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
@@ -117,7 +117,7 @@ ASLPostLabelingDelayASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "seq"
+    - type(sidecar.PostLabelingDelay) == "array"
     checks:
     - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
@@ -142,7 +142,7 @@ ASLLabelingDurationASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
     - aslcontext.n_rows == sidecar.LabelingDuration.size
 
@@ -162,7 +162,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "seq"
+    - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
     - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
@@ -179,7 +179,7 @@ ASLBackgroundSuppressionNumberPulses:
     - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
-    - type(sidecar.BackgroundSuppressionPulseTime) == "seq"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -211,7 +211,7 @@ ASLEchoTimeASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "EchoTime"
-    - type(sidecar.EchoTime) == "seq"
+    - type(sidecar.EchoTime) == "array"
     checks:
     - aslcontext.n_rows == sidecar.EchoTime.size
 

From 4e9b98077c695e902b620dc08d9128419eac2093 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:35:29 -0400
Subject: [PATCH 308/347] Revert extra change.

---
 src/schema/rules/sidecars/eeg.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 224558cc06..4b1902bd23 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -89,7 +89,7 @@ EEGCoordsystemGeneral:
         IntendedFor:
             level: OPTIONAL
             addendum: |
-                This identifies the MRI or CT scan associations with the electrodes,
+                This identifies the MRI or CT scan associated with the electrodes,
                 landmarks, and fiducials.
 
 # Fields relating to the EEG electrode positions

From eb58a91f66a79311e60856f33f35393f83d7023d Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 10:51:13 -0700
Subject: [PATCH 309/347] generate common_derivatives datatypes from all other
 existing datatypes. Add anatomical volumetric, mask and segmentation
 derivatives

---
 .../rules/datatypes/common_derivatives.yaml   | 413 ++++++++++++++++++
 src/schema/rules/datatypes/derivatives.yaml   | 158 ++++++-
 2 files changed, 558 insertions(+), 13 deletions(-)
 create mode 100644 src/schema/rules/datatypes/common_derivatives.yaml

diff --git a/src/schema/rules/datatypes/common_derivatives.yaml b/src/schema/rules/datatypes/common_derivatives.yaml
new file mode 100644
index 0000000000..48c3744f8d
--- /dev/null
+++ b/src/schema/rules/datatypes/common_derivatives.yaml
@@ -0,0 +1,413 @@
+---
+anat_nonparametric_common:
+  $ref: schema.rules.datatypes.anat.nonparametric
+  entities:
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_parametric_common:
+  $ref: schema.rules.datatypes.anat.parametric
+  entities:
+    $ref: schema.rules.datatypes.anat.parametric.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_defacemask_common:
+  $ref: schema.rules.datatypes.anat.defacemask
+  entities:
+    $ref: schema.rules.datatypes.anat.defacemask.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_multiecho_common:
+  $ref: schema.rules.datatypes.anat.multiecho
+  entities:
+    $ref: schema.rules.datatypes.anat.multiecho.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_multiflip_common:
+  $ref: schema.rules.datatypes.anat.multiflip
+  entities:
+    $ref: schema.rules.datatypes.anat.multiflip.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_multiinversion_common:
+  $ref: schema.rules.datatypes.anat.multiinversion
+  entities:
+    $ref: schema.rules.datatypes.anat.multiinversion.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_mp2rage_common:
+  $ref: schema.rules.datatypes.anat.mp2rage
+  entities:
+    $ref: schema.rules.datatypes.anat.mp2rage.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_vfamt_common:
+  $ref: schema.rules.datatypes.anat.vfamt
+  entities:
+    $ref: schema.rules.datatypes.anat.vfamt.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+anat_mtr_common:
+  $ref: schema.rules.datatypes.anat.mtr
+  entities:
+    $ref: schema.rules.datatypes.anat.mtr.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+beh_timeseries_common:
+  $ref: schema.rules.datatypes.beh.timeseries
+  entities:
+    $ref: schema.rules.datatypes.beh.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+beh_noncontinuous_common:
+  $ref: schema.rules.datatypes.beh.noncontinuous
+  entities:
+    $ref: schema.rules.datatypes.beh.noncontinuous.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+dwi_dwi_common:
+  $ref: schema.rules.datatypes.dwi.dwi
+  entities:
+    $ref: schema.rules.datatypes.dwi.dwi.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+dwi_sbref_common:
+  $ref: schema.rules.datatypes.dwi.sbref
+  entities:
+    $ref: schema.rules.datatypes.dwi.sbref.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+dwi_timeseries_common:
+  $ref: schema.rules.datatypes.dwi.timeseries
+  entities:
+    $ref: schema.rules.datatypes.dwi.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_eeg_common:
+  $ref: schema.rules.datatypes.eeg.eeg
+  entities:
+    $ref: schema.rules.datatypes.eeg.eeg.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_channels_common:
+  $ref: schema.rules.datatypes.eeg.channels
+  entities:
+    $ref: schema.rules.datatypes.eeg.channels.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_coordsystem_common:
+  $ref: schema.rules.datatypes.eeg.coordsystem
+  entities:
+    $ref: schema.rules.datatypes.eeg.coordsystem.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_electrodes_common:
+  $ref: schema.rules.datatypes.eeg.electrodes
+  entities:
+    $ref: schema.rules.datatypes.eeg.electrodes.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_events_common:
+  $ref: schema.rules.datatypes.eeg.events
+  entities:
+    $ref: schema.rules.datatypes.eeg.events.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_photo_common:
+  $ref: schema.rules.datatypes.eeg.photo
+  entities:
+    $ref: schema.rules.datatypes.eeg.photo.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+eeg_timeseries_common:
+  $ref: schema.rules.datatypes.eeg.timeseries
+  entities:
+    $ref: schema.rules.datatypes.eeg.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_fieldmaps_common:
+  $ref: schema.rules.datatypes.fmap.fieldmaps
+  entities:
+    $ref: schema.rules.datatypes.fmap.fieldmaps.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_pepolar_common:
+  $ref: schema.rules.datatypes.fmap.pepolar
+  entities:
+    $ref: schema.rules.datatypes.fmap.pepolar.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_TB1DAM_common:
+  $ref: schema.rules.datatypes.fmap.TB1DAM
+  entities:
+    $ref: schema.rules.datatypes.fmap.TB1DAM.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_TB1EPI_common:
+  $ref: schema.rules.datatypes.fmap.TB1EPI
+  entities:
+    $ref: schema.rules.datatypes.fmap.TB1EPI.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_RFFieldMaps_common:
+  $ref: schema.rules.datatypes.fmap.RFFieldMaps
+  entities:
+    $ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_TB1SRGE_common:
+  $ref: schema.rules.datatypes.fmap.TB1SRGE
+  entities:
+    $ref: schema.rules.datatypes.fmap.TB1SRGE.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+fmap_parametric_common:
+  $ref: schema.rules.datatypes.fmap.parametric
+  entities:
+    $ref: schema.rules.datatypes.fmap.parametric.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+func_func_common:
+  $ref: schema.rules.datatypes.func.func
+  entities:
+    $ref: schema.rules.datatypes.func.func.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+func_phase_common:
+  $ref: schema.rules.datatypes.func.phase
+  entities:
+    $ref: schema.rules.datatypes.func.phase.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+func_events_common:
+  $ref: schema.rules.datatypes.func.events
+  entities:
+    $ref: schema.rules.datatypes.func.events.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+func_timeseries_common:
+  $ref: schema.rules.datatypes.func.timeseries
+  entities:
+    $ref: schema.rules.datatypes.func.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_ieeg_common:
+  $ref: schema.rules.datatypes.ieeg.ieeg
+  entities:
+    $ref: schema.rules.datatypes.ieeg.ieeg.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_channels_common:
+  $ref: schema.rules.datatypes.ieeg.channels
+  entities:
+    $ref: schema.rules.datatypes.ieeg.channels.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_coordsystem_common:
+  $ref: schema.rules.datatypes.ieeg.coordsystem
+  entities:
+    $ref: schema.rules.datatypes.ieeg.coordsystem.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_electrodes_common:
+  $ref: schema.rules.datatypes.ieeg.electrodes
+  entities:
+    $ref: schema.rules.datatypes.ieeg.electrodes.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_events_common:
+  $ref: schema.rules.datatypes.ieeg.events
+  entities:
+    $ref: schema.rules.datatypes.ieeg.events.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_photo_common:
+  $ref: schema.rules.datatypes.ieeg.photo
+  entities:
+    $ref: schema.rules.datatypes.ieeg.photo.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+ieeg_timeseries_common:
+  $ref: schema.rules.datatypes.ieeg.timeseries
+  entities:
+    $ref: schema.rules.datatypes.ieeg.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_meg_common:
+  $ref: schema.rules.datatypes.meg.meg
+  entities:
+    $ref: schema.rules.datatypes.meg.meg.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_calibration_common:
+  $ref: schema.rules.datatypes.meg.calibration
+  entities:
+    $ref: schema.rules.datatypes.meg.calibration.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_crosstalk_common:
+  $ref: schema.rules.datatypes.meg.crosstalk
+  entities:
+    $ref: schema.rules.datatypes.meg.crosstalk.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_headshape_common:
+  $ref: schema.rules.datatypes.meg.headshape
+  entities:
+    $ref: schema.rules.datatypes.meg.headshape.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_markers_common:
+  $ref: schema.rules.datatypes.meg.markers
+  entities:
+    $ref: schema.rules.datatypes.meg.markers.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_coordsystem_common:
+  $ref: schema.rules.datatypes.meg.coordsystem
+  entities:
+    $ref: schema.rules.datatypes.meg.coordsystem.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_channels_common:
+  $ref: schema.rules.datatypes.meg.channels
+  entities:
+    $ref: schema.rules.datatypes.meg.channels.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_events_common:
+  $ref: schema.rules.datatypes.meg.events
+  entities:
+    $ref: schema.rules.datatypes.meg.events.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_photo_common:
+  $ref: schema.rules.datatypes.meg.photo
+  entities:
+    $ref: schema.rules.datatypes.meg.photo.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+meg_timeseries_common:
+  $ref: schema.rules.datatypes.meg.timeseries
+  entities:
+    $ref: schema.rules.datatypes.meg.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+micr_microscopy_common:
+  $ref: schema.rules.datatypes.micr.microscopy
+  entities:
+    $ref: schema.rules.datatypes.micr.microscopy.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+micr_photo_common:
+  $ref: schema.rules.datatypes.micr.photo
+  entities:
+    $ref: schema.rules.datatypes.micr.photo.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+perf_asl_common:
+  $ref: schema.rules.datatypes.perf.asl
+  entities:
+    $ref: schema.rules.datatypes.perf.asl.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+perf_aslcontext_common:
+  $ref: schema.rules.datatypes.perf.aslcontext
+  entities:
+    $ref: schema.rules.datatypes.perf.aslcontext.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+perf_asllabeling_common:
+  $ref: schema.rules.datatypes.perf.asllabeling
+  entities:
+    $ref: schema.rules.datatypes.perf.asllabeling.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+perf_timeseries_common:
+  $ref: schema.rules.datatypes.perf.timeseries
+  entities:
+    $ref: schema.rules.datatypes.perf.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+pet_pet_common:
+  $ref: schema.rules.datatypes.pet.pet
+  entities:
+    $ref: schema.rules.datatypes.pet.pet.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+pet_blood_common:
+  $ref: schema.rules.datatypes.pet.blood
+  entities:
+    $ref: schema.rules.datatypes.pet.blood.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+pet_events_common:
+  $ref: schema.rules.datatypes.pet.events
+  entities:
+    $ref: schema.rules.datatypes.pet.events.entities
+    space: OPTIONAL
+    desc: OPTIONAL
+
+pet_timeseries_common:
+  $ref: schema.rules.datatypes.pet.timeseries
+  entities:
+    $ref: schema.rules.datatypes.pet.timeseries.entities
+    space: OPTIONAL
+    desc: OPTIONAL
diff --git a/src/schema/rules/datatypes/derivatives.yaml b/src/schema/rules/datatypes/derivatives.yaml
index a79ce0468e..3e47493a13 100644
--- a/src/schema/rules/datatypes/derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives.yaml
@@ -1,36 +1,168 @@
 ---
-- name: "derivatives_common"
-  # all datatypes
-  additional_entities:
+anat_parametric_volumetric:
+  $ref: schema.rules.datatypes.anat.parametric
+  entities:
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    desc: OPTIONAL
+
+anat_nonparametric_volumetric:
+  $ref: schema.rules.datatypes.anat.nonparametric
+  entities:
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    desc: OPTIONAL
+
+dwi_volumetric:
+  $ref: schema.rules.datatypes.dwi.dwi
+  entities:
+    $ref: schema.rules.datatypes.dwi.dwi.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
     desc: OPTIONAL
 
-- name: "volumetric_preproc"
-  # nii, niigz in pet and mri
-  additional_entities:
+func_volumetric:
+  $ref: schema.rules.datatypes.func.func
+  entities:
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     res: OPTIONAL
     den: OPTIONAL
     desc: OPTIONAL
 
-- name: "mask"
-  # anat, func, dwi
+anat_parametric_mask:
   suffixes:
-  - desg
+  - mask
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.anat.parametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+
+anat_nonparametric_mask:
+  suffixes:
+  - mask
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+
+dwi_mask:
+  suffixes:
+  - mask
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.dwi.dwi.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+
+func_mask:
+  suffixes:
+  - mask
   extensions:
-  additional_entities:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.func.func.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+
+anat_parametric_discrete_segmentation:
+  suffixes:
+  - mask
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     res: OPTIONAL
     den: OPTIONAL
     label: OPTIONAL
     desc: OPTIONAL
-- name: "discreate_segmentation"
-  # anat, func, dwi
+
+anat_nonparametric_discrete_segmentation:
+  suffixes:
+  - mask
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+    label: OPTIONAL
+    desc: OPTIONAL
+
+func_discrete_segmentation:
   suffixes:
   - desg
   extensions:
   - .nii.gz
-  additional_entities:
+  entities:
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     res: OPTIONAL
     den: OPTIONAL
+
+dwi_discrete_segmentation:
+  suffixes:
+  - desg
+  extensions:
+  - .nii.gz
+  entities:
+    $ref: schema.rules.datatypes.dwi.dwi.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+
+anat_parametric_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.derivatives.anat_parametric_discrete_segmentation
+  suffixes:
+  - probseg
+  entities:
+    $ref: schema.rules.datatypes.derivatives.anat_parametric_discrete_segmentation.entities
+    label: OPTIONAL
+
+anat_nonparametric_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.derivatives.anat_nonparametric_discrete_segmentation
+  suffixes:
+  - probseg
+  entities:
+    $ref: schema.rules.datatypes.derivatives.anat_nonparametric_discrete_segmentation.entities
+    label: OPTIONAL
+
+func_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.derivatives.func_discrete_segmentation
+  suffixes:
+  - probseg
+  entities:
+    $ref: schema.rules.datatypes.derivatives.func_discrete_segmentation.entities
+    label: OPTIONAL
+
+dwi_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.derivatives.dwi_discrete_segmentation
+  suffixes:
+  - probseg
+  entities:
+    $ref: schema.rules.datatypes.derivatives.dwi_discrete_segmentation.entities
+    label: OPTIONAL

From 75153bda268e189d20f77fc0fde008c656bf8f7c Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 10:54:47 -0700
Subject: [PATCH 310/347] yamllint fix for  sidecars common_derivatives

---
 src/schema/rules/sidecars/common_derivative.yaml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
index 503662ad2c..6c50981c06 100644
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ b/src/schema/rules/sidecars/common_derivative.yaml
@@ -37,7 +37,7 @@ MaskDerivatives:
     fields:
         RawSources: REQUIRED
         Type: RECOMMENDED
-        Atlas: OPTIONAL 
+        Atlas: OPTIONAL
         Resolution: OPTIONAL
         Density: OPTIONAL
 
@@ -53,9 +53,9 @@ SegmentationCommon:
     selectors:
     - dataset.DatasetType == "derivative"
     - suffix in ["dseg", "probseg"]
-    fields: 
+    fields:
         Type: RECOMMENDED
-        Atlas: OPTIONAL 
+        Atlas: OPTIONAL
         Resolution: OPTIONAL
         Density: OPTIONAL
 
@@ -83,4 +83,3 @@ ImageDerivativeDenEntity:
     - entities contains "den"
     fields:
         Density: REQUIRED
-

From 08b0467b2960980927b8e09c50eb721fa298382d Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 10:51:48 -0700
Subject: [PATCH 311/347] Latin

---
 src/schema/meta/context.yaml                  | 4 ++--
 src/schema/rules/sidecars/asl_validation.yaml | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 3defdfcb36..bea9de4a90 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -90,7 +90,7 @@ context:
             description: "Entities parsed from the current filename"
             type: object
         datatype:
-            description: "Datatype of current file, e.g., anat"
+            description: "Datatype of current file, for examples, anat"
             type: string
         suffix:
             description: "Suffix of current file"
@@ -99,7 +99,7 @@ context:
             description: "Extension of current file including initial dot"
             type: string
         modality:
-            description: "Modality of current file, e.g., MRI"
+            description: "Modality of current file, for examples, MRI"
             type: string
 
         sidecar:
diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 392b9bf7db..fec43aa19e 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -86,8 +86,8 @@ ASLPostLabelingDelayNiftiLength:
         labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
         (for 3D acquisition) or first slice (for 2D acquisition).
         Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a
+        In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
+        in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a
         zero.
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
@@ -108,9 +108,9 @@ ASLPostLabelingDelayASLContextLength:
         middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
         the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
         Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
         in the acquisition order.
-        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a zero.
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:

From 318e5add889f5bc292fe9565eca295097bebba0d Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 11:00:27 -0700
Subject: [PATCH 312/347] Update src/schema/rules/datatypes/derivatives.yaml

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 src/schema/rules/datatypes/derivatives.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/datatypes/derivatives.yaml b/src/schema/rules/datatypes/derivatives.yaml
index 3e47493a13..b5821e9e66 100644
--- a/src/schema/rules/datatypes/derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives.yaml
@@ -126,7 +126,7 @@ func_discrete_segmentation:
 
 dwi_discrete_segmentation:
   suffixes:
-  - desg
+  - dseg
   extensions:
   - .nii.gz
   entities:

From 1f6e4d284d27d339f7ac5af427d0fcc188bae07e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 11:09:30 -0700
Subject: [PATCH 313/347] STY: fix YAML lint

---
 src/schema/rules/sidecars/asl_validation.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index fec43aa19e..309b6a2cf9 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -87,8 +87,8 @@ ASLPostLabelingDelayNiftiLength:
         (for 3D acquisition) or first slice (for 2D acquisition).
         Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
         In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
-        in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a
-        zero.
+        in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is
+        indicated by a zero.
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:

From 2eae61c24332fc3fd645ff7ab1d1eee132f41879 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 13 Apr 2022 09:35:36 -0700
Subject: [PATCH 314/347] SCHEMA: Encode requirement levels for
 dataset_description and genetic_info

---
 src/schema/rules/dataset_metadata.yaml | 40 ++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 src/schema/rules/dataset_metadata.yaml

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
new file mode 100644
index 0000000000..9e0c8fd28c
--- /dev/null
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -0,0 +1,40 @@
+dataset_description:
+    path: /dataset_description.json
+    fields:
+        Name: REQUIRED
+        BIDSVersion: REQUIRED
+        DatasetType: RECOMMENDED
+        License: RECOMMENDED
+        Authors: OPTIONAL
+        Acknowledgements: OPTIONAL
+        HowToAcknowledge: OPTIONAL
+        Funding: OPTIONAL
+        EthicsApprovals: OPTIONAL
+        ReferencesAndLinks: OPTIONAL
+        DatasetDOI: OPTIONAL
+        GeneratedBy: RECOMMENDED
+        SourceDatasets: RECOMMENDED
+
+derivative_description:
+    path: /dataset_description.json
+    selectors:
+        dataset.DatasetType == "derivative"
+    fields:
+        GeneratedBy: REQUIRED
+
+dataset_description_with_genetics:
+    path: /dataset_description.json
+    selectors:
+        dataset.genetic_info
+    fields:
+        Genetics: REQUIRED
+
+genetic_info:
+    path: /genetic_info.json
+    fields:
+        GeneticLevel: REQUIRED
+        SampleOrigin: REQUIRED
+        AnalyticalApproach: OPTIONAL
+        TissueOrigin: OPTIONAL
+        BrainLocation: OPTIONAL
+        CellType: OPTIONAL

From a79d5dbdb422642211d6fc6c9c844eb9c0f45b51 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 13 Apr 2022 09:47:47 -0700
Subject: [PATCH 315/347] WIP: Example of nested structures

---
 src/schema/rules/dataset_metadata.yaml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 9e0c8fd28c..c04cc54768 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -13,6 +13,14 @@ dataset_description:
         ReferencesAndLinks: OPTIONAL
         DatasetDOI: OPTIONAL
         GeneratedBy: RECOMMENDED
+        GeneratedBy[].Name: REQUIRED
+        GeneratedBy[].Version: RECOMMENDED
+        GeneratedBy[].Description: OPTIONAL
+        GeneratedBy[].CodeURL: OPTIONAL
+        GeneratedBy[].Container: OPTIONAL
+        GeneratedBy[].Container.Type: RECOMMENDED
+        GeneratedBy[].Container.Tag: RECOMMENDED
+        GeneratedBy[].Container.URI: RECOMMENDED
         SourceDatasets: RECOMMENDED
 
 derivative_description:
@@ -28,6 +36,9 @@ dataset_description_with_genetics:
         dataset.genetic_info
     fields:
         Genetics: REQUIRED
+        Genetics.Dataset: REQUIRED
+        Genetics.Database: OPTIONAL
+        Genetics.Descriptors: OPTIONAL
 
 genetic_info:
     path: /genetic_info.json

From 9684bbf31327ae15d6cb5ac8e1ee9492f9188b80 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 13 Apr 2022 10:03:27 -0700
Subject: [PATCH 316/347] Make path a selector

---
 src/schema/rules/dataset_metadata.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index c04cc54768..1d7a8dbb72 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -1,5 +1,6 @@
 dataset_description:
-    path: /dataset_description.json
+    selectors:
+    - path: /dataset_description.json
     fields:
         Name: REQUIRED
         BIDSVersion: REQUIRED

From d8facfe6f9c58547b19182b18792d1958423e7ad Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 07:25:46 -0700
Subject: [PATCH 317/347] Update selectors to fit context schema

---
 src/schema/rules/dataset_metadata.yaml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 1d7a8dbb72..868ded8e8f 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -1,6 +1,6 @@
 dataset_description:
     selectors:
-    - path: /dataset_description.json
+    - path == /dataset_description.json
     fields:
         Name: REQUIRED
         BIDSVersion: REQUIRED
@@ -25,16 +25,16 @@ dataset_description:
         SourceDatasets: RECOMMENDED
 
 derivative_description:
-    path: /dataset_description.json
     selectors:
-        dataset.DatasetType == "derivative"
+    - path == /dataset_description.json
+    - dataset.dataset_description.DatasetType == "derivative"
     fields:
         GeneratedBy: REQUIRED
 
 dataset_description_with_genetics:
-    path: /dataset_description.json
     selectors:
-        dataset.genetic_info
+    - path == /dataset_description.json
+    - dataset.files contains "/genetic_info.json"
     fields:
         Genetics: REQUIRED
         Genetics.Dataset: REQUIRED
@@ -42,7 +42,8 @@ dataset_description_with_genetics:
         Genetics.Descriptors: OPTIONAL
 
 genetic_info:
-    path: /genetic_info.json
+    selectors:
+    - path == /genetic_info.json
     fields:
         GeneticLevel: REQUIRED
         SampleOrigin: REQUIRED

From 93ebdbe01819721c1c44e048f7b88632c3bdd5dd Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 10:18:45 -0700
Subject: [PATCH 318/347] Update selectors to match current context object

---
 src/schema/rules/dataset_metadata.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 868ded8e8f..fb1878845b 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -1,6 +1,6 @@
 dataset_description:
     selectors:
-    - path == /dataset_description.json
+    - path == "/dataset_description.json"
     fields:
         Name: REQUIRED
         BIDSVersion: REQUIRED
@@ -26,14 +26,14 @@ dataset_description:
 
 derivative_description:
     selectors:
-    - path == /dataset_description.json
-    - dataset.dataset_description.DatasetType == "derivative"
+    - path == "/dataset_description.json"
+    - json.DatasetType == "derivative"
     fields:
         GeneratedBy: REQUIRED
 
 dataset_description_with_genetics:
     selectors:
-    - path == /dataset_description.json
+    - path == "/dataset_description.json"
     - dataset.files contains "/genetic_info.json"
     fields:
         Genetics: REQUIRED
@@ -43,7 +43,7 @@ dataset_description_with_genetics:
 
 genetic_info:
     selectors:
-    - path == /genetic_info.json
+    - path == "/genetic_info.json"
     fields:
         GeneticLevel: REQUIRED
         SampleOrigin: REQUIRED

From 49ee3fd91191992ecc9733dfa0839053dae16131 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 14 Apr 2022 10:19:23 -0700
Subject: [PATCH 319/347] Implement gh-1068

---
 src/schema/rules/dataset_metadata.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index fb1878845b..8212279a15 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -6,7 +6,7 @@ dataset_description:
         BIDSVersion: REQUIRED
         DatasetType: RECOMMENDED
         License: RECOMMENDED
-        Authors: OPTIONAL
+        Authors: RECOMMENDED
         Acknowledgements: OPTIONAL
         HowToAcknowledge: OPTIONAL
         Funding: OPTIONAL

From d96fed41ab71d40b56bfa150235d0ecde407cfab Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 10:17:25 -0700
Subject: [PATCH 320/347] STY: indent 2

---
 src/schema/rules/dataset_metadata.yaml | 92 +++++++++++++-------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 8212279a15..4b69e5643e 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -1,53 +1,53 @@
 dataset_description:
-    selectors:
-    - path == "/dataset_description.json"
-    fields:
-        Name: REQUIRED
-        BIDSVersion: REQUIRED
-        DatasetType: RECOMMENDED
-        License: RECOMMENDED
-        Authors: RECOMMENDED
-        Acknowledgements: OPTIONAL
-        HowToAcknowledge: OPTIONAL
-        Funding: OPTIONAL
-        EthicsApprovals: OPTIONAL
-        ReferencesAndLinks: OPTIONAL
-        DatasetDOI: OPTIONAL
-        GeneratedBy: RECOMMENDED
-        GeneratedBy[].Name: REQUIRED
-        GeneratedBy[].Version: RECOMMENDED
-        GeneratedBy[].Description: OPTIONAL
-        GeneratedBy[].CodeURL: OPTIONAL
-        GeneratedBy[].Container: OPTIONAL
-        GeneratedBy[].Container.Type: RECOMMENDED
-        GeneratedBy[].Container.Tag: RECOMMENDED
-        GeneratedBy[].Container.URI: RECOMMENDED
-        SourceDatasets: RECOMMENDED
+  selectors:
+  - path == "/dataset_description.json"
+  fields:
+    Name: REQUIRED
+    BIDSVersion: REQUIRED
+    DatasetType: RECOMMENDED
+    License: RECOMMENDED
+    Authors: RECOMMENDED
+    Acknowledgements: OPTIONAL
+    HowToAcknowledge: OPTIONAL
+    Funding: OPTIONAL
+    EthicsApprovals: OPTIONAL
+    ReferencesAndLinks: OPTIONAL
+    DatasetDOI: OPTIONAL
+    GeneratedBy: RECOMMENDED
+    GeneratedBy[].Name: REQUIRED
+    GeneratedBy[].Version: RECOMMENDED
+    GeneratedBy[].Description: OPTIONAL
+    GeneratedBy[].CodeURL: OPTIONAL
+    GeneratedBy[].Container: OPTIONAL
+    GeneratedBy[].Container.Type: RECOMMENDED
+    GeneratedBy[].Container.Tag: RECOMMENDED
+    GeneratedBy[].Container.URI: RECOMMENDED
+    SourceDatasets: RECOMMENDED
 
 derivative_description:
-    selectors:
-    - path == "/dataset_description.json"
-    - json.DatasetType == "derivative"
-    fields:
-        GeneratedBy: REQUIRED
+  selectors:
+  - path == "/dataset_description.json"
+  - json.DatasetType == "derivative"
+  fields:
+    GeneratedBy: REQUIRED
 
 dataset_description_with_genetics:
-    selectors:
-    - path == "/dataset_description.json"
-    - dataset.files contains "/genetic_info.json"
-    fields:
-        Genetics: REQUIRED
-        Genetics.Dataset: REQUIRED
-        Genetics.Database: OPTIONAL
-        Genetics.Descriptors: OPTIONAL
+  selectors:
+  - path == "/dataset_description.json"
+  - dataset.files contains "/genetic_info.json"
+  fields:
+    Genetics: REQUIRED
+    Genetics.Dataset: REQUIRED
+    Genetics.Database: OPTIONAL
+    Genetics.Descriptors: OPTIONAL
 
 genetic_info:
-    selectors:
-    - path == "/genetic_info.json"
-    fields:
-        GeneticLevel: REQUIRED
-        SampleOrigin: REQUIRED
-        AnalyticalApproach: OPTIONAL
-        TissueOrigin: OPTIONAL
-        BrainLocation: OPTIONAL
-        CellType: OPTIONAL
+  selectors:
+  - path == "/genetic_info.json"
+  fields:
+    GeneticLevel: REQUIRED
+    SampleOrigin: REQUIRED
+    AnalyticalApproach: OPTIONAL
+    TissueOrigin: OPTIONAL
+    BrainLocation: OPTIONAL
+    CellType: OPTIONAL

From 1461c52a35b38779406d4d6d8ca2f7ae7631daba Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 10:19:16 -0700
Subject: [PATCH 321/347] Tag issues 113 and 128

---
 src/schema/rules/dataset_metadata.yaml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 4b69e5643e..cc3ef04575 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -6,7 +6,14 @@ dataset_description:
     BIDSVersion: REQUIRED
     DatasetType: RECOMMENDED
     License: RECOMMENDED
-    Authors: RECOMMENDED
+    Authors:
+      level: RECOMMENDED
+      issue:
+        name: NO_AUTHORS
+        message: |
+          The Authors field of dataset_description.json should contain an array of fields -
+          with one author per field. This was triggered because there are no authors, which
+          will make DOI registration from dataset metadata impossible.
     Acknowledgements: OPTIONAL
     HowToAcknowledge: OPTIONAL
     Funding: OPTIONAL
@@ -38,6 +45,12 @@ dataset_description_with_genetics:
   fields:
     Genetics: REQUIRED
     Genetics.Dataset: REQUIRED
+      level: REQUIRED
+      issue:
+        name: NO_GENETIC_DATABASE
+        message: |
+          A genetic_info.json file is present but no Database field present in Genetics
+          object in dataset_description.json.
     Genetics.Database: OPTIONAL
     Genetics.Descriptors: OPTIONAL
 

From 0b4158aa4b5713586e231dc1a10bd199e9a06923 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 10:31:00 -0700
Subject: [PATCH 322/347] Use curly-bracket syntax

---
 src/schema/rules/dataset_metadata.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index cc3ef04575..3619a6c992 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -26,9 +26,9 @@ dataset_description:
     GeneratedBy[].Description: OPTIONAL
     GeneratedBy[].CodeURL: OPTIONAL
     GeneratedBy[].Container: OPTIONAL
-    GeneratedBy[].Container.Type: RECOMMENDED
-    GeneratedBy[].Container.Tag: RECOMMENDED
-    GeneratedBy[].Container.URI: RECOMMENDED
+    GeneratedBy[].Container{}.Type: RECOMMENDED
+    GeneratedBy[].Container{}.Tag: RECOMMENDED
+    GeneratedBy[].Container{}.URI: RECOMMENDED
     SourceDatasets: RECOMMENDED
 
 derivative_description:
@@ -44,15 +44,15 @@ dataset_description_with_genetics:
   - dataset.files contains "/genetic_info.json"
   fields:
     Genetics: REQUIRED
-    Genetics.Dataset: REQUIRED
+    Genetics{}.Dataset: REQUIRED
       level: REQUIRED
       issue:
         name: NO_GENETIC_DATABASE
         message: |
           A genetic_info.json file is present but no Database field present in Genetics
           object in dataset_description.json.
-    Genetics.Database: OPTIONAL
-    Genetics.Descriptors: OPTIONAL
+    Genetics{}.Database: OPTIONAL
+    Genetics{}.Descriptors: OPTIONAL
 
 genetic_info:
   selectors:

From 8714e1da57b26d013af28aca00fb6e2f5a9e4509 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 11:25:59 -0700
Subject: [PATCH 323/347] ---

---
 src/schema/rules/dataset_metadata.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 3619a6c992..d4b1aef063 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -1,3 +1,4 @@
+---
 dataset_description:
   selectors:
   - path == "/dataset_description.json"

From 4c2af1c858f43e50209c31955611d4d9d2c54a8e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 11:33:03 -0700
Subject: [PATCH 324/347] YAML: syntax error

---
 src/schema/rules/dataset_metadata.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index d4b1aef063..4e9a6e89dc 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -45,7 +45,7 @@ dataset_description_with_genetics:
   - dataset.files contains "/genetic_info.json"
   fields:
     Genetics: REQUIRED
-    Genetics{}.Dataset: REQUIRED
+    Genetics{}.Dataset:
       level: REQUIRED
       issue:
         name: NO_GENETIC_DATABASE

From 5e116de926855f9493e55ba411c439e96e5f973e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 11:46:56 -0700
Subject: [PATCH 325/347] Conform to issue syntax

---
 src/schema/rules/dataset_metadata.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 4e9a6e89dc..4171faf186 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -10,7 +10,7 @@ dataset_description:
     Authors:
       level: RECOMMENDED
       issue:
-        name: NO_AUTHORS
+        code: NO_AUTHORS
         message: |
           The Authors field of dataset_description.json should contain an array of fields -
           with one author per field. This was triggered because there are no authors, which
@@ -48,7 +48,7 @@ dataset_description_with_genetics:
     Genetics{}.Dataset:
       level: REQUIRED
       issue:
-        name: NO_GENETIC_DATABASE
+        code: NO_GENETIC_DATABASE
         message: |
           A genetic_info.json file is present but no Database field present in Genetics
           object in dataset_description.json.

From 109eee98d145c32d9bccb12a1c2a125c64a874f1 Mon Sep 17 00:00:00 2001
From: Eric Earl <eric.earl@nih.gov>
Date: Fri, 15 Apr 2022 13:34:47 -0700
Subject: [PATCH 326/347] Conform schema/rules for sidecars and tabular_data

Did my best to conform all these rules to the sprint standard decisions.
---
 src/schema/rules/sidecars/asl.yaml            | 144 +++++-----
 src/schema/rules/sidecars/asl_validation.yaml | 269 ++++++++++--------
 src/schema/rules/sidecars/beh.yaml            |  16 +-
 src/schema/rules/sidecars/continuous.yaml     |  16 +-
 src/schema/rules/sidecars/dwi.yaml            |  12 +-
 src/schema/rules/sidecars/eeg.yaml            | 110 +++----
 src/schema/rules/sidecars/entities.yaml       |  26 +-
 .../rules/sidecars/events_validation.yaml     |  13 +-
 src/schema/rules/sidecars/fmap.yaml           |  22 +-
 .../rules/sidecars/fmap_validation.yaml       |  18 +-
 src/schema/rules/sidecars/func.yaml           |  66 ++---
 src/schema/rules/sidecars/ieeg.yaml           |  95 ++++---
 src/schema/rules/sidecars/meg.yaml            | 149 +++++-----
 src/schema/rules/sidecars/micr.yaml           |  70 ++---
 src/schema/rules/sidecars/mri.yaml            | 184 ++++++------
 src/schema/rules/sidecars/pet.yaml            | 160 +++++------
 src/schema/rules/tabular_data/eeg.yaml        |  47 +--
 src/schema/rules/tabular_data/ieeg.yaml       |  59 ++--
 src/schema/rules/tabular_data/meg.yaml        |  27 +-
 src/schema/rules/tabular_data/pet.yaml        |  28 +-
 20 files changed, 798 insertions(+), 733 deletions(-)

diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 81c10c6846..2d4aa50065 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -13,28 +13,29 @@ MRIASLTextOnly:
     - datatype == "perf"
     - suffix == "asl"
     fields:
-        MagneticFieldStrength: REQUIRED
-        MRAcquisitionType: REQUIRED
-        EchoTime: REQUIRED
+        MagneticFieldStrength: required
+        MRAcquisitionType: required
+        EchoTime: required
         SliceTiming:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `MRAcquisitionType` is defined as `2D`
-        RepetitionTimePreparation: REQUIRED
+            level: recommended
+            level_addendum: required if `MRAcquisitionType` is defined as `2D`
+        RepetitionTimePreparation: required
         FlipAngle:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `LookLocker` is `true`
+            level: recommended
+            level_addendum: required if `LookLocker` is `true`
 
 MRIASLTextOnlySliceTiming:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "MRAcquisitionType"
     - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming:
-            level: REQUIRED
+            level: required
             issue:
-                name: SLICE_TIMING_NOT_DEFINED_2D_ASL
+                code: SLICE_TIMING_NOT_DEFINED_2D_ASL
                 message: |
                     You should define `SliceTiming` for this file, because `SequenceType` is sets
                     to a 2D sequence. `SliceTiming` is the time at which each slice was
@@ -44,7 +45,7 @@ MRIASLTextOnlySliceTiming:
                     of volume acquisition. The list goes through the slices along the slice
                     axis in the slice encoding dimension (see below). Note that to ensure the
                     proper interpretation of the `SliceTiming` field, it is important to check
-                    if the OPTIONAL `SliceEncodingDirection` exists. In particular, if
+                    if the optional `SliceEncodingDirection` exists. In particular, if
                     `SliceEncodingDirection` is negative, the entries in `SliceTiming` are
                     defined in reverse order with respect to the slice axis, such that the
                     final entry in the `SliceTiming` list is the time of acquisition of slice 0.
@@ -55,12 +56,13 @@ MRIASLTextOnlyFlipAngle:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "LookLocker"
     - sidecar.LookLocker == true
     fields:
         FlipAngle:
-            level: REQUIRED
+            level: required
             issue:
-                name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+                code: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
                     You should define `FlipAngle` for this file, in case of a
                     LookLocker acquisition. `FlipAngle` is the flip angle (FA)
@@ -81,42 +83,43 @@ MRIASLCommonMetadataFields:
     - datatype == "perf"
     - suffix == "asl"
     fields:
-        ArterialSpinLabelingType: REQUIRED
-        PostLabelingDelay: REQUIRED
-        BackgroundSuppression: REQUIRED
-        M0Type: REQUIRED
-        TotalAcquiredPairs: REQUIRED
-        VascularCrushing: RECOMMENDED
-        AcquisitionVoxelSize: RECOMMENDED
+        ArterialSpinLabelingType: required
+        PostLabelingDelay: required
+        BackgroundSuppression: required
+        M0Type: required
+        TotalAcquiredPairs: required
+        VascularCrushing: recommended
+        AcquisitionVoxelSize: recommended
         M0Estimate:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `M0Type` is `Estimate`
+            level: optional
+            level_addendum: required if `M0Type` is `Estimate`
         BackgroundSuppressionNumberPulses:
-            level: OPTIONAL
-            level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
+            level: optional
+            level_addendum: recommended if `BackgroundSuppression` is `true`
         BackgroundSuppressionPulseTime:
-            level: OPTIONAL
-            level_addendum: RECOMMENDED if `BackgroundSuppression` is `true`
+            level: optional
+            level_addendum: recommended if `BackgroundSuppression` is `true`
         VascularCrushingVENC:
-            level: OPTIONAL
-            level_addendum: RECOMMENDED if `VascularCrushing` is `true`
-        LabelingOrientation: RECOMMENDED
-        LabelingDistance: RECOMMENDED
-        LabelingLocationDescription: RECOMMENDED
-        LookLocker: OPTIONAL
-        LabelingEfficiency: OPTIONAL
+            level: optional
+            level_addendum: recommended if `VascularCrushing` is `true`
+        LabelingOrientation: recommended
+        LabelingDistance: recommended
+        LabelingLocationDescription: recommended
+        LookLocker: optional
+        LabelingEfficiency: optional
 
 MRIASLCommonMetadataFieldsM0Type:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "M0Type"
     - sidecar.M0Type == "Estimate"
     fields:
         M0Estimate:
-            level: REQUIRED
+            level: required
             issue:
-                name: M0ESTIMATE_NOT_DEFINED
+                code: M0ESTIMATE_NOT_DEFINED
                 message: |
                     You must define `M0Estimate` for this file, because `M0Type` is set to
                     'Estimate'. `M0Estimate` is a single numerical whole-brain M0 value
@@ -128,82 +131,90 @@ MRIASLCommonMetadataFieldsBackgroundSuppression:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "BackgroundSuppression"
     - sidecar.BackgroundSuppression == true
     fields:
-        BackgroundSuppressionNumberPulses: RECOMMENDED
-        BackgroundSuppressionPulseTime: RECOMMENDED
+        BackgroundSuppressionNumberPulses: recommended
+        BackgroundSuppressionPulseTime: recommended
 
 MRIASLCommonMetadataFieldsVascularCrushing:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "VascularCrushing"
     - sidecar.VascularCrushing == true
     fields:
-        VascularCrushingVENC: RECOMMENDED
+        VascularCrushingVENC: recommended
 
 MRIASLPCASLSpecific:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "ArterialSpinLabelingType"
     - sidecar.ArterialSpinLabelingType in ["CASL", "PCASL"]
     fields:
-        LabelingDuration: REQUIRED
-        LabelingPulseAverageGradient: RECOMMENDED
-        LabelingPulseMaximumGradient: RECOMMENDED
-        LabelingPulseAverageB1: RECOMMENDED
-        LabelingPulseDuration: RECOMMENDED
-        LabelingPulseFlipAngle: RECOMMENDED
-        LabelingPulseInterval: RECOMMENDED
+        LabelingDuration: required
+        LabelingPulseAverageGradient: recommended
+        LabelingPulseMaximumGradient: recommended
+        LabelingPulseAverageB1: recommended
+        LabelingPulseDuration: recommended
+        LabelingPulseFlipAngle: recommended
+        LabelingPulseInterval: recommended
 
 MRIASLPCASLSpecific2:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "ArterialSpinLabelingType"
     - sidecar.ArterialSpinLabelingType == "PCASL"
     fields:
-        PCASLType: RECOMMENDED
+        PCASLType: recommended
 
 MRIASLCASLSpecific:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "ArterialSpinLabelingType"
     - sidecar.ArterialSpinLabelingType == "CASL"
     fields:
-        CASLType: RECOMMENDED
+        CASLType: recommended
 
 MRIASLPASLSpecific:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "ArterialSpinLabelingType"
     - sidecar.ArterialSpinLabelingType == "PASL"
     fields:
-        BolusCutOffFlag: REQUIRED
-        PASLType: RECOMMENDED
-        LabelingSlabThickness: RECOMMENDED
+        BolusCutOffFlag: required
+        PASLType: recommended
+        LabelingSlabThickness: recommended
         BolusCutOffDelayTime:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `BolusCutOffFlag` is `true`
+            level: optional
+            level_addendum: required if `BolusCutOffFlag` is `true`
         BolusCutOffTechnique:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `BolusCutOffFlag` is `true`
+            level: optional
+            level_addendum: required if `BolusCutOffFlag` is `true`
 
 MRIASLPASLSpecificBolusCutOffFlag:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
+    - sidecar contains "ArterialSpinLabelingType"
     - sidecar.ArterialSpinLabelingType == "PASL"
+    - sidecar contains "BolusCutOffFlag"
     - sidecar.BolusCutOffFlag == true
     fields:
         BolusCutOffDelayTime:
-            level: REQUIRED
+            level: required
             issue:
-                name: PASL_BOLUS_CUT_OFF_DELAY_TIME
+                code: PASL_BOLUS_CUT_OFF_DELAY_TIME
                 message: |
                     It is required to define 'BolusCutOffDelayTime' for this file,
                     when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is
@@ -215,9 +226,9 @@ MRIASLPASLSpecificBolusCutOffFlag:
                     bolus cut-off saturation pulses are provided. Based on DICOM Tag
                     0018,925F ASL Bolus Cut-off Delay Time.
         BolusCutOffTechnique:
-            level: REQUIRED
+            level: required
             issue:
-                name: PASL_BOLUS_CUT_OFF_TECHINIQUE
+                code: PASL_BOLUS_CUT_OFF_TECHINIQUE
                 message: |
                     It is required to define `BolusCutOffTechnique` for this file,
                     when `BolusCutOffFlag` is set to `true`. `BolusCutOffTechnique`,
@@ -232,23 +243,24 @@ MRIASLM0ScanTextOnly:
     - datatype == "perf"
     - suffix == "m0scan"
     fields:
-        EchoTime: REQUIRED
-        RepetitionTimePreparation: REQUIRED
+        EchoTime: required
+        RepetitionTimePreparation: required
         FlipAngle:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `LookLocker` is `true`
+            level: recommended
+            level_addendum: required if `LookLocker` is `true`
 
 MRIASLM0ScanTextOnlyFlipAngle:
     selectors:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "m0scan"
+    - sidecar contains "LookLocker"
     - sidecar.LookLocker == true
     fields:
         FlipAngle:
-            level: REQUIRED
+            level: required
             issue:
-                name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+                code: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
                     You should define `FlipAngle` for this file, in case of a LookLocker
                     acquisition. `FlipAngle` is the flip angle (FA) for the acquisition,
@@ -267,7 +279,7 @@ MRIASLM0Scan:
     - suffix == "m0scan"
     fields:
         IntendedFor:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 This is used to refer to the ASL time series for which the `*_m0scan.nii[.gz]` is intended.
-        AcquisitionVoxelSize: RECOMMENDED
+        AcquisitionVoxelSize: recommended
diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 392b9bf7db..1ed38e1d90 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -3,19 +3,20 @@
 
 # 157
 ASLLabelingDurationNiftiLength:
-    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
-    description: |
-        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
-        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
-        specified.
-        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
-        zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
-        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-    level: error
+    issue:
+        code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+        message: |
+            The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
+            'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+            corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+            In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
+            specified.
+            In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+            an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
+            zero.
+            In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+            `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+        level: error
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
@@ -25,11 +26,12 @@ ASLLabelingDurationNiftiLength:
 
 # 165
 ASLContextConsistent:
-    code: ASLCONTEXT_TSV_NOT_CONSISTENT
-    description: |
-        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
-        values in the NIfTI header.
-    level: error
+    issue:
+        code: ASLCONTEXT_TSV_NOT_CONSISTENT
+        message: |
+            The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+            values in the NIfTI header.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -38,16 +40,17 @@ ASLContextConsistent:
 
 # 168
 ASLFlipAngleNiftiLength:
-    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
-    description: |
-        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
-        'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
-        Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
-        The data type number may apply to files from any MRI modality concerned with a single value for this field,
-        or to the files in a file collection where the value of this field is iterated using the flip entity.
-        The data type array provides a value for each volume in a 4D dataset and should only be used when the
-        volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
-    level: error
+    issue:
+        code: FLIP_ANGLE_NOT_MATCHING_NIFTI
+        message: |
+            The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+            'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+            Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+            The data type number may apply to files from any MRI modality concerned with a single value for this field,
+            or to the files in a file collection where the value of this field is iterated using the flip entity.
+            The data type array provides a value for each volume in a 4D dataset and should only be used when the
+            volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+        level: error
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
@@ -57,17 +60,18 @@ ASLFlipAngleNiftiLength:
 
 # 172
 ASLFlipAngleASLContextLength:
-    code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-       The number of values for 'FlipAngle' for this file does not match the number of volumes in the
-       'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-       'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
-       Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
-       The data type number may apply to files from any MRI modality concerned with a single value for this field,
-       or to the files in a file collection where the value of this field is iterated using the flip entity.
-       The data type array provides a value for each volume in a 4D dataset and should only be used when the volume
-       timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
-    level: error
+    issue:
+        code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
+        message: |
+            The number of values for 'FlipAngle' for this file does not match the number of volumes in the
+            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+            Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+            The data type number may apply to files from any MRI modality concerned with a single value for this field,
+            or to the files in a file collection where the value of this field is iterated using the flip entity.
+            The data type array provides a value for each volume in a 4D dataset and should only be used when the volume
+            timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -78,19 +82,20 @@ ASLFlipAngleASLContextLength:
 
 # 173
 ASLPostLabelingDelayNiftiLength:
-    code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
-    description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
-        header.
-        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
-        labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
-        (for 3D acquisition) or first slice (for 2D acquisition).
-        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a
-        zero.
-        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-    level: error
+    issue:
+        code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
+        message: |
+            The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
+            header.
+            'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
+            labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
+            (for 3D acquisition) or first slice (for 2D acquisition).
+            Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+            In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+            in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a
+            zero.
+            Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+        level: error
     selectors:
     - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
@@ -100,19 +105,20 @@ ASLPostLabelingDelayNiftiLength:
 
 # 174
 ASLPostLabelingDelayASLContextLength:
-    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
-        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
-        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
-        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order.
-        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
-        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-    level: error
+    issue:
+        code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
+        message: |
+            The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+            in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+            middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+            the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+            Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+            In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+            in the acquisition order.
+            Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+            Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -123,21 +129,22 @@ ASLPostLabelingDelayASLContextLength:
 
 # 175
 ASLLabelingDurationASLContextLength:
-    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-        The number of values for 'LabelingDuration' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
-        a scalar must be specified.
-        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
-        `LabelingDuration` of zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes
-        specified in `*_aslcontext.tsv`.
-        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-    level: error
+    issue:
+        code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+        message: |
+            The number of values for 'LabelingDuration' for this file does not match the number of volumes
+            in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+            corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+            In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+            a scalar must be specified.
+            In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+            an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+            `LabelingDuration` of zero.
+            In case an array of numbers is provided, its length should be equal to the number of volumes
+            specified in `*_aslcontext.tsv`.
+            Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -148,16 +155,17 @@ ASLLabelingDurationASLContextLength:
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
-    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
-        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
-        The data type number may apply to files from any MRI modality concerned with a single value for this field.
-        The data type array provides a value for each volume in a 4D dataset and should only be used when the
-        volume timing is critical for interpretation of the data, such as in ASL.
-    level: error
+    issue:
+        code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+        message: |
+            The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+            volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+            re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+            The data type number may apply to files from any MRI modality concerned with a single value for this field.
+            The data type array provides a value for each volume in a 4D dataset and should only be used when the
+            volume timing is critical for interpretation of the data, such as in ASL.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -168,13 +176,14 @@ ASLRepetitionTimePreparationASLContextLength:
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
-    code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
-    description: |
-        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
-        'BackgroundSuppressionPulseTime'.
-        'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
-        Note that this excludes any effect of background suppression pulses applied before the labeling.
-    level: warning
+    issue:
+        code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
+        message: |
+            The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
+            'BackgroundSuppressionPulseTime'.
+            'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
+            Note that this excludes any effect of background suppression pulses applied before the labeling.
+        level: warning
     selectors:
     - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
@@ -185,13 +194,14 @@ ASLBackgroundSuppressionNumberPulses:
 
 # 181
 ASLTotalAcquiredVolumesASLContextLength:
-    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
-    description: |
-        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
-        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-    level: warning
+    issue:
+        code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+        message: |
+            The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+            volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        level: warning
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -201,12 +211,13 @@ ASLTotalAcquiredVolumesASLContextLength:
 
 # 196
 ASLEchoTimeASLContextLength:
-    code: ECHO_TIME_NOT_CONSISTENT
-    description: |
-        The number of values for 'EchoTime' for this file does not match number of volumes in the
-        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
-    level: warning
+    issue:
+        code: ECHO_TIME_NOT_CONSISTENT
+        message: |
+            The number of values for 'EchoTime' for this file does not match number of volumes in the
+            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+            'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
+        level: warning
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
@@ -217,43 +228,49 @@ ASLEchoTimeASLContextLength:
 
 # 198
 ASLM0TypeAbsentScan:
-    code: M0Type_SET_INCORRECTLY_TO_ABSENT
-    description: |
-        You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
-        '*_m0scan.json', or defining the 'M0Estimate' field.
-        This is not allowed, please check that this field are filled correctly.
-    level: error
+    issue:
+        code: M0Type_SET_INCORRECTLY_TO_ABSENT
+        message: |
+            You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
+            '*_m0scan.json', or defining the 'M0Estimate' field.
+            This is not allowed, please check that this field are filled correctly.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
     - associations contains "m0scan"
+    - sidecar contains "M0Type"
     checks:
     - sidecar.M0Type != "absent"
 
 # 199
 ASLM0TypeAbsentASLContext:
-    code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
-    description: |
-        You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
-        This is not allowed, please check that this field are filled correctly.
-    level: error
+    issue:
+        code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
+        message: |
+            You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
+            This is not allowed, please check that this field are filled correctly.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
     - aslcontext.volume_type contains "m0scan"
+    - sidecar contains "M0Type"
     checks:
     - sidecar.M0Type != "absent"
 
 # 202
 ASLM0TypeIncorrect:
-    code: M0Type_SET_INCORRECTLY
-    description: |
-        M0Type was not defined correctly.
-        If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
-    level: error
+    issue:
+        code: M0Type_SET_INCORRECTLY
+        message: |
+            M0Type was not defined correctly.
+            If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
+        level: error
     selectors:
     - suffix == "asl"
     - associations contains "aslcontext"
+    - sidecar contains "M0Type"
     - sidecar.M0Type == "separate"
     checks:
     - associations contains "m0scan"
diff --git a/src/schema/rules/sidecars/beh.yaml b/src/schema/rules/sidecars/beh.yaml
index 74052ff92a..dc863f12c4 100644
--- a/src/schema/rules/sidecars/beh.yaml
+++ b/src/schema/rules/sidecars/beh.yaml
@@ -11,11 +11,11 @@ BEHTabularData:
     selectors:
     - suffix in ["beh", "events"]
     fields:
-        TaskName: RECOMMENDED
-        Instructions: RECOMMENDED
-        TaskDescription: RECOMMENDED
-        CogAtlasID: RECOMMENDED
-        CogPOID: RECOMMENDED
-        InstitutionName: RECOMMENDED
-        InstitutionAddress: RECOMMENDED
-        InstitutionalDepartmentName: RECOMMENDED
+        TaskName: recommended
+        Instructions: recommended
+        TaskDescription: recommended
+        CogAtlasID: recommended
+        CogPOID: recommended
+        InstitutionName: recommended
+        InstitutionAddress: recommended
+        InstitutionalDepartmentName: recommended
diff --git a/src/schema/rules/sidecars/continuous.yaml b/src/schema/rules/sidecars/continuous.yaml
index 9325f4daf0..cdfe0e1ef4 100644
--- a/src/schema/rules/sidecars/continuous.yaml
+++ b/src/schema/rules/sidecars/continuous.yaml
@@ -11,16 +11,16 @@ Continuous:
     selectors:
     - suffix in ["physio", "stim"]
     fields:
-        SamplingFrequency: REQUIRED
-        StartTime: REQUIRED
-        Columns: REQUIRED
+        SamplingFrequency: required
+        StartTime: required
+        Columns: required
 
-# Other RECOMMENDED metadata for physiological data
+# Other recommended metadata for physiological data
 Physio:
     selectors:
     - suffix == "physio"
     fields:
-        Manufacturer: RECOMMENDED
-        ManufacturersModelName: RECOMMENDED
-        SoftwareVersions: RECOMMENDED
-        DeviceSerialNumber: RECOMMENDED
+        Manufacturer: recommended
+        ManufacturersModelName: recommended
+        SoftwareVersions: recommended
+        DeviceSerialNumber: recommended
diff --git a/src/schema/rules/sidecars/dwi.yaml b/src/schema/rules/sidecars/dwi.yaml
index aea15ca5e2..0f25d3ee1a 100644
--- a/src/schema/rules/sidecars/dwi.yaml
+++ b/src/schema/rules/sidecars/dwi.yaml
@@ -10,16 +10,16 @@
 # NOTE: I don't think this can be schemafied, since it depends on owner intent.
 MRIDiffusionMultipart:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "dwi"
     fields:
-        MultipartID: REQUIRED
+        MultipartID: required
 
-# Other RECOMMENDED metadata
+# Other recommended metadata
 MRIDiffusionOtherMetadata:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "dwi"
     fields:
-        PhaseEncodingDirection: RECOMMENDED
-        TotalReadoutTime: RECOMMENDED
+        PhaseEncodingDirection: recommended
+        TotalReadoutTime: recommended
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index d1a217e3f2..ec630cfcea 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -14,32 +14,32 @@ EEGGeneric:
     - suffix == "eeg"
     fields:
         TaskName:
-            level: REQUIRED
+            level: required
             description_addendum: |
-                A RECOMMENDED convention is to name resting state task using labels
+                A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
-EEGRecommended:
+EEGrecommended:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
     fields:
-        InstitutionName: RECOMMENDED
-        InstitutionAddress: RECOMMENDED
-        InstitutionalDepartmentName: RECOMMENDED
-        Manufacturer: RECOMMENDED
-        ManufacturersModelName: RECOMMENDED
-        SoftwareVersions: RECOMMENDED
-        TaskDescription: RECOMMENDED
+        InstitutionName: recommended
+        InstitutionAddress: recommended
+        InstitutionalDepartmentName: recommended
+        Manufacturer: recommended
+        ManufacturersModelName: recommended
+        SoftwareVersions: recommended
+        TaskDescription: recommended
         Instructions:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
-        CogAtlasID: RECOMMENDED
-        CogPOID: RECOMMENDED
-        DeviceSerialNumber: RECOMMENDED
+        CogAtlasID: recommended
+        CogPOID: recommended
+        DeviceSerialNumber: recommended
 
 EEGRequired:
     selectors:
@@ -47,37 +47,37 @@ EEGRequired:
     - datatype == "eeg"
     - suffix == "eeg"
     fields:
-        EEGReference: REQUIRED
+        EEGReference: required
         SamplingFrequency:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
-        PowerLineFrequency: REQUIRED
-        SoftwareFilters: REQUIRED
+        PowerLineFrequency: required
+        SoftwareFilters: required
 
-EEGMoreRecommended:
+EEGMorerecommended:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
     fields:
-        CapManufacturer: RECOMMENDED
-        CapManufacturersModelName: RECOMMENDED
-        EEGChannelCount: RECOMMENDED
-        ECGChannelCount: RECOMMENDED
-        EMGChannelCount: RECOMMENDED
-        EOGChannelCount: RECOMMENDED
-        MiscChannelCount: RECOMMENDED
-        TriggerChannelCount: RECOMMENDED
-        RecordingDuration: RECOMMENDED
-        RecordingType: RECOMMENDED
-        EpochLength: RECOMMENDED
-        EEGGround: RECOMMENDED
-        HeadCircumference: RECOMMENDED
-        EEGPlacementScheme: RECOMMENDED
-        HardwareFilters: RECOMMENDED
-        SubjectArtefactDescription: RECOMMENDED
+        CapManufacturer: recommended
+        CapManufacturersModelName: recommended
+        EEGChannelCount: recommended
+        ECGChannelCount: recommended
+        EMGChannelCount: recommended
+        EOGChannelCount: recommended
+        MiscChannelCount: recommended
+        TriggerChannelCount: recommended
+        RecordingDuration: recommended
+        RecordingType: recommended
+        EpochLength: recommended
+        EEGGround: recommended
+        HeadCircumference: recommended
+        EEGPlacementScheme: recommended
+        HardwareFilters: recommended
+        SubjectArtefactDescription: recommended
 
 # General fields
 EEGCoordsystemGeneral:
@@ -87,7 +87,7 @@ EEGCoordsystemGeneral:
     - suffix == "coordsystem"
     fields:
         IntendedFor:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
                 This identifies the MRI or CT scan associated with the electrodes,
                 landmarks, and fiducials.
@@ -99,20 +99,21 @@ EEGCoordsystemPositions:
     - datatype == "eeg"
     - suffix == "coordsystem"
     fields:
-        EEGCoordinateSystem: REQUIRED
-        EEGCoordinateUnits: REQUIRED
+        EEGCoordinateSystem: required
+        EEGCoordinateUnits: required
         EEGCoordinateSystemDescription:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `EEGCoordinateSystem` is `"Other"`
+            level: recommended
+            level_addendum: required if `EEGCoordinateSystem` is `"Other"`
 
 EEGCoordsystemOther:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
+    - sidecar contains "EEGCoordinateSystem"
     - sidecar.EEGCoordinateSystem == "Other"
     fields:
-        EEGCoordinateSystemDescription: REQUIRED
+        EEGCoordinateSystemDescription: required
 
 # Fields relating to the position of fiducials measured during an EEG session/run
 EEGCoordsystemFiducials:
@@ -121,13 +122,13 @@ EEGCoordsystemFiducials:
     - datatype == "eeg"
     - suffix == "coordsystem"
     fields:
-        FiducialsDescription: OPTIONAL
-        FiducialsCoordinates: RECOMMENDED
-        FiducialsCoordinateSystem: RECOMMENDED
-        FiducialsCoordinateUnits: RECOMMENDED
+        FiducialsDescription: optional
+        FiducialsCoordinates: recommended
+        FiducialsCoordinateSystem: recommended
+        FiducialsCoordinateUnits: recommended
         FiducialsCoordinateSystemDescription:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `FiducialsCoordinateSystem` is `"Other"`
+            level: recommended
+            level_addendum: required if `FiducialsCoordinateSystem` is `"Other"`
 
 EEGCoordsystemOtherFiducialCoordinateSystem:
     selectors:
@@ -136,7 +137,7 @@ EEGCoordsystemOtherFiducialCoordinateSystem:
     - suffix == "coordsystem"
     - FiducialsCoordinateSystem == "Other"
     fields:
-        FiducialsCoordinateSystemDescription: REQUIRED
+        FiducialsCoordinateSystemDescription: required
 
 # Fields relating to the position of anatomical landmark measured during an EEG session/run
 EEGCoordsystemLandmark:
@@ -145,20 +146,21 @@ EEGCoordsystemLandmark:
     - datatype == "eeg"
     - suffix == "coordsystem"
     fields:
-        AnatomicalLandmarkCoordinates: RECOMMENDED
+        AnatomicalLandmarkCoordinates: recommended
         AnatomicalLandmarkCoordinateSystem:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Preferably the same as the `EEGCoordinateSystem`.
-        AnatomicalLandmarkCoordinateUnits: RECOMMENDED
+        AnatomicalLandmarkCoordinateUnits: recommended
         AnatomicalLandmarkCoordinateSystemDescription:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `AnatomicalLandmarkCoordinateSystem` is `"Other"`
+            level: recommended
+            level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `"Other"`
 
 EEGCoordsystemAnatomicalLandmarkCoordinateSystemDescription:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
+    - sidecar contains "AnatomicalLandmarkCoordinateSystem"
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
     fields:
-        AnatomicalLandmarkCoordinateSystemDescription: REQUIRED
+        AnatomicalLandmarkCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/entities.yaml b/src/schema/rules/sidecars/entities.yaml
index 3fcc796da6..3147815569 100644
--- a/src/schema/rules/sidecars/entities.yaml
+++ b/src/schema/rules/sidecars/entities.yaml
@@ -13,58 +13,58 @@ EntitiesTaskMetadata:
     selectors:
     - entities contains "task"
     fields:
-        TaskName: RECOMMENDED
+        TaskName: recommended
 
 EntitiesCeMetadata:
     selectors:
     - entities contains "ce"
     fields:
-        ContrastBolusIngredient: OPTIONAL
+        ContrastBolusIngredient: optional
 
 EntitiesTrcMetadata:
     selectors:
     - entities contains "trc"
     fields:
-        TracerName: REQUIRED
+        TracerName: required
 
 EntitiesStainMetadata:
     selectors:
     - entities contains "stain"
     fields:
-        SampleStaining: RECOMMENDED
-        SamplePrimaryAntibodies: RECOMMENDED
-        SampleSecondaryAntibodies: RECOMMENDED
+        SampleStaining: recommended
+        SamplePrimaryAntibodies: recommended
+        SampleSecondaryAntibodies: recommended
 
 EntitiesEchoMetadata:
     selectors:
     - entities contains "echo"
     fields:
-        EchoTime: REQUIRED
+        EchoTime: required
 
 EntitiesFlipMetadata:
     selectors:
     - entities contains "flip"
     fields:
-        FlipAngle: REQUIRED
+        FlipAngle: required
 
 EntitiesInvMetadata:
     selectors:
     - entities contains "inv"
     fields:
-        InversionTime: REQUIRED
+        InversionTime: required
 
 EntitiesMTMetadata:
     selectors:
     - entities contains "mt"
     fields:
-        MTState: REQUIRED
+        MTState: required
 
 EntitiesPartMetadata:
     selectors:
     - entities.part == "phase"
     fields:
         Units:
-            level: REQUIRED
+            level: required
             rules:
             - value in ["rad", "arbitrary"]
 
@@ -72,10 +72,10 @@ EntitiesResMetadata:
     selectors:
     - entities contains "res"
     fields:
-        Resolution: REQUIRED
+        Resolution: required
 
 EntitiesDenMetadata:
     selectors:
     - entities contains "den"
     fields:
-        Density: REQUIRED
+        Density: required
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
index 4e735a38e0..58774358b9 100644
--- a/src/schema/rules/sidecars/events_validation.yaml
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -3,14 +3,15 @@
 
 # 25
 EventsMissing:
-    code: EVENTS_TSV_MISSING
-    description: |
-        Task scans should have a corresponding events.tsv file.
-        If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
-    level: warning  # could be an error with the proper selectors, I think
+    issue:
+        code: EVENTS_TSV_MISSING
+        message: |
+            Task scans should have a corresponding events.tsv file.
+            If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
+        level: warning  # could be an error with the proper selectors, I think
     selectors:
     - entities contains "task"
     - entities.task != "rest"
-    - entities.task not contains "rest"  # Alternative for including the word "rest"
+    - entities.task not(contains "rest")  # Alternative for including the word "rest"
     checks:
     - associations contains "events"
diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
index 48291235be..9d9b7b7b05 100644
--- a/src/schema/rules/sidecars/fmap.yaml
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -12,7 +12,7 @@ MRIFieldmapB0FieldIdentifier:
     - modality == "MRI"
     - datatype == "fmap"
     fields:
-        B0FieldIdentifier: RECOMMENDED
+        B0FieldIdentifier: recommended
 
 MRIFieldmapIntendedFor:
     selectors:
@@ -20,9 +20,9 @@ MRIFieldmapIntendedFor:
     - datatype == "fmap"
     fields:
         IntendedFor:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
-                This field is OPTIONAL, and in case the fieldmaps do not correspond
+                This field is optional, and in case the fieldmaps do not correspond
                 to any particular scans, it does not have to be filled.
 
 # Case 1: Phase-difference map and at least one magnitude image
@@ -32,8 +32,8 @@ MRIFieldmapPhaseDifferencePhasediff:
     - datatype == "fmap"
     - suffix == "phasediff"
     fields:
-        EchoTime1: REQUIRED
-        EchoTime2: REQUIRED
+        EchoTime1: required
+        EchoTime2: required
 
 MRIFieldmapPhaseDifferenceMagnitude1:
     selectors:
@@ -41,7 +41,7 @@ MRIFieldmapPhaseDifferenceMagnitude1:
     - datatype == "fmap"
     - suffix == "magnitude1"
     fields:
-        EchoTime1: REQUIRED
+        EchoTime1: required
 
 MRIFieldmapPhaseDifferenceMagnitude2:
     selectors:
@@ -49,7 +49,7 @@ MRIFieldmapPhaseDifferenceMagnitude2:
     - datatype == "fmap"
     - suffix == "magnitude2"
     fields:
-        EchoTime2: REQUIRED
+        EchoTime2: required
 
 # Case 2: Two phase maps and two magnitude images
 # NOTE: Need to check for presence of related files.
@@ -61,7 +61,7 @@ MRIFieldmapTwoPhase:
     - datatype == "fmap"
     - suffix in ["phase1", "phase2", "magnitude1", "magnitude2"]
     fields:
-        EchoTime__fmap: REQUIRED
+        EchoTime__fmap: required
 
 # Case 3: Direct field mapping
 MRIFieldmapDirectFieldMapping:
@@ -71,7 +71,7 @@ MRIFieldmapDirectFieldMapping:
     - suffix in ["phase", "fieldmap"]
     fields:
         Units:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 Fieldmaps must be in units of Hertz (`"Hz"`),
                 radians per second (`"rad/s"`), or Tesla (`"T"`).
@@ -83,5 +83,5 @@ MRIFieldmapPepolar:
     - datatype == "fmap"
     - suffix == "epi"
     fields:
-        PhaseEncodingDirection: REQUIRED
-        TotalReadoutTime: REQUIRED
+        PhaseEncodingDirection: required
+        TotalReadoutTime: required
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/sidecars/fmap_validation.yaml
index 53c231d89e..b33cf18c90 100644
--- a/src/schema/rules/sidecars/fmap_validation.yaml
+++ b/src/schema/rules/sidecars/fmap_validation.yaml
@@ -3,10 +3,11 @@
 
 # 91
 FmapFieldmapWithoutMagnitude:
-    code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
-    description: |
-        '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
-    level: error
+    issue:
+        code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
+        message: |
+            '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
+        level: error
     selectors:
     - suffix == "fieldmap"
     checks:
@@ -14,10 +15,11 @@ FmapFieldmapWithoutMagnitude:
 
 # 92
 FmapPhasediffWithoutMagnitude:
-    code: MISSING_MAGNITUDE1_FILE
-    description: |
-        Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
-    level: warning
+    issue:
+        code: MISSING_MAGNITUDE1_FILE
+        message: |
+            Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
+        level: warning
     selectors:
     - suffix == "phasediff"
     checks:
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 43bd5f286f..ffdcb45108 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -11,100 +11,100 @@
 # Required fields
 MRIFuncRequired:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     fields:
-        RepetitionTime: REQUIRED
-        VolumeTiming: REQUIRED
+        RepetitionTime: required
+        VolumeTiming: required
         TaskName:
-            level: REQUIRED
+            level: required
             description_addendum: |
-                A RECOMMENDED convention is to name resting state task using labels
+                A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
 # Timing Parameters
 MRIFuncTimingParameters:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     fields:
-        NumberOfVolumesDiscardedByScanner: RECOMMENDED
-        NumberOfVolumesDiscardedByUser: RECOMMENDED
-        DelayTime: RECOMMENDED
+        NumberOfVolumesDiscardedByScanner: recommended
+        NumberOfVolumesDiscardedByUser: recommended
+        DelayTime: recommended
         AcquisitionDuration:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                REQUIRED for sequences that are described with the `VolumeTiming`
+                required for sequences that are described with the `VolumeTiming`
                 field and that do not have the `SliceTiming` field set to allow for
                 accurate calculation of "acquisition time"
             issue:
                 name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
                 message: |
                     The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
-        DelayAfterTrigger: RECOMMENDED
+        DelayAfterTrigger: recommended
 
 # The mutual exclusion table, spread across 5 definitions
-# NOTE: This introduces a PROHIBITED level
+# NOTE: This introduces a prohibited level
 MRIFuncTimingParametersMutualExclusion1:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     - sidecar contains "RepetitionTime"
     fields:
-        AcquisitionDuration: PROHIBITED
-        VolumeTiming: PROHIBITED
+        AcquisitionDuration: prohibited
+        VolumeTiming: prohibited
 
 MRIFuncTimingParametersMutualExclusion2:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     - sidecar contains "SliceTiming"
     - sidecar contains "VolumeTiming"
     fields:
-        RepetitionTime: PROHIBITED
-        DelayTime: PROHIBITED
+        RepetitionTime: prohibited
+        DelayTime: prohibited
 
 MRIFuncTimingParametersMutualExclusion3:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     - sidecar contains "AcquisitionDuration"
     - sidecar contains "VolumeTiming"
     fields:
-        RepetitionTime: PROHIBITED
-        DelayTime: PROHIBITED
+        RepetitionTime: prohibited
+        DelayTime: prohibited
 
 MRIFuncTimingParametersMutualExclusion4:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     - sidecar contains "RepetitionTime"
     - sidecar contains "SliceTiming"
     fields:
-        AcquisitionDuration: PROHIBITED
-        VolumeTiming: PROHIBITED
+        AcquisitionDuration: prohibited
+        VolumeTiming: prohibited
 
 MRIFuncTimingParametersMutualExclusion5:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     - sidecar contains "RepetitionTime"
     - sidecar contains "DelayTime"
     fields:
-        AcquisitionDuration: PROHIBITED
-        VolumeTiming: PROHIBITED
+        AcquisitionDuration: prohibited
+        VolumeTiming: prohibited
 
 # fMRI task information
 MRIFuncTaskInformation:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "func"
     fields:
         Instructions:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
-        TaskDescription: RECOMMENDED
-        CogAtlasID: RECOMMENDED
-        CogPOID: RECOMMENDED
+        TaskDescription: recommended
+        CogAtlasID: recommended
+        CogPOID: recommended
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index 8cc9290d72..9f51287f3b 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -14,34 +14,34 @@ iEEGGeneric:
     - suffix == "ieeg"
     fields:
         TaskName:
-            level: REQUIRED
+            level: required
             description_addendum: |
-                A RECOMMENDED convention is to name resting state task using labels
+                A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
-iEEGRecommended:
+iEEGrecommended:
     selectors:
     - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
     fields:
-        InstitutionName: RECOMMENDED
-        InstitutionAddress: RECOMMENDED
-        InstitutionalDepartmentName: RECOMMENDED
+        InstitutionName: recommended
+        InstitutionAddress: recommended
+        InstitutionalDepartmentName: recommended
         Manufacturer:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: For example, `"TDT"`, `"Blackrock"`.
-        ManufacturersModelName: RECOMMENDED
-        SoftwareVersions: RECOMMENDED
-        TaskDescription: RECOMMENDED
+        ManufacturersModelName: recommended
+        SoftwareVersions: recommended
+        TaskDescription: recommended
         Instructions:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
-        CogAtlasID: RECOMMENDED
-        CogPOID: RECOMMENDED
-        DeviceSerialNumber: RECOMMENDED
+        CogAtlasID: recommended
+        CogPOID: recommended
+        DeviceSerialNumber: recommended
 
 # Specific iEEG fields MUST be present
 iEEGRequired:
@@ -50,14 +50,14 @@ iEEGRequired:
     - datatype == "ieeg"
     - suffix == "ieeg"
     fields:
-        iEEGReference: REQUIRED
+        iEEGReference: required
         SamplingFrequency:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
-        PowerLineFrequency: REQUIRED
-        SoftwareFilters": REQUIRED
+        PowerLineFrequency: required
+        SoftwareFilters": required
 
 # Specific iEEG fields SHOULD be present
 iEEGMoreRecommended:
@@ -66,25 +66,25 @@ iEEGMoreRecommended:
     - datatype == "ieeg"
     - suffix == "ieeg"
     fields:
-        DCOffsetCorrection: DEPRECATED
-        HardwareFilters: RECOMMENDED
-        ElectrodeManufacturer: RECOMMENDED
-        ElectrodeManufacturersModelName: RECOMMENDED
-        ECOGChannelCount: RECOMMENDED
-        SEEGChannelCount: RECOMMENDED
-        EEGChannelCount: RECOMMENDED
-        EOGChannelCount: RECOMMENDED
-        ECGChannelCount: RECOMMENDED
-        EMGChannelCount: RECOMMENDED
-        MiscChannelCount: RECOMMENDED
-        TriggerChannelCount: RECOMMENDED
-        RecordingDuration: RECOMMENDED
-        RecordingType: RECOMMENDED
-        EpochLength: RECOMMENDED
-        iEEGGround: RECOMMENDED
-        iEEGPlacementScheme: RECOMMENDED
-        iEEGElectrodeGroups: RECOMMENDED
-        SubjectArtefactDescription: RECOMMENDED
+        DCOffsetCorrection: deprecated
+        HardwareFilters: recommended
+        ElectrodeManufacturer: recommended
+        ElectrodeManufacturersModelName: recommended
+        ECOGChannelCount: recommended
+        SEEGChannelCount: recommended
+        EEGChannelCount: recommended
+        EOGChannelCount: recommended
+        ECGChannelCount: recommended
+        EMGChannelCount: recommended
+        MiscChannelCount: recommended
+        TriggerChannelCount: recommended
+        RecordingDuration: recommended
+        RecordingType: recommended
+        EpochLength: recommended
+        iEEGGround: recommended
+        iEEGPlacementScheme: recommended
+        iEEGElectrodeGroups: recommended
+        SubjectArtefactDescription: recommended
 
 # Specific iEEG fields MAY be present
 iEEGOptional:
@@ -93,8 +93,8 @@ iEEGOptional:
     - datatype == "ieeg"
     - suffix == "ieeg"
     fields:
-        ElectricalStimulation: OPTIONAL
-        ElectricalStimulationParameters: OPTIONAL
+        ElectricalStimulation: optional
+        ElectricalStimulationParameters: optional
 
 # General fields
 iEEGCoordsystemGeneral:
@@ -104,7 +104,7 @@ iEEGCoordsystemGeneral:
     - suffix == "coordsystem"
     fields:
         IntendedFor:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
                 If only a surface reconstruction is available, this should point to
                 the surface reconstruction file.
@@ -125,19 +125,20 @@ iEEGCoordsystemPositions:
     - datatype == "ieeg"
     - suffix == "coordsystem"
     fields:
-        iEEGCoordinateSystem: REQUIRED
-        iEEGCoordinateUnits: REQUIRED
+        iEEGCoordinateSystem: required
+        iEEGCoordinateUnits: required
         iEEGCoordinateSystemDescription:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if `iEEGCoordinateSystem` is `"Other"`
-        iEEGCoordinateProcessingDescription: RECOMMENDED
-        iEEGCoordinateProcessingReference: RECOMMENDED
+            level: recommended
+            level_addendum: required if `iEEGCoordinateSystem` is `"Other"`
+        iEEGCoordinateProcessingDescription: recommended
+        iEEGCoordinateProcessingReference: recommended
 
 iEEGCoordsystemOther:
     selectors:
     - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "coordsystem"
+    - sidecar contains "iEEGCoordinateSystem"
     - sidecar.iEEGCoordinateSystem == "Other"
     fields:
-        iEEGCoordinateSystemDescription: REQUIRED
+        iEEGCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index aa822ab4cc..e969c5d91f 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -16,9 +16,9 @@ MEGGeneric:
     - suffix == "meg"
     fields:
         TaskName:
-            level: REQUIRED
+            level: required
             description_addendum: |
-                A RECOMMENDED convention is to name resting state task using labels
+                A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
 MEGRecommended:
@@ -27,11 +27,11 @@ MEGRecommended:
     - datatype == "meg"
     - suffix == "meg"
     fields:
-        InstitutionName: RECOMMENDED
-        InstitutionAddress: RECOMMENDED
-        InstitutionalDepartmentName: RECOMMENDED
+        InstitutionName: recommended
+        InstitutionAddress: recommended
+        InstitutionalDepartmentName: recommended
         Manufacturer:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 For MEG scanners, this must be one of:
                 `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
@@ -39,20 +39,20 @@ MEGRecommended:
                 See [Appendix VII](/99-appendices/07-meg-systems.html) for
                 preferred names.
         ManufacturersModelName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 See [Appendix VII](/99-appendices/07-meg-systems.html) for
                 preferred names.
-        SoftwareVersions: RECOMMENDED
-        TaskDescription: RECOMMENDED
+        SoftwareVersions: recommended
+        TaskDescription: recommended
         Instructions:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 This is especially important in context of resting state recordings and
                 distinguishing between eyes open and eyes closed paradigms.
-        CogAtlasID: RECOMMENDED
-        CogPOID: RECOMMENDED
-        DeviceSerialNumber: RECOMMENDED
+        CogAtlasID: recommended
+        CogPOID: recommended
+        DeviceSerialNumber: recommended
 
 # Specific MEG fields MUST be present
 MEGRequired:
@@ -62,15 +62,15 @@ MEGRequired:
     - suffix == "meg"
     fields:
         SamplingFrequency:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 The sampling frequency of data channels that deviate from the main sampling
                 frequency SHOULD be specified in the `channels.tsv` file.
-        PowerLineFrequency: REQUIRED
-        DewarPosition: REQUIRED
-        SoftwareFilters: REQUIRED
-        DigitizedLandmarks: REQUIRED
-        DigitizedHeadPoints: REQUIRED
+        PowerLineFrequency: required
+        DewarPosition: required
+        SoftwareFilters: required
+        DigitizedLandmarks: required
+        DigitizedHeadPoints: required
 
 # Specific MEG fields SHOULD be present
 MEGMoreRecommended:
@@ -79,25 +79,25 @@ MEGMoreRecommended:
     - datatype == "meg"
     - suffix == "meg"
     fields:
-        MEGChannelCount: RECOMMENDED
-        MEGREFChannelCount: RECOMMENDED
-        EEGChannelCount: RECOMMENDED
-        ECOGChannelCount: RECOMMENDED
-        SEEGChannelCount: RECOMMENDED
-        EOGChannelCount: RECOMMENDED
-        ECGChannelCount: RECOMMENDED
-        EMGChannelCount: RECOMMENDED
-        MiscChannelCount: RECOMMENDED
-        TriggerChannelCount: RECOMMENDED
-        RecordingDuration: RECOMMENDED
-        RecordingType: RECOMMENDED
-        EpochLength: RECOMMENDED
-        ContinuousHeadLocalization: RECOMMENDED
-        HeadCoilFrequency: RECOMMENDED
-        MaxMovement: RECOMMENDED
-        SubjectArtefactDescription: RECOMMENDED
-        AssociatedEmptyRoom: RECOMMENDED
-        HardwareFilters: RECOMMENDED
+        MEGChannelCount: recommended
+        MEGREFChannelCount: recommended
+        EEGChannelCount: recommended
+        ECOGChannelCount: recommended
+        SEEGChannelCount: recommended
+        EOGChannelCount: recommended
+        ECGChannelCount: recommended
+        EMGChannelCount: recommended
+        MiscChannelCount: recommended
+        TriggerChannelCount: recommended
+        RecordingDuration: recommended
+        RecordingType: recommended
+        EpochLength: recommended
+        ContinuousHeadLocalization: recommended
+        HeadCoilFrequency: recommended
+        MaxMovement: recommended
+        SubjectArtefactDescription: recommended
+        AssociatedEmptyRoom: recommended
+        HardwareFilters: recommended
 
 # Specific EEG fields
 # NOTE: I'm not sure if "EEG is present" is enough to indicate simultaneous EEG/MEG.
@@ -108,10 +108,10 @@ MEGwithEEG:
     - suffix == "meg"
     - dataset.modalities contains "EEG"
     fields:
-        EEGPlacementScheme: OPTIONAL
-        CapManufacturer: OPTIONAL
-        CapManufacturersModelName: OPTIONAL
-        EEGReference: OPTIONAL
+        EEGPlacementScheme: optional
+        CapManufacturer: optional
+        CapManufacturersModelName: optional
+        EEGReference: optional
 
 # MEG and EEG sensors
 MEGCoordsystemWithEEG:
@@ -120,21 +120,21 @@ MEGCoordsystemWithEEG:
     - datatype == "meg"
     - suffix == "coordsystem"
     fields:
-        MEGCoordinateSystem: REQUIRED
-        MEGCoordinateUnits: REQUIRED
+        MEGCoordinateSystem: required
+        MEGCoordinateUnits: required
         MEGCoordinateSystemDescription:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `MEGCoordinateSystem` is `Other`
+            level: optional
+            level_addendum: required if `MEGCoordinateSystem` is `Other`
         EEGCoordinateSystem:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
                 See [Recording EEG simultaneously with MEG]
                 (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
                 Preferably the same as the `MEGCoordinateSystem`.
-        EEGCoordinateUnits: OPTIONAL
+        EEGCoordinateUnits: optional
         EEGCoordinateSystemDescription:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `EEGCoordinateSystem` is `Other`
+            level: optional
+            level_addendum: required if `EEGCoordinateSystem` is `Other`
             description_addendum: |
                 See [Recording EEG simultaneously with MEG]
                 (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
@@ -145,9 +145,10 @@ MEGCoordsystemWithEEGMEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
+    - sidecar contains "MEGCoordinateSystem"
     - sidecar.MEGCoordinateSystem == "Other"
     fields:
-        MEGCoordinateSystemDescription: REQUIRED
+        MEGCoordinateSystemDescription: required
 
 # NOTE: Not sure if this requires simult. EEG
 MEGCoordsystemWithEEGEEGCoordinateSystem:
@@ -155,9 +156,10 @@ MEGCoordsystemWithEEGEEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
+    - sidecar contains "EEGCoordinateSystem"
     - sidecar.EEGCoordinateSystem == "Other"
     fields:
-        EEGCoordinateSystemDescription: REQUIRED
+        EEGCoordinateSystemDescription: required
 
 # Head localization coils
 MEGCoordsystemHeadLocalizationCoils:
@@ -166,21 +168,22 @@ MEGCoordsystemHeadLocalizationCoils:
     - datatype == "meg"
     - suffix == "coordsystem"
     fields:
-        HeadCoilCoordinates: OPTIONAL
-        HeadCoilCoordinateSystem: OPTIONAL
-        HeadCoilCoordinateUnits: OPTIONAL
+        HeadCoilCoordinates: optional
+        HeadCoilCoordinateSystem: optional
+        HeadCoilCoordinateUnits: optional
         HeadCoilCoordinateSystemDescription:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `HeadCoilCoordinateSystem` is `Other`
+            level: optional
+            level_addendum: required if `HeadCoilCoordinateSystem` is `Other`
 
 MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
     selectors:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
+    - sidecar contains "HeadCoilCoordinateSystem"
     - sidecar.HeadCoilCoordinateSystem == "Other"
     fields:
-        HeadCoilCoordinateSystemDescription: REQUIRED
+        HeadCoilCoordinateSystemDescription: required
 
 # Digitized head points
 MEGCoordsystemDigitizedHeadPoints:
@@ -189,21 +192,22 @@ MEGCoordsystemDigitizedHeadPoints:
     - datatype == "meg"
     - suffix == "coordsystem"
     fields:
-        DigitizedHeadPoints: OPTIONAL
-        DigitizedHeadPointsCoordinateSystem: OPTIONAL
-        DigitizedHeadPointsCoordinateUnits: OPTIONAL
+        DigitizedHeadPoints: optional
+        DigitizedHeadPointsCoordinateSystem: optional
+        DigitizedHeadPointsCoordinateUnits: optional
         DigitizedHeadPointsCoordinateSystemDescription:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `DigitizedHeadPointsCoordinateSystem` is `Other`
+            level: optional
+            level_addendum: required if `DigitizedHeadPointsCoordinateSystem` is `Other`
 
 MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
     selectors:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
+    - sidecar contains "DigitizedHeadPointsCoordinateSystem"
     - sidecar.DigitizedHeadPointsCoordinateSystem == "Other"
     fields:
-        DigitizedHeadPointsCoordinateSystemDescription: REQUIRED
+        DigitizedHeadPointsCoordinateSystemDescription: required
 
 # Anatomical MRI
 MEGCoordsystemAnatomicalMRI:
@@ -214,7 +218,7 @@ MEGCoordsystemAnatomicalMRI:
     - dataset.modalities contains "anat"
     fields:
         IntendedFor:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
                 This is used to identify the structural MRI(s),
                 possibly of different types if a list is specified,
@@ -227,24 +231,25 @@ MEGCoordsystemAnatomicalLandmarks:
     - datatype == "meg"
     - suffix == "coordsystem"
     fields:
-        AnatomicalLandmarkCoordinates: OPTIONAL
+        AnatomicalLandmarkCoordinates: optional
         AnatomicalLandmarkCoordinateSystem:
-            level: OPTIONAL
+            level: optional
             description_addendum: |
                 Preferably the same as the `MEGCoordinateSystem`.
-        AnatomicalLandmarkCoordinateUnits: OPTIONAL
+        AnatomicalLandmarkCoordinateUnits: optional
         AnatomicalLandmarkCoordinateSystemDescription:
-            level: OPTIONAL
-            level_addendum: REQUIRED if `AnatomicalLandmarkCoordinateSystem` is `Other`
+            level: optional
+            level_addendum: required if `AnatomicalLandmarkCoordinateSystem` is `Other`
 
 MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
     selectors:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
+    - sidecar contains "AnatomicalLandmarkCoordinateSystem"
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
     fields:
-        AnatomicalLandmarkCoordinateSystemDescription: REQUIRED
+        AnatomicalLandmarkCoordinateSystemDescription: required
 
 # Fiducials information
 MEGCoordsystemFiducialsInformation:
@@ -253,4 +258,4 @@ MEGCoordsystemFiducialsInformation:
     - datatype == "meg"
     - suffix == "coordsystem"
     fields:
-        FiducialsDescription: OPTIONAL
+        FiducialsDescription: optional
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
index a8b3d66ad1..99413ad890 100644
--- a/src/schema/rules/sidecars/micr.yaml
+++ b/src/schema/rules/sidecars/micr.yaml
@@ -9,71 +9,71 @@
 # Device Hardware
 MicroscopyDeviceHardware:
     selectors:
-    - modality == "MICR"
+    - modality == "micr"
     - datatype == "micr"
     fields:
-        Manufacturer: RECOMMENDED
-        ManufacturersModelName: RECOMMENDED
-        DeviceSerialNumber: RECOMMENDED
-        StationName: RECOMMENDED
-        SoftwareVersions: RECOMMENDED
-        InstitutionName: RECOMMENDED
-        InstitutionAddress: RECOMMENDED
-        InstitutionalDepartmentName: RECOMMENDED
+        Manufacturer: recommended
+        ManufacturersModelName: recommended
+        DeviceSerialNumber: recommended
+        StationName: recommended
+        SoftwareVersions: recommended
+        InstitutionName: recommended
+        InstitutionAddress: recommended
+        InstitutionalDepartmentName: recommended
 
 # Image Acquisition
 MicroscopyImageAcquisition:
     selectors:
-    - modality == "MICR"
+    - modality == "micr"
     - datatype == "micr"
     fields:
-        PixelSize: REQUIRED
-        PixelSizeUnits: REQUIRED
-        Immersion: OPTIONAL
-        NumericalAperture: OPTIONAL
-        Magnification: OPTIONAL
-        ImageAcquisitionProtocol: OPTIONAL
-        OtherAcquisitionParameters: OPTIONAL
+        PixelSize: required
+        PixelSizeUnits: required
+        Immersion: optional
+        NumericalAperture: optional
+        Magnification: optional
+        ImageAcquisitionProtocol: optional
+        OtherAcquisitionParameters: optional
 
 # Sample
 MicroscopySample:
     selectors:
-    - modality == "MICR"
+    - modality == "micr"
     - datatype == "micr"
     fields:
         BodyPart:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: |
                 From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/
                 output/chtml/part16/chapter_L.html#chapter_L)
                 (for example `"BRAIN"`).
-        BodyPartDetails: RECOMMENDED
-        BodyPartDetailsOntology: OPTIONAL
-        SampleEnvironment: RECOMMENDED
-        SampleEmbedding: OPTIONAL
-        SampleFixation: OPTIONAL
-        SampleStaining: RECOMMENDED
-        SamplePrimaryAntibody: RECOMMENDED
-        SampleSecondaryAntibody: RECOMMENDED
-        SliceThickness: OPTIONAL
-        TissueDeformationScaling: OPTIONAL
-        SampleExtractionProtocol: OPTIONAL
-        SampleExtractionInstitution: OPTIONAL
+        BodyPartDetails: recommended
+        BodyPartDetailsOntology: optional
+        SampleEnvironment: recommended
+        SampleEmbedding: optional
+        SampleFixation: optional
+        SampleStaining: recommended
+        SamplePrimaryAntibody: recommended
+        SampleSecondaryAntibody: recommended
+        SliceThickness: optional
+        TissueDeformationScaling: optional
+        SampleExtractionProtocol: optional
+        SampleExtractionInstitution: optional
 
 # Chunk Transformations
 MicroscopyChunkTransformations:
     selectors:
-    - modality == "MICR"
+    - modality == "micr"
     - datatype == "micr"
     - entities contains "chunk"
     fields:
-        ChunkTransformationMatrix: RECOMMENDED
+        ChunkTransformationMatrix: recommended
 
 MicroscopyChunkTransformationsMatrixAxis:
     selectors:
-    - modality == "MICR"
+    - modality == "micr"
     - datatype == "micr"
     - entities contains "chunk"
     - sidecar contains "ChunkTransformationMatrix"
     fields:
-        ChunkTransformationMatrixAxis: REQUIRED
+        ChunkTransformationMatrixAxis: required
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 67bec335f5..19ddb3a526 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -9,114 +9,118 @@
 # MRI Common metadata fields
 MRIScannerHardware:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
         Manufacturer:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
         ManufacturersModelName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
         DeviceSerialNumber:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`.
         StationName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 1010 `Station Name`.
         SoftwareVersions:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`.
         HardcopyDeviceSoftwareVersion: DEPRECATED
         MagneticFieldStrength:
-            level: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
-        ReceiveCoilName: RECOMMENDED
-        ReceiveCoilActiveElements: RECOMMENDED
-        GradientSetType: RECOMMENDED
-        MRTransmitCoilSequence: RECOMMENDED
-        MatrixCoilMode: RECOMMENDED
-        CoilCombinationMethod: RECOMMENDED
+            level: recommended, but required for Arterial Spin Labeling
+        ReceiveCoilName: recommended
+        ReceiveCoilActiveElements: recommended
+        GradientSetType: recommended
+        MRTransmitCoilSequence: recommended
+        MatrixCoilMode: recommended
+        CoilCombinationMethod: recommended
 
 MRISequenceSpecifics:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
-        PulseSequenceType: RECOMMENDED
-        ScanningSequence: RECOMMENDED
-        SequenceVariant: RECOMMENDED
-        ScanOptions: RECOMMENDED
-        SequenceName: RECOMMENDED
-        PulseSequenceDetails: RECOMMENDED
+        PulseSequenceType: recommended
+        ScanningSequence: recommended
+        SequenceVariant: recommended
+        ScanOptions: recommended
+        SequenceName: recommended
+        PulseSequenceDetails: recommended
         NonlinearGradientCorrection: |
-            RECOMMENDED, but REQUIRED if [PET](./09-positron-emission-tomography.md) data are present
-        MRAcquisitionType: RECOMMENDED, but REQUIRED for Arterial Spin Labeling
-        MTState: RECOMMENDED
-        MTOffsetFrequency: OPTIONAL
-        MTPulseBandwidth: OPTIONAL
-        MTNumberOfPulses: OPTIONAL
-        MTPulseShape: OPTIONAL
-        MTPulseDuration: OPTIONAL
-        SpoilingState: RECOMMENDED
-        SpoilingType: OPTIONAL
-        SpoilingRFPhaseIncrement: OPTIONAL
-        SpoilingGradientMoment: OPTIONAL
-        SpoilingGradientDuration: OPTIONAL
+            recommended, but required if [PET](./09-positron-emission-tomography.md) data are present
+        MRAcquisitionType: recommended, but required for Arterial Spin Labeling
+        MTState: recommended
+        MTOffsetFrequency: optional
+        MTPulseBandwidth: optional
+        MTNumberOfPulses: optional
+        MTPulseShape: optional
+        MTPulseDuration: optional
+        SpoilingState: recommended
+        SpoilingType: optional
+        SpoilingRFPhaseIncrement: optional
+        SpoilingGradientMoment: optional
+        SpoilingGradientDuration: optional
 
 PETMRISequenceSpecifics:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - dataset.modalities contains "PET"
     fields:
-        NonLinearGradientCorrection: REQUIRED
+        NonLinearGradientCorrection: required
 
 ASLMRISequenceSpecifics:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "perf"
     fields:
-        MRAcquisitionType: REQUIRED
+        MRAcquisitionType: required
 
 MTParameters:
     selectors:
-    - sidecar.MTState == True
+    - sidecar contains "MTState"
+    - sidecar.MTState == "True"
     fields:
-        MTOffsetFrequency: RECOMMENDED
-        MTPulseBandwidth: RECOMMENDED
-        MTNumberOfPulses: RECOMMENDED
-        MTPulseShape: RECOMMENDED
-        MTPulseDuration: RECOMMENDED
+        MTOffsetFrequency: recommended
+        MTPulseBandwidth: recommended
+        MTNumberOfPulses: recommended
+        MTPulseShape: recommended
+        MTPulseDuration: recommended
 
 SpoilingType:
     selectors:
+    - sidecar contains "SpoilingState"
     - sidecar.SpoilingState == True
     fields:
-        SpoilingType: RECOMMENDED
+        SpoilingType: recommended
 
 SpoilingRF:
     selectors:
+    - sidecar contains "SpoilingType"
     - sidecar.SpoilingType in ["RF", "COMBINED"]
     fields:
-        SpoilingRFPhaseIncrement: RECOMMENDED
+        SpoilingRFPhaseIncrement: recommended
 
 SpoilingGradient:
     selectors:
+    - sidecar contains "SpoilingType"
     - sidecar.SpoilingType in ["GRADIENT", "COMBINED"]
     fields:
-        SpoilingGradientMoment: RECOMMENDED
-        SpoilingGradientDuration: RECOMMENDED
+        SpoilingGradientMoment: recommended
+        SpoilingGradientDuration: recommended
 
 MRISpatialEncoding:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
-        NumberShots: RECOMMENDED
-        ParallelReductionFactorInPlane: RECOMMENDED
-        ParallelAcquisitionTechnique: RECOMMENDED
-        PartialFourier: RECOMMENDED
-        PartialFourierDirection: RECOMMENDED
+        NumberShots: recommended
+        ParallelReductionFactorInPlane: recommended
+        ParallelAcquisitionTechnique: recommended
+        PartialFourier: recommended
+        PartialFourierDirection: recommended
         PhaseEncodingDirection:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                This parameter is REQUIRED if corresponding fieldmap data is present
+                This parameter is required if corresponding fieldmap data is present
                 or when using multiple runs with different phase encoding directions
                 (which can be later used for field inhomogeneity correction).
             issue:
@@ -124,9 +128,9 @@ MRISpatialEncoding:
                 issue: |
                     You have to define 'PhaseEncodingDirection' for this file.
         EffectiveEchoSpacing:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                <sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data
+                <sup>2</sup> This parameter is required if corresponding fieldmap data
                 is present.
             issue:
                 name: EFFECTIVE_ECHO_SPACING_NOT_DEFINED
@@ -134,9 +138,9 @@ MRISpatialEncoding:
                     You should define 'EffectiveEchoSpacing' for this file. If you don't
                     provide this information field map correction will not be possible.
         TotalReadoutTime:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                <sup>3</sup> This parameter is REQUIRED if corresponding 'field/distortion' maps
+                <sup>3</sup> This parameter is required if corresponding 'field/distortion' maps
                 acquired with opposing phase encoding directions are present
                 (see [Case 4: Multiple phase encoded
                 directions](#case-4-multiple-phase-encoded-directions-pepolar)).
@@ -144,16 +148,16 @@ MRISpatialEncoding:
                 name: TOTAL_READOUT_TIME_MUST_DEFINE
                 message: |
                     You have to define 'TotalReadoutTime' for this file.
-        MixingTime: RECOMMENDED
+        MixingTime: recommended
 
 MRITimingParameters:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
         EchoTime:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                REQUIRED if corresponding fieldmap data is present,
+                required if corresponding fieldmap data is present,
                 or the data comes from a multi-echo sequence or Arterial Spin Labeling.
             issue:
                 name: ECHO_TIME_NOT_DEFINED
@@ -167,39 +171,40 @@ MRITimingParameters:
                     The data type array provides a value for each volume in a 4D dataset and
                     should only be used when the volume timing is critical for interpretation
                     of the data, such as in ASL or variable echo time fMRI sequences.
-        InversionTime: RECOMMENDED
+        InversionTime: recommended
         SliceTiming:
-            level: RECOMMENDED
+            level: recommended
             level_addendum: |
-                REQUIRED for sparse sequences that do not have the `DelayTime` field set,
+                required for sparse sequences that do not have the `DelayTime` field set,
                 and Arterial Spin Labeling with `MRAcquisitionType` set on `2D`.
-        SliceEncodingDirection: RECOMMENDED
-        DwellTime: RECOMMENDED
+        SliceEncodingDirection: recommended
+        DwellTime: recommended
 
 SliceTimingASL:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "perf"
     - suffix in ["asl", "m0scan"]
+    - sidecar contains "MRAcquisitionType"
     - sidecar.MRAcquisitionType == "2D"
     fields:
-        SliceTiming: REQUIRED
+        SliceTiming: required
 
 # This is technically for sparse sequences only, but I don't know how to encode that.
 SliceTimingSparse:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar contains "DelayTime"
     fields:
-        SliceTiming: REQUIRED
+        SliceTiming: required
 
 MRIRFandContrast:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
         FlipAngle:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if LookLocker is set to `true`.
+            level: recommended
+            level_addendum: required if LookLocker is set to `true`.
             issue:
                 name: LOOK_LOCKER_FLIP_ANGLE_MISSING
                 message: |
@@ -214,44 +219,45 @@ MRIRFandContrast:
                     in a 4D dataset and should only be used when the volume timing is
                     critical for interpretation of the data, such as in ASL or
                     variable flip angle fMRI sequences.
-        NegativeContrast: OPTIONAL
+        NegativeContrast: optional
 
 MRIFlipAngleLookLocker:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
+    - sidecar contains "LookLocker"
     - sidecar.LookLocker == True
     fields:
-        FlipAngle: REQUIRED
+        FlipAngle: required
 
 MRISliceAcceleration:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
-        MultibandAccelerationFactor: RECOMMENDED
+        MultibandAccelerationFactor: recommended
 
 MRIAnatomicalLandmarks:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
-        AnatomicalLandmarkCoordinates__mri: RECOMMENDED
+        AnatomicalLandmarkCoordinates__mri: recommended
 
 MRIEchoPlanarImagingAndB0Mapping:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
-        B0FieldIdentifier: RECOMMENDED
-        B0FieldSource: RECOMMENDED
+        B0FieldIdentifier: recommended
+        B0FieldSource: recommended
 
 MRIInstitutionInformation:
     selectors:
-    - modality == "MRI"
+    - modality == "mri"
     fields:
         InstitutionName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
         InstitutionAddress:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
         InstitutionalDepartmentName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index 5ee41b1f23..6399eb5e69 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -2,182 +2,182 @@
 # PET common metadata fields
 PETScannerHardware:
     selectors:
-    - modality == "PET"
+    - modality == "pet"
     fields:
         Manufacturer:
-            level: REQUIRED
+            level: required
             description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`.
         ManufacturersModelName:
-            level: REQUIRED
+            level: required
             description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`.
         Units:
-            level: REQUIRED
+            level: required
             description_addendum: |
                 SI unit for radioactivity (Becquerel) should be used (for example, "Bq/mL").
                 Corresponds to DICOM Tag 0054, 1001 `Units`.
         InstitutionName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`.
         InstitutionAddress:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`.
         InstitutionalDepartmentName:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
         BodyPart:
-            level: RECOMMENDED
+            level: recommended
             description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
 
 PETRadioChemistry:
     selectors:
-    - modality == "PET"
+    - modality == "pet"
     fields:
         TracerName:
-            level: REQUIRED
+            level: required
         TracerRadionuclide:
-            level: REQUIRED
+            level: required
         InjectedRadioactivity:
-            level: REQUIRED
+            level: required
         InjectedRadioactivityUnits:
-            level: REQUIRED
+            level: required
         InjectedMass:
-            level: REQUIRED
+            level: required
         InjectedMassUnits:
-            level: REQUIRED
+            level: required
         SpecificRadioactivity:
-            level: REQUIRED
+            level: required
         SpecificRadioactivityUnits:
-            level: REQUIRED
+            level: required
         ModeOfAdministration:
-            level: REQUIRED
+            level: required
         TracerRadLex:
-            level: RECOMMENDED
+            level: recommended
         TracerSNOMED:
-            level: RECOMMENDED
+            level: recommended
         TracerMolecularWeight:
-            level: RECOMMENDED
+            level: recommended
         TracerMolecularWeightUnits:
-            level: RECOMMENDED
+            level: recommended
         InjectedMassPerWeight:
-            level: RECOMMENDED
+            level: recommended
         InjectedMassPerWeightUnits:
-            level: RECOMMENDED
+            level: recommended
         SpecificRadioactivityMeasTime:
-            level: RECOMMENDED
+            level: recommended
         MolarActivity:
-            level: RECOMMENDED
+            level: recommended
         MolarActivityUnits:
-            level: RECOMMENDED
+            level: recommended
         MolarActivityMeasTime:
-            level: RECOMMENDED
+            level: recommended
         InfusionRadioactivity:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+            level: recommended
+            level_addendum: required if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
         InfusionStart:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+            level: recommended
+            level_addendum: required if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
         InfusionSpeed:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+            level: recommended
+            level_addendum: required if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
         InfusionSpeedUnits:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+            level: recommended
+            level_addendum: required if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
         InjectedVolume:
-            level: RECOMMENDED
-            level_addendum: REQUIRED if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
+            level: recommended
+            level_addendum: required if PETRadioChemistry.fields.ModeOfAdministration == 'bolus-infusion'
         Purity:
-            level: RECOMMENDED
+            level: recommended
 
-# PET Infusion conditionally REQUIRED entities
+# PET Infusion conditionally required entities
 EntitiesBolusMetadata:
     selectors:
-    - modality == 'PET'
+    - modality == "pet"
     - sidecar.ModeOfAdministration == 'bolus-infusion'
     fields:
         InfusionRadioactivity:
-            level: REQUIRED
+            level: required
         InfusionStart:
-            level: REQUIRED
+            level: required
         InfusionSpeed:
-            level: REQUIRED
+            level: required
         InfusionSpeedUnits:
-            level: REQUIRED
+            level: required
         InjectedVolume:
-            level: REQUIRED
+            level: required
 
 PETPharmaceuticals:
     selectors:
-    - modality == "PET"
+    - modality == "pet"
     fields:
         PharmaceuticalName:
-            level: RECOMMENDED
+            level: recommended
         PharmaceuticalDoseAmount:
-            level: RECOMMENDED
+            level: recommended
         PharmaCeuticalDoseUnits:
-            level: RECOMMENDED
+            level: recommended
         PharmaCeuticalDoseRegimen:
-            level: RECOMMENDED
+            level: recommended
         PharmaCeuticalDoseTime:
-            level: RECOMMENDED
+            level: recommended
         Anaesthesia:
-            level: OPTIONAL
+            level: optional
 
 PETTime:
     selectors:
-    - modality == "PET"
+    - modality == "pet"
     fields:
         TimeZero:
-            level: REQUIRED
+            level: required
         ScanStart:
-            level: REQUIRED
+            level: required
         InjectionStart:
-            level: REQUIRED
+            level: required
         FramesTimesStart:
-            level: REQUIRED
+            level: required
         FrameDuration:
-            level: REQUIRED
+            level: required
         InjectionEnd:
-            level: RECOMMENDED
+            level: recommended
         ScanDate:
-            level: DEPRECATED
+            level: deprecated
 
 PETReconstruction:
     selectors:
-    - modality == "PET"
+    - modality == "pet"
     fields:
         AcquisitionMode:
-            level: REQUIRED
+            level: required
         ImageDecayCorrected:
-            level: REQUIRED
+            level: required
         ImageDecayCorrectionTime:
-            level: REQUIRED
+            level: required
         ReconMethodName:
-            level: REQUIRED
+            level: required
         ReconMethodParameterLabels:
-            level: REQUIRED
+            level: required
         ReconMethodParameterUnits:
-            level: REQUIRED
+            level: required
         ReconMethodParameterValues:
-            level: REQUIRED
+            level: required
         ReconFilterType:
-            level: REQUIRED
+            level: required
         ReconFilterSize:
-            level: REQUIRED
+            level: required
         AttenuationCorrection:
-            level: REQUIRED
+            level: required
         ReconMethodImplementationVersion:
-            level: RECOMMENDED
+            level: recommended
         AttenuationCorrectionMethodReference:
-            level: RECOMMENDED
+            level: recommended
         ScaleFactor:
-            level: RECOMMENDED
+            level: recommended
         ScatterFraction:
-            level: RECOMMENDED
+            level: recommended
         DecayCorrectionFactor:
-            level: RECOMMENDED
+            level: recommended
         DoseCalibrationFactor:
-            level: RECOMMENDED
+            level: recommended
         PromptRate:
-            level: RECOMMENDED
+            level: recommended
         SinglesRate:
-            level: RECOMMENDED
+            level: recommended
diff --git a/src/schema/rules/tabular_data/eeg.yaml b/src/schema/rules/tabular_data/eeg.yaml
index ee987de4f7..742a6856ec 100644
--- a/src/schema/rules/tabular_data/eeg.yaml
+++ b/src/schema/rules/tabular_data/eeg.yaml
@@ -4,19 +4,22 @@ EEGChannels:
     - datatype == "eeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type__eeg_channels, units]
+    initial_columns:
+    - name__channels
+    - type__eeg_channels
+    - units
     columns:
-        name__channels: REQUIRED
-        type__eeg_channels: REQUIRED
-        units: REQUIRED
-        description: OPTIONAL
-        sampling_frequency: OPTIONAL
-        reference: OPTIONAL
-        low_cutoff: OPTIONAL
-        high_cutoff: OPTIONAL
-        notch: OPTIONAL
-        status: OPTIONAL
-        status_descriptions: OPTIONAL
+        name__channels: required
+        type__eeg_channels: required
+        units: required
+        description: optional
+        sampling_frequency: optional
+        reference: optional
+        low_cutoff: optional
+        high_cutoff: optional
+        notch: optional
+        status: optional
+        status_descriptions: optional
     additional_columns: allowed_if_defined
 
 EEGElectrodes:
@@ -24,13 +27,17 @@ EEGElectrodes:
     - datatype == "eeg"
     - suffix == "electrodes"
     - extension == ".tsv"
-    initial_columns: [name__electrodes, x, y, z]
+    initial_columns:
+    - name__electrodes
+    - x
+    - y
+    - z
     columns:
-        name__electrodes: REQUIRED
-        x: REQUIRED
-        y: REQUIRED
-        z: REQUIRED
-        type__electrodes: RECOMMENDED
-        material: RECOMMENDED
-        impedance: RECOMMENDED
+        name__electrodes: required
+        x: required
+        y: required
+        z: required
+        type__electrodes: recommended
+        material: recommended
+        impedance: recommended
     additional_columns: allowed_if_defined
diff --git a/src/schema/rules/tabular_data/ieeg.yaml b/src/schema/rules/tabular_data/ieeg.yaml
index faa968f160..36bde71c54 100644
--- a/src/schema/rules/tabular_data/ieeg.yaml
+++ b/src/schema/rules/tabular_data/ieeg.yaml
@@ -4,20 +4,23 @@ iEEGChannels:
     - datatype == "ieeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type__ieeg_channels, units]
+    initial_columns:
+    - name__channels
+    - type__ieeg_channels
+    - units
     columns:
-        name__channels: REQUIRED
-        type__ieeg_channels: REQUIRED
-        units: REQUIRED
-        low_cutoff: REQUIRED
-        high_cutoff: REQUIRED
-        reference: OPTIONAL
-        group: OPTIONAL
-        sampling_frequency: OPTIONAL
-        description: OPTIONAL
-        notch: OPTIONAL
-        status: OPTIONAL
-        status_descriptions: OPTIONAL
+        name__channels: required
+        type__ieeg_channels: required
+        units: required
+        low_cutoff: required
+        high_cutoff: required
+        reference: optional
+        group: optional
+        sampling_frequency: optional
+        description: optional
+        notch: optional
+        status: optional
+        status_descriptions: optional
     additional_columns: allowed_if_defined
 
 iEEGElectrodes:
@@ -25,18 +28,22 @@ iEEGElectrodes:
     - datatype == "ieeg"
     - suffix == "electrodes"
     - extension == ".tsv"
-    initial_columns: [name__electrodes, x, y, z]
+    initial_columns:
+    - name__electrodes
+    - x
+    - y
+    - z
     columns:
-        name__electrodes: REQUIRED
-        x: REQUIRED
-        y: REQUIRED
-        z: REQUIRED
-        size: REQUIRED
-        material: RECOMMENDED
-        manufacturer: RECOMMENDED
-        group: RECOMMENDED
-        hemisphere: RECOMMENDED
-        type__electrodes: OPTIONAL
-        impedance: OPTIONAL
-        dimension: OPTIONAL
+        name__electrodes: required
+        x: required
+        y: required
+        z: required
+        size: required
+        material: recommended
+        manufacturer: recommended
+        group: recommended
+        hemisphere: recommended
+        type__electrodes: optional
+        impedance: optional
+        dimension: optional
     additional_columns: allowed_if_defined
diff --git a/src/schema/rules/tabular_data/meg.yaml b/src/schema/rules/tabular_data/meg.yaml
index f5bc01862a..ce364796cf 100644
--- a/src/schema/rules/tabular_data/meg.yaml
+++ b/src/schema/rules/tabular_data/meg.yaml
@@ -4,17 +4,20 @@ MEGChannels:
     - datatype == "eeg"
     - suffix == "channels"
     - extension == ".tsv"
-    initial_columns: [name__channels, type__meg_channels, units]
+    initial_columns:
+    - name__channels
+    - type__meg_channels
+    - units
     columns:
-        name__channels: REQUIRED
-        type__meg_channels: REQUIRED
-        units: REQUIRED
-        description: OPTIONAL
-        sampling_frequency: OPTIONAL
-        low_cutoff: OPTIONAL
-        high_cutoff: OPTIONAL
-        notch: OPTIONAL
-        software_filters: OPTIONAL
-        status: OPTIONAL
-        status_descriptions: OPTIONAL
+        name__channels: required
+        type__meg_channels: required
+        units: required
+        description: optional
+        sampling_frequency: optional
+        low_cutoff: optional
+        high_cutoff: optional
+        notch: optional
+        software_filters: optional
+        status: optional
+        status_descriptions: optional
     additional_columns: allowed_if_defined
diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index 1960b34fd7..82e0059c22 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -5,46 +5,48 @@ Blood:
     - suffix == "blood"
     - extension == ".tsv"
     columns:
-        time: REQUIRED
-        plasma_radioactivity: OPTIONAL
-        metabolite_parent_fraction: OPTIONAL
-        metabolite_polar_fraction: OPTIONAL
-        hplc_recovery_fractions: OPTIONAL
-        whole_blood_radioactivity: OPTIONAL
+        time: required
+        plasma_radioactivity: optional
+        metabolite_parent_fraction: optional
+        metabolite_polar_fraction: optional
+        hplc_recovery_fractions: optional
+        whole_blood_radioactivity: optional
 
 BloodPlasma:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar.PlasmaAvail
+    - sidecar contains "PlasmaAvail"
     columns:
-        plasma_radioactivity: REQUIRED
+        plasma_radioactivity: required
 
 BloodMetabolite:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar.MetaboliteAvail
+    - sidecar contains "MetaboliteAvail"
     columns:
-        metabolite_parent_fraction: REQUIRED
-        metabolite_polar_fraction: RECOMMENDED
+        metabolite_parent_fraction: required
+        metabolite_polar_fraction: recommended
 
 BloodMetaboliteCorrection:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
+    - sidecar contains "MetaboliteRecoveryCorrectionApplied"
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
     columns:
-        hplc_recovery_fractions: REQUIRED
+        hplc_recovery_fractions: required
 
 BloodWholeBlood:
     selectors:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
+    - sidecar contains "WholeBloodAvail"
     - sidecar.WholeBloodAvail == true
     columns:
-        whole_blood_radioactivity: REQUIRED
+        whole_blood_radioactivity: required

From e230fd8502a592fb427f76d7f26d9cd59fa3bb01 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 13:36:46 -0700
Subject: [PATCH 327/347] continue to bring derivatives schema in line with
 spec.

---
 .../{ => derivatives}/common_derivatives.yaml |  2 +-
 .../common_imaging_derivatives.yaml}          | 66 +++++++++++---
 .../rules/sidecars/common_derivative.yaml     | 85 -------------------
 .../derivatives/common_derivatives.yaml       | 85 +++++++++++++++++++
 .../derivatives/common_derivatives.yaml       | 11 +++
 5 files changed, 149 insertions(+), 100 deletions(-)
 rename src/schema/rules/datatypes/{ => derivatives}/common_derivatives.yaml (99%)
 rename src/schema/rules/datatypes/{derivatives.yaml => derivatives/common_imaging_derivatives.yaml} (73%)
 delete mode 100644 src/schema/rules/sidecars/common_derivative.yaml
 create mode 100644 src/schema/rules/sidecars/derivatives/common_derivatives.yaml
 create mode 100644 src/schema/rules/tabular_data/derivatives/common_derivatives.yaml

diff --git a/src/schema/rules/datatypes/common_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
similarity index 99%
rename from src/schema/rules/datatypes/common_derivatives.yaml
rename to src/schema/rules/datatypes/derivatives/common_derivatives.yaml
index 48c3744f8d..4f64c515df 100644
--- a/src/schema/rules/datatypes/common_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
@@ -1,4 +1,4 @@
----
+q:-
 anat_nonparametric_common:
   $ref: schema.rules.datatypes.anat.nonparametric
   entities:
diff --git a/src/schema/rules/datatypes/derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
similarity index 73%
rename from src/schema/rules/datatypes/derivatives.yaml
rename to src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index b5821e9e66..d85bd543cb 100644
--- a/src/schema/rules/datatypes/derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -89,7 +89,7 @@ func_mask:
 
 anat_parametric_discrete_segmentation:
   suffixes:
-  - mask
+  - dseg
   extensions:
   - .nii.gz
   entities:
@@ -97,12 +97,10 @@ anat_parametric_discrete_segmentation:
     space: OPTIONAL
     res: OPTIONAL
     den: OPTIONAL
-    label: OPTIONAL
-    desc: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
   suffixes:
-  - mask
+  - dseg
   extensions:
   - .nii.gz
   entities:
@@ -110,8 +108,6 @@ anat_nonparametric_discrete_segmentation:
     space: OPTIONAL
     res: OPTIONAL
     den: OPTIONAL
-    label: OPTIONAL
-    desc: OPTIONAL
 
 func_discrete_segmentation:
   suffixes:
@@ -136,33 +132,75 @@ dwi_discrete_segmentation:
     den: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.derivatives.anat_parametric_discrete_segmentation
   suffixes:
   - probseg
+  extensions:
+  - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.derivatives.anat_parametric_discrete_segmentation.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.derivatives.anat_nonparametric_discrete_segmentation
   suffixes:
   - probseg
+  extensions:
+  - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.derivatives.anat_nonparametric_discrete_segmentation.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
     label: OPTIONAL
 
 func_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.derivatives.func_discrete_segmentation
   suffixes:
   - probseg
+  extensions:
+  - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.derivatives.func_discrete_segmentation.entities
+    $ref: schema.rules.datatypes.func.func.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.derivatives.dwi_discrete_segmentation
   suffixes:
   - probseg
+  extensions:
+  - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.derivatives.dwi_discrete_segmentation.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
     label: OPTIONAL
+
+anat_parametic_discrete_surface:
+  suffixes:
+  - dseg
+  extensions:
+  - label.gii
+  - dlabel.nii
+  entities:
+    $ref: schema.rules.datatypes.anat.parametric.entities
+    hemi: OPTIONAL
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
+
+anat_nonparametic_discrete_surface:
+  suffixes:
+  - dseg
+  extensions:
+  - label.gii
+  - dlabel.nii
+  entities:
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    hemi: OPTIONAL
+    space: OPTIONAL
+    res: OPTIONAL
+    den: OPTIONAL
diff --git a/src/schema/rules/sidecars/common_derivative.yaml b/src/schema/rules/sidecars/common_derivative.yaml
deleted file mode 100644
index 6c50981c06..0000000000
--- a/src/schema/rules/sidecars/common_derivative.yaml
+++ /dev/null
@@ -1,85 +0,0 @@
----
-CommonDerivativeFields:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    fields:
-    - Description: RECOMMENDED
-    - Sources: OPTIONAL
-    - RawSources: OPTIONAL
-
-SpatialReferenceEntity:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - entities contains "space"
-    fields:
-        SpatialReference: RECOMMENDED
-
-SpatialReferenceNonStandard:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - not(entities.space in schema.objects.metadata._StandardTemplateCoordSys)
-    fields:
-        SpatialReference: REQUIRED
-
-SpatialReferenceNoEntity:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - not(entities contains "space")
-    fields:
-        SpatialReference: REQUIRED
-
-# this needs to come before density and resolution overrides selected in a
-# different way
-MaskDerivatives:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - suffix == "mask"
-    fields:
-        RawSources: REQUIRED
-        Type: RECOMMENDED
-        Atlas: OPTIONAL
-        Resolution: OPTIONAL
-        Density: OPTIONAL
-
-MaskDerivativesAtlas:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - suffix == "mask"
-    - entities contains "label"
-    fields:
-        atlas: RECOMMENDED
-
-SegmentationCommon:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - suffix in ["dseg", "probseg"]
-    fields:
-        Type: RECOMMENDED
-        Atlas: OPTIONAL
-        Resolution: OPTIONAL
-        Density: OPTIONAL
-
-# Derivatives -> Imaging data types
-ImageDerivatives:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - modality in ["mri", "pet"]
-    - extension in [".nii", ".nii.gz"]
-    fields:
-        SkullStripped: REQUIRED
-
-ImageDerivativeResEntity:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - modality in ["mri", "pet"]
-    - entities contains "res"
-    fields:
-        Resolution: REQUIRED
-
-ImageDerivativeDenEntity:
-    selectors:
-    - dataset.DatasetType == "derivative"
-    - modality in ["mri", "pet"]
-    - entities contains "den"
-    fields:
-        Density: REQUIRED
diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
new file mode 100644
index 0000000000..87a59eca78
--- /dev/null
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -0,0 +1,85 @@
+---
+CommonDerivativeFields:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  fields:
+    Description: RECOMMENDED
+    Sources: OPTIONAL
+    RawSources: OPTIONAL
+
+SpatialReferenceEntity:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - entities contains "space"
+  fields:
+    SpatialReference: RECOMMENDED
+
+SpatialReferenceNonStandard:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - not(entities.space in schema.objects.metadata._StandardTemplateCoordSys)
+  fields:
+    SpatialReference: REQUIRED
+
+SpatialReferenceNoEntity:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - not(entities contains "space")
+  fields:
+    SpatialReference: REQUIRED
+
+# this needs to come before density and resolution overrides selected in a
+# different way
+MaskDerivatives:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix == "mask"
+  fields:
+    RawSources: REQUIRED
+    Type: RECOMMENDED
+    Atlas: OPTIONAL
+    Resolution: OPTIONAL
+    Density: OPTIONAL
+
+MaskDerivativesAtlas:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix == "mask"
+  - entities contains "label"
+  fields:
+    atlas: RECOMMENDED
+
+SegmentationCommon:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix in ["dseg", "probseg"]
+  fields:
+    Type: RECOMMENDED
+    Atlas: OPTIONAL
+    Resolution: OPTIONAL
+    Density: OPTIONAL
+
+# Derivatives -> Imaging data types
+ImageDerivatives:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - modality in ["mri", "pet"]
+  - extension in [".nii", ".nii.gz"]
+  fields:
+    SkullStripped: REQUIRED
+
+ImageDerivativeResEntity:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - modality in ["mri", "pet"]
+  - entities contains "res"
+  fields:
+    Resolution: REQUIRED
+
+ImageDerivativeDenEntity:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - modality in ["mri", "pet"]
+  - entities contains "den"
+  fields:
+    Density: REQUIRED
diff --git a/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
new file mode 100644
index 0000000000..237b111436
--- /dev/null
+++ b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
@@ -0,0 +1,11 @@
+---
+SegmentationLookup:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix in ["dseg" "probseg"]
+  columns:
+    index: REQUIRED
+    name: REQUIRED
+    abbreviation: OPTIONAL
+    color: OPTIONAL
+    mapping: OPTIONAL

From 425fee66bdb09ca4b8a2c885f481a0a07354df75 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 13:38:25 -0700
Subject: [PATCH 328/347] fix datatypes/derivatives/common_derivatives.yaml
 header

---
 src/schema/rules/datatypes/derivatives/common_derivatives.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
index 4f64c515df..48c3744f8d 100644
--- a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
@@ -1,4 +1,4 @@
-q:-
+---
 anat_nonparametric_common:
   $ref: schema.rules.datatypes.anat.nonparametric
   entities:

From ea25b43872d3444292a5229a35365ed6e8953c0d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 15 Apr 2022 16:52:10 -0400
Subject: [PATCH 329/347] Apply suggestions from code review

---
 src/schema/rules/sidecars/eeg.yaml  | 4 ++--
 src/schema/rules/sidecars/ieeg.yaml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index ec630cfcea..eb54527c81 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -19,7 +19,7 @@ EEGGeneric:
                 A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
-EEGrecommended:
+EEGRecommended:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
@@ -56,7 +56,7 @@ EEGRequired:
         PowerLineFrequency: required
         SoftwareFilters: required
 
-EEGMorerecommended:
+EEGMoreRecommended:
     selectors:
     - modality == "eeg"
     - datatype == "eeg"
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index 9f51287f3b..d7763546f3 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -19,7 +19,7 @@ iEEGGeneric:
                 A recommended convention is to name resting state task using labels
                 beginning with `rest`.
 
-iEEGrecommended:
+iEEGRecommended:
     selectors:
     - modality == "ieeg"
     - datatype == "ieeg"

From 79f7946e7fb566d457a4d20da59140a3eae2977e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 14:08:58 -0700
Subject: [PATCH 330/347] STY: pacify yaml linter

---
 src/schema/rules/sidecars/asl_validation.yaml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 3f461396de..c2310ff937 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -6,7 +6,8 @@ ASLLabelingDurationNiftiLength:
     issue:
         code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
         message: |
-            The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
+            The number of values for 'LabelingDuration' for this file does not match the 4th dimension
+            of the NIfTI header.
             'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
             corresponding to the temporal width of the labeling bolus for `(P)CASL`.
             In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
@@ -49,7 +50,8 @@ ASLFlipAngleNiftiLength:
             The data type number may apply to files from any MRI modality concerned with a single value for this field,
             or to the files in a file collection where the value of this field is iterated using the flip entity.
             The data type array provides a value for each volume in a 4D dataset and should only be used when the
-            volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+            volume timing is critical for interpretation of the data, such as in ASL or variable flip
+            angle fMRI sequences.
         level: error
     selectors:
     - suffix == "asl"
@@ -91,7 +93,8 @@ ASLPostLabelingDelayNiftiLength:
             labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
             (for 3D acquisition) or first slice (for 2D acquisition).
             Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
+            In the latter case, the array of numbers contains the PLD of each volume
+            (that is, each 'control' and 'label')
             in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is
             indicated by a zero.
             Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
@@ -114,7 +117,8 @@ ASLPostLabelingDelayASLContextLength:
             middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
             the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
             Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
+            In the latter case, the array of numbers contains the PLD of each volume
+            (that is, each 'control' and 'label')
             in the acquisition order.
             Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a zero.
             Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.

From 32c29551f4036319bea742f412c57a1310a882da Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 14:15:22 -0700
Subject: [PATCH 331/347] Move validation yaml files to checks subdir

---
 .../rules/{sidecars/asl_validation.yaml => checks/asl.yaml}       | 0
 .../rules/{sidecars/dwi_validation.yaml => checks/dwi.yaml}       | 0
 .../rules/{sidecars/events_validation.yaml => checks/events.yaml} | 0
 .../rules/{sidecars/fmap_validation.yaml => checks/fmap.yaml}     | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename src/schema/rules/{sidecars/asl_validation.yaml => checks/asl.yaml} (100%)
 rename src/schema/rules/{sidecars/dwi_validation.yaml => checks/dwi.yaml} (100%)
 rename src/schema/rules/{sidecars/events_validation.yaml => checks/events.yaml} (100%)
 rename src/schema/rules/{sidecars/fmap_validation.yaml => checks/fmap.yaml} (100%)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/checks/asl.yaml
similarity index 100%
rename from src/schema/rules/sidecars/asl_validation.yaml
rename to src/schema/rules/checks/asl.yaml
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/checks/dwi.yaml
similarity index 100%
rename from src/schema/rules/sidecars/dwi_validation.yaml
rename to src/schema/rules/checks/dwi.yaml
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/checks/events.yaml
similarity index 100%
rename from src/schema/rules/sidecars/events_validation.yaml
rename to src/schema/rules/checks/events.yaml
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/checks/fmap.yaml
similarity index 100%
rename from src/schema/rules/sidecars/fmap_validation.yaml
rename to src/schema/rules/checks/fmap.yaml

From 2db6b95f223e8e5e84cb513662b4252fc0c7bb29 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 15 Apr 2022 14:26:52 -0700
Subject: [PATCH 332/347] STY: Conform checks to 2-space convention

---
 src/schema/rules/checks/asl.yaml    | 472 ++++++++++++++--------------
 src/schema/rules/checks/dwi.yaml    |  88 +++---
 src/schema/rules/checks/events.yaml |  24 +-
 src/schema/rules/checks/fmap.yaml   |  36 +--
 4 files changed, 310 insertions(+), 310 deletions(-)

diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml
index c2310ff937..47d6d3c110 100644
--- a/src/schema/rules/checks/asl.yaml
+++ b/src/schema/rules/checks/asl.yaml
@@ -3,278 +3,278 @@
 
 # 157
 ASLLabelingDurationNiftiLength:
-    issue:
-        code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
-        message: |
-            The number of values for 'LabelingDuration' for this file does not match the 4th dimension
-            of the NIfTI header.
-            'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-            corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-            In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
-            specified.
-            In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-            an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
-            zero.
-            In case an array of numbers is provided, its length should be equal to the number of volumes specified in
-            `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
-    checks:
-    - nifti_header.dim[4] == len(sidecar.LabelingDuration)
+  issue:
+    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+    message: |
+      The number of values for 'LabelingDuration' for this file does not match the 4th dimension
+      of the NIfTI header.
+      'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+      corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+      In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
+      specified.
+      In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+      an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
+      zero.
+      In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+      `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - sidecar contains "LabelingDuration"
+  - type(sidecar.LabelingDuration) == "array"
+  checks:
+  - nifti_header.dim[4] == len(sidecar.LabelingDuration)
 
 # 165
 ASLContextConsistent:
-    issue:
-        code: ASLCONTEXT_TSV_NOT_CONSISTENT
-        message: |
-            The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
-            values in the NIfTI header.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    checks:
-    - nifti_header.dim[4] == associations.aslcontext.n_rows
+  issue:
+    code: ASLCONTEXT_TSV_NOT_CONSISTENT
+    message: |
+      The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+      values in the NIfTI header.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  checks:
+  - nifti_header.dim[4] == associations.aslcontext.n_rows
 
 # 168
 ASLFlipAngleNiftiLength:
-    issue:
-        code: FLIP_ANGLE_NOT_MATCHING_NIFTI
-        message: |
-            The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
-            'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
-            Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
-            The data type number may apply to files from any MRI modality concerned with a single value for this field,
-            or to the files in a file collection where the value of this field is iterated using the flip entity.
-            The data type array provides a value for each volume in a 4D dataset and should only be used when the
-            volume timing is critical for interpretation of the data, such as in ASL or variable flip
-            angle fMRI sequences.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
-    checks:
-    - nifti_header.dim[4] == len(sidecar.FlipAngle)
+  issue:
+    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
+    message: |
+      The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+      'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+      Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+      The data type number may apply to files from any MRI modality concerned with a single value for this field,
+      or to the files in a file collection where the value of this field is iterated using the flip entity.
+      The data type array provides a value for each volume in a 4D dataset and should only be used when the
+      volume timing is critical for interpretation of the data, such as in ASL or variable flip
+      angle fMRI sequences.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - sidecar contains "FlipAngle"
+  - type(sidecar.FlipAngle) == "array"
+  checks:
+  - nifti_header.dim[4] == len(sidecar.FlipAngle)
 
 # 172
 ASLFlipAngleASLContextLength:
-    issue:
-        code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
-        message: |
-            The number of values for 'FlipAngle' for this file does not match the number of volumes in the
-            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
-            Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
-            The data type number may apply to files from any MRI modality concerned with a single value for this field,
-            or to the files in a file collection where the value of this field is iterated using the flip entity.
-            The data type array provides a value for each volume in a 4D dataset and should only be used when the volume
-            timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
-    checks:
-    - aslcontext.n_rows == sidecar.FlipAngle.size
+  issue:
+    code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
+    message: |
+      The number of values for 'FlipAngle' for this file does not match the number of volumes in the
+      'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees.
+      Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
+      The data type number may apply to files from any MRI modality concerned with a single value for this field,
+      or to the files in a file collection where the value of this field is iterated using the flip entity.
+      The data type array provides a value for each volume in a 4D dataset and should only be used when the volume
+      timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "FlipAngle"
+  - type(sidecar.FlipAngle) == "array"
+  checks:
+  - aslcontext.n_rows == sidecar.FlipAngle.size
 
 # 173
 ASLPostLabelingDelayNiftiLength:
-    issue:
-        code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
-        message: |
-            The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
-            header.
-            'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
-            labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
-            (for 3D acquisition) or first slice (for 2D acquisition).
-            Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume
-            (that is, each 'control' and 'label')
-            in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is
-            indicated by a zero.
-            Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
-    checks:
-    - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
+  issue:
+    code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
+    message: |
+      The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
+      header.
+      'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
+      labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
+      (for 3D acquisition) or first slice (for 2D acquisition).
+      Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+      In the latter case, the array of numbers contains the PLD of each volume
+      (that is, each 'control' and 'label')
+      in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is
+      indicated by a zero.
+      Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - sidecar contains "PostLabelingDelay"
+  - type(sidecar.PostLabelingDelay) == "array"
+  checks:
+  - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
 # 174
 ASLPostLabelingDelayASLContextLength:
-    issue:
-        code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
-        message: |
-            The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
-            in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
-            middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
-            the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
-            Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume
-            (that is, each 'control' and 'label')
-            in the acquisition order.
-            Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a zero.
-            Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
-    checks:
-    - aslcontext.n_rows == sidecar.PostLabelingDelay.size
+  issue:
+    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
+    message: |
+      The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+      in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+      middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+      the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+      Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+      In the latter case, the array of numbers contains the PLD of each volume
+      (that is, each 'control' and 'label')
+      in the acquisition order.
+      Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a zero.
+      Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "PostLabelingDelay"
+  - type(sidecar.PostLabelingDelay) == "array"
+  checks:
+  - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
 # 175
 ASLLabelingDurationASLContextLength:
-    issue:
-        code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
-        message: |
-            The number of values for 'LabelingDuration' for this file does not match the number of volumes
-            in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-            corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-            In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
-            a scalar must be specified.
-            In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-            an array of numbers must be specified, for which any `m0scan` in the timeseries has a
-            `LabelingDuration` of zero.
-            In case an array of numbers is provided, its length should be equal to the number of volumes
-            specified in `*_aslcontext.tsv`.
-            Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
-    checks:
-    - aslcontext.n_rows == sidecar.LabelingDuration.size
+  issue:
+    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+    message: |
+      The number of values for 'LabelingDuration' for this file does not match the number of volumes
+      in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+      corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+      In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+      a scalar must be specified.
+      In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+      an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+      `LabelingDuration` of zero.
+      In case an array of numbers is provided, its length should be equal to the number of volumes
+      specified in `*_aslcontext.tsv`.
+      Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "LabelingDuration"
+  - type(sidecar.LabelingDuration) == "array"
+  checks:
+  - aslcontext.n_rows == sidecar.LabelingDuration.size
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
-    issue:
-        code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
-        message: |
-            The number of values of 'RepetitionTimePreparation' for this file does not match the number of
-            volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
-            re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
-            The data type number may apply to files from any MRI modality concerned with a single value for this field.
-            The data type array provides a value for each volume in a 4D dataset and should only be used when the
-            volume timing is critical for interpretation of the data, such as in ASL.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "array"
-    checks:
-    - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
+  issue:
+    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+    message: |
+      The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+      volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+      re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+      The data type number may apply to files from any MRI modality concerned with a single value for this field.
+      The data type array provides a value for each volume in a 4D dataset and should only be used when the
+      volume timing is critical for interpretation of the data, such as in ASL.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "RepetitionTimePreparation"
+  - type(sidecar.RepetitionTimePreparation) == "array"
+  checks:
+  - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
-    issue:
-        code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
-        message: |
-            The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
-            'BackgroundSuppressionPulseTime'.
-            'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
-            Note that this excludes any effect of background suppression pulses applied before the labeling.
-        level: warning
-    selectors:
-    - suffix == "asl"
-    - sidecar contains "BackgroundSuppressionNumberPulses"
-    - sidecar contains "BackgroundSuppressionPulseTime"
-    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
-    checks:
-    - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
+  issue:
+    code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
+    message: |
+      The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
+      'BackgroundSuppressionPulseTime'.
+      'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
+      Note that this excludes any effect of background suppression pulses applied before the labeling.
+    level: warning
+  selectors:
+  - suffix == "asl"
+  - sidecar contains "BackgroundSuppressionNumberPulses"
+  - sidecar contains "BackgroundSuppressionPulseTime"
+  - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+  checks:
+  - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
 # 181
 ASLTotalAcquiredVolumesASLContextLength:
-    issue:
-        code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
-        message: |
-            The number of values for 'TotalAcquiredVolumes' for this file does not match number of
-            volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
-            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        level: warning
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "TotalAcquiredVolumes"
-    checks:
-    - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
+  issue:
+    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+    message: |
+      The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+      volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+      'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+    level: warning
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "TotalAcquiredVolumes"
+  checks:
+  - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
 
 # 196
 ASLEchoTimeASLContextLength:
-    issue:
-        code: ECHO_TIME_NOT_CONSISTENT
-        message: |
-            The number of values for 'EchoTime' for this file does not match number of volumes in the
-            'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-            'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
-        level: warning
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "EchoTime"
-    - type(sidecar.EchoTime) == "array"
-    checks:
-    - aslcontext.n_rows == sidecar.EchoTime.size
+  issue:
+    code: ECHO_TIME_NOT_CONSISTENT
+    message: |
+      The number of values for 'EchoTime' for this file does not match number of volumes in the
+      'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+      'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
+    level: warning
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "EchoTime"
+  - type(sidecar.EchoTime) == "array"
+  checks:
+  - aslcontext.n_rows == sidecar.EchoTime.size
 
 # 198
 ASLM0TypeAbsentScan:
-    issue:
-        code: M0Type_SET_INCORRECTLY_TO_ABSENT
-        message: |
-            You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
-            '*_m0scan.json', or defining the 'M0Estimate' field.
-            This is not allowed, please check that this field are filled correctly.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - associations contains "m0scan"
-    - sidecar contains "M0Type"
-    checks:
-    - sidecar.M0Type != "absent"
+  issue:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT
+    message: |
+      You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
+      '*_m0scan.json', or defining the 'M0Estimate' field.
+      This is not allowed, please check that this field are filled correctly.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - associations contains "m0scan"
+  - sidecar contains "M0Type"
+  checks:
+  - sidecar.M0Type != "absent"
 
 # 199
 ASLM0TypeAbsentASLContext:
-    issue:
-        code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
-        message: |
-            You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
-            This is not allowed, please check that this field are filled correctly.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - aslcontext.volume_type contains "m0scan"
-    - sidecar contains "M0Type"
-    checks:
-    - sidecar.M0Type != "absent"
+  issue:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
+    message: |
+      You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
+      This is not allowed, please check that this field are filled correctly.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - aslcontext.volume_type contains "m0scan"
+  - sidecar contains "M0Type"
+  checks:
+  - sidecar.M0Type != "absent"
 
 # 202
 ASLM0TypeIncorrect:
-    issue:
-        code: M0Type_SET_INCORRECTLY
-        message: |
-            M0Type was not defined correctly.
-            If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
-        level: error
-    selectors:
-    - suffix == "asl"
-    - associations contains "aslcontext"
-    - sidecar contains "M0Type"
-    - sidecar.M0Type == "separate"
-    checks:
-    - associations contains "m0scan"
+  issue:
+    code: M0Type_SET_INCORRECTLY
+    message: |
+      M0Type was not defined correctly.
+      If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
+    level: error
+  selectors:
+  - suffix == "asl"
+  - associations contains "aslcontext"
+  - sidecar contains "M0Type"
+  - sidecar.M0Type == "separate"
+  checks:
+  - associations contains "m0scan"
diff --git a/src/schema/rules/checks/dwi.yaml b/src/schema/rules/checks/dwi.yaml
index e67f05359f..260b71f6bd 100644
--- a/src/schema/rules/checks/dwi.yaml
+++ b/src/schema/rules/checks/dwi.yaml
@@ -3,59 +3,59 @@
 
 # 29
 DWIVolumeCount:
-    code: VOLUME_COUNT_MISMATCH
-    description: |
-        The number of volumes in this scan does not match the number of volumes in the
-        corresponding .bvec and .bval files.
-    level: error
-    selectors:
-    - suffix == "dwi"
-    - associations contains "bval"
-    - associations contains "bvec"
-    checks:
-    - associations.bval.n_cols == nifti_header.dim[4]
-    - associations.bvec.n_cols == nifti_header.dim[4]
+  code: VOLUME_COUNT_MISMATCH
+  description: |
+    The number of volumes in this scan does not match the number of volumes in the
+    corresponding .bvec and .bval files.
+  level: error
+  selectors:
+  - suffix == "dwi"
+  - associations contains "bval"
+  - associations contains "bvec"
+  checks:
+  - associations.bval.n_cols == nifti_header.dim[4]
+  - associations.bvec.n_cols == nifti_header.dim[4]
 
 # 30
 DWIBvalRows:
-    code: BVAL_MULTIPLE_ROWS
-    description: |
-        '.bval' files should contain exactly one row of volumes.
-    level: error
-    selectors:
-    - extension == "bval"
-    checks:
-    - data.n_rows == 1
+  code: BVAL_MULTIPLE_ROWS
+  description: |
+    '.bval' files should contain exactly one row of volumes.
+  level: error
+  selectors:
+  - extension == "bval"
+  checks:
+  - data.n_rows == 1
 
 # 31
 DWIBvecRows:
-    code: BVEC_NUMBER_ROWS
-    description: |
-        '.bvec' files should contain exactly three rows of volumes.
-    level: error
-    selectors:
-    - extension == "bvec"
-    checks:
-    - data.n_rows == 3
+  code: BVEC_NUMBER_ROWS
+  description: |
+    '.bvec' files should contain exactly three rows of volumes.
+  level: error
+  selectors:
+  - extension == "bvec"
+  checks:
+  - data.n_rows == 3
 
 # 32
 DWIMissingBvec:
-    code: DWI_MISSING_BVEC
-    description: |
-        DWI scans must have a corresponding .bvec file.
-    level: error
-    selectors:
-    - suffix == "dwi"
-    checks:
-    - associations contains "bvec"
+  code: DWI_MISSING_BVEC
+  description: |
+    DWI scans must have a corresponding .bvec file.
+  level: error
+  selectors:
+  - suffix == "dwi"
+  checks:
+  - associations contains "bvec"
 
 # 33
 DWIMissingBval:
-    code: DWI_MISSING_BVAL
-    description: |
-        DWI scans must have a corresponding .bval file.
-    level: error
-    selectors:
-    - suffix == "dwi"
-    checks:
-    - associations contains "bval"
+  code: DWI_MISSING_BVAL
+  description: |
+    DWI scans must have a corresponding .bval file.
+  level: error
+  selectors:
+  - suffix == "dwi"
+  checks:
+  - associations contains "bval"
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 58774358b9..ed70539e86 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -3,15 +3,15 @@
 
 # 25
 EventsMissing:
-    issue:
-        code: EVENTS_TSV_MISSING
-        message: |
-            Task scans should have a corresponding events.tsv file.
-            If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
-        level: warning  # could be an error with the proper selectors, I think
-    selectors:
-    - entities contains "task"
-    - entities.task != "rest"
-    - entities.task not(contains "rest")  # Alternative for including the word "rest"
-    checks:
-    - associations contains "events"
+  issue:
+    code: EVENTS_TSV_MISSING
+    message: |
+      Task scans should have a corresponding events.tsv file.
+      If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
+    level: warning  # could be an error with the proper selectors, I think
+  selectors:
+  - entities contains "task"
+  - entities.task != "rest"
+  - entities.task not(contains "rest")  # Alternative for including the word "rest"
+  checks:
+  - associations contains "events"
diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
index b33cf18c90..ed880bf19f 100644
--- a/src/schema/rules/checks/fmap.yaml
+++ b/src/schema/rules/checks/fmap.yaml
@@ -3,24 +3,24 @@
 
 # 91
 FmapFieldmapWithoutMagnitude:
-    issue:
-        code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
-        message: |
-            '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
-        level: error
-    selectors:
-    - suffix == "fieldmap"
-    checks:
-    - associations contains "magnitude"
+  issue:
+    code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
+    message: |
+      '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
+    level: error
+  selectors:
+  - suffix == "fieldmap"
+  checks:
+  - associations contains "magnitude"
 
 # 92
 FmapPhasediffWithoutMagnitude:
-    issue:
-        code: MISSING_MAGNITUDE1_FILE
-        message: |
-            Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
-        level: warning
-    selectors:
-    - suffix == "phasediff"
-    checks:
-    - associations contains "magnitude1"
+  issue:
+    code: MISSING_MAGNITUDE1_FILE
+    message: |
+      Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
+    level: warning
+  selectors:
+  - suffix == "phasediff"
+  checks:
+  - associations contains "magnitude1"

From 0976edaf01d62fb08e38f1cd873d5e6916d8aa98 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 15:00:09 -0700
Subject: [PATCH 333/347] add refs that contain datatype to common imaging
 derivatives

---
 .../derivatives/common_imaging_derivatives.yaml  | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index d85bd543cb..0d5c0654cb 100644
--- a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -36,6 +36,7 @@ func_volumetric:
     desc: OPTIONAL
 
 anat_parametric_mask:
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - mask
   extensions:
@@ -49,6 +50,7 @@ anat_parametric_mask:
     desc: OPTIONAL
 
 anat_nonparametric_mask:
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - mask
   extensions:
@@ -62,6 +64,7 @@ anat_nonparametric_mask:
     desc: OPTIONAL
 
 dwi_mask:
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - mask
   extensions:
@@ -75,6 +78,7 @@ dwi_mask:
     desc: OPTIONAL
 
 func_mask:
+  $ref: schema.rules.datatypes.func.func
   suffixes:
   - mask
   extensions:
@@ -88,6 +92,7 @@ func_mask:
     desc: OPTIONAL
 
 anat_parametric_discrete_segmentation:
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
@@ -99,6 +104,7 @@ anat_parametric_discrete_segmentation:
     den: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
@@ -110,8 +116,9 @@ anat_nonparametric_discrete_segmentation:
     den: OPTIONAL
 
 func_discrete_segmentation:
+  $ref: schema.rules.datatypes.func.func
   suffixes:
-  - desg
+  - dseg
   extensions:
   - .nii.gz
   entities:
@@ -121,6 +128,7 @@ func_discrete_segmentation:
     den: OPTIONAL
 
 dwi_discrete_segmentation:
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - dseg
   extensions:
@@ -132,6 +140,7 @@ dwi_discrete_segmentation:
     den: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - probseg
   extensions:
@@ -144,6 +153,7 @@ anat_parametric_probabilistic_segmentation:
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - probseg
   extensions:
@@ -156,6 +166,7 @@ anat_nonparametric_probabilistic_segmentation:
     label: OPTIONAL
 
 func_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.func.func
   suffixes:
   - probseg
   extensions:
@@ -168,6 +179,7 @@ func_probabilistic_segmentation:
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - probseg
   extensions:
@@ -180,6 +192,7 @@ dwi_probabilistic_segmentation:
     label: OPTIONAL
 
 anat_parametic_discrete_surface:
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
@@ -193,6 +206,7 @@ anat_parametic_discrete_surface:
     den: OPTIONAL
 
 anat_nonparametic_discrete_surface:
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:

From f29eabfa757282fea131ebece8b10a33d4f0ddc0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 15 Apr 2022 15:01:27 -0700
Subject: [PATCH 334/347] add missing periods and use full entity name in
 dataype common imaging derivatives add missing comma in tabular
 common_derivatives

---
 .../common_imaging_derivatives.yaml           | 84 +++++++++----------
 .../derivatives/common_derivatives.yaml       |  2 +-
 2 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index 0d5c0654cb..796449fa74 100644
--- a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -4,8 +4,8 @@ anat_parametric_volumetric:
   entities:
     $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     desc: OPTIONAL
 
 anat_nonparametric_volumetric:
@@ -13,8 +13,8 @@ anat_nonparametric_volumetric:
   entities:
     $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     desc: OPTIONAL
 
 dwi_volumetric:
@@ -22,8 +22,8 @@ dwi_volumetric:
   entities:
     $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     desc: OPTIONAL
 
 func_volumetric:
@@ -31,8 +31,8 @@ func_volumetric:
   entities:
     $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_mask:
@@ -44,8 +44,8 @@ anat_parametric_mask:
   entities:
     $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
     desc: OPTIONAL
 
@@ -58,8 +58,8 @@ anat_nonparametric_mask:
   entities:
     $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
     desc: OPTIONAL
 
@@ -72,8 +72,8 @@ dwi_mask:
   entities:
     $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
     desc: OPTIONAL
 
@@ -86,8 +86,8 @@ func_mask:
   entities:
     $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
     desc: OPTIONAL
 
@@ -100,8 +100,8 @@ anat_parametric_discrete_segmentation:
   entities:
     $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
   $ref: schema.rules.datatypes.anat.nonparametric
@@ -112,8 +112,8 @@ anat_nonparametric_discrete_segmentation:
   entities:
     $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
 
 func_discrete_segmentation:
   $ref: schema.rules.datatypes.func.func
@@ -124,8 +124,8 @@ func_discrete_segmentation:
   entities:
     $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
 
 dwi_discrete_segmentation:
   $ref: schema.rules.datatypes.dwi.dwi
@@ -136,8 +136,8 @@ dwi_discrete_segmentation:
   entities:
     $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
   $ref: schema.rules.datatypes.anat.parametric
@@ -148,8 +148,8 @@ anat_parametric_probabilistic_segmentation:
   entities:
     $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
@@ -161,8 +161,8 @@ anat_nonparametric_probabilistic_segmentation:
   entities:
     $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
 
 func_probabilistic_segmentation:
@@ -174,8 +174,8 @@ func_probabilistic_segmentation:
   entities:
     $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
@@ -187,8 +187,8 @@ dwi_probabilistic_segmentation:
   entities:
     $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
     label: OPTIONAL
 
 anat_parametic_discrete_surface:
@@ -196,25 +196,25 @@ anat_parametic_discrete_surface:
   suffixes:
   - dseg
   extensions:
-  - label.gii
-  - dlabel.nii
+  - .label.gii
+  - .dlabel.nii
   entities:
     $ref: schema.rules.datatypes.anat.parametric.entities
-    hemi: OPTIONAL
+    hemisphere:: OPTIONAL
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
 
 anat_nonparametic_discrete_surface:
   $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
-  - label.gii
-  - dlabel.nii
+  - .label.gii
+  - .dlabel.nii
   entities:
     $ref: schema.rules.datatypes.anat.nonparametric.entities
-    hemi: OPTIONAL
+    hemisphere:: OPTIONAL
     space: OPTIONAL
-    res: OPTIONAL
-    den: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
diff --git a/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
index 237b111436..880a779309 100644
--- a/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
@@ -2,7 +2,7 @@
 SegmentationLookup:
   selectors:
   - dataset.DatasetType == "derivative"
-  - suffix in ["dseg" "probseg"]
+  - suffix in ["dseg", "probseg"]
   columns:
     index: REQUIRED
     name: REQUIRED

From ddab685f097cdd536f9e0df66c92971196beeceb Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Sat, 16 Apr 2022 12:51:30 -0700
Subject: [PATCH 335/347] DOC: Fix iEEG channel object name

---
 src/schema/objects/columns.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index b9547f176f..4b73c82942 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -525,7 +525,7 @@ type__meg_channels:
   - HLU
   - FITERR
   - OTHER
-type__ieg_channels:
+type__ieeg_channels:
   name: type
   description: |
     Type of channel; MUST use the channel types listed below.

From d9e38fa9b45f1d39528bf10baeab30196e6b86e5 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 18 Apr 2022 10:46:36 -0500
Subject: [PATCH 336/347] change  to _ref in schema

---
 .../derivatives/common_derivatives.yaml       | 236 +++++++++---------
 .../common_imaging_derivatives.yaml           |  72 +++---
 2 files changed, 154 insertions(+), 154 deletions(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
index 48c3744f8d..ef5e726473 100644
--- a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
@@ -1,413 +1,413 @@
 ---
 anat_nonparametric_common:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_common:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_defacemask_common:
-  $ref: schema.rules.datatypes.anat.defacemask
+  _ref: schema.rules.datatypes.anat.defacemask
   entities:
-    $ref: schema.rules.datatypes.anat.defacemask.entities
+    _ref: schema.rules.datatypes.anat.defacemask.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiecho_common:
-  $ref: schema.rules.datatypes.anat.multiecho
+  _ref: schema.rules.datatypes.anat.multiecho
   entities:
-    $ref: schema.rules.datatypes.anat.multiecho.entities
+    _ref: schema.rules.datatypes.anat.multiecho.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiflip_common:
-  $ref: schema.rules.datatypes.anat.multiflip
+  _ref: schema.rules.datatypes.anat.multiflip
   entities:
-    $ref: schema.rules.datatypes.anat.multiflip.entities
+    _ref: schema.rules.datatypes.anat.multiflip.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiinversion_common:
-  $ref: schema.rules.datatypes.anat.multiinversion
+  _ref: schema.rules.datatypes.anat.multiinversion
   entities:
-    $ref: schema.rules.datatypes.anat.multiinversion.entities
+    _ref: schema.rules.datatypes.anat.multiinversion.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mp2rage_common:
-  $ref: schema.rules.datatypes.anat.mp2rage
+  _ref: schema.rules.datatypes.anat.mp2rage
   entities:
-    $ref: schema.rules.datatypes.anat.mp2rage.entities
+    _ref: schema.rules.datatypes.anat.mp2rage.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_vfamt_common:
-  $ref: schema.rules.datatypes.anat.vfamt
+  _ref: schema.rules.datatypes.anat.vfamt
   entities:
-    $ref: schema.rules.datatypes.anat.vfamt.entities
+    _ref: schema.rules.datatypes.anat.vfamt.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mtr_common:
-  $ref: schema.rules.datatypes.anat.mtr
+  _ref: schema.rules.datatypes.anat.mtr
   entities:
-    $ref: schema.rules.datatypes.anat.mtr.entities
+    _ref: schema.rules.datatypes.anat.mtr.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_timeseries_common:
-  $ref: schema.rules.datatypes.beh.timeseries
+  _ref: schema.rules.datatypes.beh.timeseries
   entities:
-    $ref: schema.rules.datatypes.beh.timeseries.entities
+    _ref: schema.rules.datatypes.beh.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_noncontinuous_common:
-  $ref: schema.rules.datatypes.beh.noncontinuous
+  _ref: schema.rules.datatypes.beh.noncontinuous
   entities:
-    $ref: schema.rules.datatypes.beh.noncontinuous.entities
+    _ref: schema.rules.datatypes.beh.noncontinuous.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_dwi_common:
-  $ref: schema.rules.datatypes.dwi.dwi
+  _ref: schema.rules.datatypes.dwi.dwi
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    _ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_sbref_common:
-  $ref: schema.rules.datatypes.dwi.sbref
+  _ref: schema.rules.datatypes.dwi.sbref
   entities:
-    $ref: schema.rules.datatypes.dwi.sbref.entities
+    _ref: schema.rules.datatypes.dwi.sbref.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_timeseries_common:
-  $ref: schema.rules.datatypes.dwi.timeseries
+  _ref: schema.rules.datatypes.dwi.timeseries
   entities:
-    $ref: schema.rules.datatypes.dwi.timeseries.entities
+    _ref: schema.rules.datatypes.dwi.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_eeg_common:
-  $ref: schema.rules.datatypes.eeg.eeg
+  _ref: schema.rules.datatypes.eeg.eeg
   entities:
-    $ref: schema.rules.datatypes.eeg.eeg.entities
+    _ref: schema.rules.datatypes.eeg.eeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_channels_common:
-  $ref: schema.rules.datatypes.eeg.channels
+  _ref: schema.rules.datatypes.eeg.channels
   entities:
-    $ref: schema.rules.datatypes.eeg.channels.entities
+    _ref: schema.rules.datatypes.eeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_coordsystem_common:
-  $ref: schema.rules.datatypes.eeg.coordsystem
+  _ref: schema.rules.datatypes.eeg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.eeg.coordsystem.entities
+    _ref: schema.rules.datatypes.eeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_electrodes_common:
-  $ref: schema.rules.datatypes.eeg.electrodes
+  _ref: schema.rules.datatypes.eeg.electrodes
   entities:
-    $ref: schema.rules.datatypes.eeg.electrodes.entities
+    _ref: schema.rules.datatypes.eeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_events_common:
-  $ref: schema.rules.datatypes.eeg.events
+  _ref: schema.rules.datatypes.eeg.events
   entities:
-    $ref: schema.rules.datatypes.eeg.events.entities
+    _ref: schema.rules.datatypes.eeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_photo_common:
-  $ref: schema.rules.datatypes.eeg.photo
+  _ref: schema.rules.datatypes.eeg.photo
   entities:
-    $ref: schema.rules.datatypes.eeg.photo.entities
+    _ref: schema.rules.datatypes.eeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_timeseries_common:
-  $ref: schema.rules.datatypes.eeg.timeseries
+  _ref: schema.rules.datatypes.eeg.timeseries
   entities:
-    $ref: schema.rules.datatypes.eeg.timeseries.entities
+    _ref: schema.rules.datatypes.eeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_fieldmaps_common:
-  $ref: schema.rules.datatypes.fmap.fieldmaps
+  _ref: schema.rules.datatypes.fmap.fieldmaps
   entities:
-    $ref: schema.rules.datatypes.fmap.fieldmaps.entities
+    _ref: schema.rules.datatypes.fmap.fieldmaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_pepolar_common:
-  $ref: schema.rules.datatypes.fmap.pepolar
+  _ref: schema.rules.datatypes.fmap.pepolar
   entities:
-    $ref: schema.rules.datatypes.fmap.pepolar.entities
+    _ref: schema.rules.datatypes.fmap.pepolar.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1DAM_common:
-  $ref: schema.rules.datatypes.fmap.TB1DAM
+  _ref: schema.rules.datatypes.fmap.TB1DAM
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1DAM.entities
+    _ref: schema.rules.datatypes.fmap.TB1DAM.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1EPI_common:
-  $ref: schema.rules.datatypes.fmap.TB1EPI
+  _ref: schema.rules.datatypes.fmap.TB1EPI
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1EPI.entities
+    _ref: schema.rules.datatypes.fmap.TB1EPI.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_RFFieldMaps_common:
-  $ref: schema.rules.datatypes.fmap.RFFieldMaps
+  _ref: schema.rules.datatypes.fmap.RFFieldMaps
   entities:
-    $ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
+    _ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1SRGE_common:
-  $ref: schema.rules.datatypes.fmap.TB1SRGE
+  _ref: schema.rules.datatypes.fmap.TB1SRGE
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1SRGE.entities
+    _ref: schema.rules.datatypes.fmap.TB1SRGE.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_parametric_common:
-  $ref: schema.rules.datatypes.fmap.parametric
+  _ref: schema.rules.datatypes.fmap.parametric
   entities:
-    $ref: schema.rules.datatypes.fmap.parametric.entities
+    _ref: schema.rules.datatypes.fmap.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_func_common:
-  $ref: schema.rules.datatypes.func.func
+  _ref: schema.rules.datatypes.func.func
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    _ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_phase_common:
-  $ref: schema.rules.datatypes.func.phase
+  _ref: schema.rules.datatypes.func.phase
   entities:
-    $ref: schema.rules.datatypes.func.phase.entities
+    _ref: schema.rules.datatypes.func.phase.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_events_common:
-  $ref: schema.rules.datatypes.func.events
+  _ref: schema.rules.datatypes.func.events
   entities:
-    $ref: schema.rules.datatypes.func.events.entities
+    _ref: schema.rules.datatypes.func.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_timeseries_common:
-  $ref: schema.rules.datatypes.func.timeseries
+  _ref: schema.rules.datatypes.func.timeseries
   entities:
-    $ref: schema.rules.datatypes.func.timeseries.entities
+    _ref: schema.rules.datatypes.func.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_ieeg_common:
-  $ref: schema.rules.datatypes.ieeg.ieeg
+  _ref: schema.rules.datatypes.ieeg.ieeg
   entities:
-    $ref: schema.rules.datatypes.ieeg.ieeg.entities
+    _ref: schema.rules.datatypes.ieeg.ieeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_channels_common:
-  $ref: schema.rules.datatypes.ieeg.channels
+  _ref: schema.rules.datatypes.ieeg.channels
   entities:
-    $ref: schema.rules.datatypes.ieeg.channels.entities
+    _ref: schema.rules.datatypes.ieeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_coordsystem_common:
-  $ref: schema.rules.datatypes.ieeg.coordsystem
+  _ref: schema.rules.datatypes.ieeg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.ieeg.coordsystem.entities
+    _ref: schema.rules.datatypes.ieeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_electrodes_common:
-  $ref: schema.rules.datatypes.ieeg.electrodes
+  _ref: schema.rules.datatypes.ieeg.electrodes
   entities:
-    $ref: schema.rules.datatypes.ieeg.electrodes.entities
+    _ref: schema.rules.datatypes.ieeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_events_common:
-  $ref: schema.rules.datatypes.ieeg.events
+  _ref: schema.rules.datatypes.ieeg.events
   entities:
-    $ref: schema.rules.datatypes.ieeg.events.entities
+    _ref: schema.rules.datatypes.ieeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_photo_common:
-  $ref: schema.rules.datatypes.ieeg.photo
+  _ref: schema.rules.datatypes.ieeg.photo
   entities:
-    $ref: schema.rules.datatypes.ieeg.photo.entities
+    _ref: schema.rules.datatypes.ieeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_timeseries_common:
-  $ref: schema.rules.datatypes.ieeg.timeseries
+  _ref: schema.rules.datatypes.ieeg.timeseries
   entities:
-    $ref: schema.rules.datatypes.ieeg.timeseries.entities
+    _ref: schema.rules.datatypes.ieeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_meg_common:
-  $ref: schema.rules.datatypes.meg.meg
+  _ref: schema.rules.datatypes.meg.meg
   entities:
-    $ref: schema.rules.datatypes.meg.meg.entities
+    _ref: schema.rules.datatypes.meg.meg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_calibration_common:
-  $ref: schema.rules.datatypes.meg.calibration
+  _ref: schema.rules.datatypes.meg.calibration
   entities:
-    $ref: schema.rules.datatypes.meg.calibration.entities
+    _ref: schema.rules.datatypes.meg.calibration.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_crosstalk_common:
-  $ref: schema.rules.datatypes.meg.crosstalk
+  _ref: schema.rules.datatypes.meg.crosstalk
   entities:
-    $ref: schema.rules.datatypes.meg.crosstalk.entities
+    _ref: schema.rules.datatypes.meg.crosstalk.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_headshape_common:
-  $ref: schema.rules.datatypes.meg.headshape
+  _ref: schema.rules.datatypes.meg.headshape
   entities:
-    $ref: schema.rules.datatypes.meg.headshape.entities
+    _ref: schema.rules.datatypes.meg.headshape.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_markers_common:
-  $ref: schema.rules.datatypes.meg.markers
+  _ref: schema.rules.datatypes.meg.markers
   entities:
-    $ref: schema.rules.datatypes.meg.markers.entities
+    _ref: schema.rules.datatypes.meg.markers.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_coordsystem_common:
-  $ref: schema.rules.datatypes.meg.coordsystem
+  _ref: schema.rules.datatypes.meg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.meg.coordsystem.entities
+    _ref: schema.rules.datatypes.meg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_channels_common:
-  $ref: schema.rules.datatypes.meg.channels
+  _ref: schema.rules.datatypes.meg.channels
   entities:
-    $ref: schema.rules.datatypes.meg.channels.entities
+    _ref: schema.rules.datatypes.meg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_events_common:
-  $ref: schema.rules.datatypes.meg.events
+  _ref: schema.rules.datatypes.meg.events
   entities:
-    $ref: schema.rules.datatypes.meg.events.entities
+    _ref: schema.rules.datatypes.meg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_photo_common:
-  $ref: schema.rules.datatypes.meg.photo
+  _ref: schema.rules.datatypes.meg.photo
   entities:
-    $ref: schema.rules.datatypes.meg.photo.entities
+    _ref: schema.rules.datatypes.meg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_timeseries_common:
-  $ref: schema.rules.datatypes.meg.timeseries
+  _ref: schema.rules.datatypes.meg.timeseries
   entities:
-    $ref: schema.rules.datatypes.meg.timeseries.entities
+    _ref: schema.rules.datatypes.meg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_microscopy_common:
-  $ref: schema.rules.datatypes.micr.microscopy
+  _ref: schema.rules.datatypes.micr.microscopy
   entities:
-    $ref: schema.rules.datatypes.micr.microscopy.entities
+    _ref: schema.rules.datatypes.micr.microscopy.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_photo_common:
-  $ref: schema.rules.datatypes.micr.photo
+  _ref: schema.rules.datatypes.micr.photo
   entities:
-    $ref: schema.rules.datatypes.micr.photo.entities
+    _ref: schema.rules.datatypes.micr.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asl_common:
-  $ref: schema.rules.datatypes.perf.asl
+  _ref: schema.rules.datatypes.perf.asl
   entities:
-    $ref: schema.rules.datatypes.perf.asl.entities
+    _ref: schema.rules.datatypes.perf.asl.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_aslcontext_common:
-  $ref: schema.rules.datatypes.perf.aslcontext
+  _ref: schema.rules.datatypes.perf.aslcontext
   entities:
-    $ref: schema.rules.datatypes.perf.aslcontext.entities
+    _ref: schema.rules.datatypes.perf.aslcontext.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asllabeling_common:
-  $ref: schema.rules.datatypes.perf.asllabeling
+  _ref: schema.rules.datatypes.perf.asllabeling
   entities:
-    $ref: schema.rules.datatypes.perf.asllabeling.entities
+    _ref: schema.rules.datatypes.perf.asllabeling.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_timeseries_common:
-  $ref: schema.rules.datatypes.perf.timeseries
+  _ref: schema.rules.datatypes.perf.timeseries
   entities:
-    $ref: schema.rules.datatypes.perf.timeseries.entities
+    _ref: schema.rules.datatypes.perf.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_pet_common:
-  $ref: schema.rules.datatypes.pet.pet
+  _ref: schema.rules.datatypes.pet.pet
   entities:
-    $ref: schema.rules.datatypes.pet.pet.entities
+    _ref: schema.rules.datatypes.pet.pet.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_blood_common:
-  $ref: schema.rules.datatypes.pet.blood
+  _ref: schema.rules.datatypes.pet.blood
   entities:
-    $ref: schema.rules.datatypes.pet.blood.entities
+    _ref: schema.rules.datatypes.pet.blood.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_events_common:
-  $ref: schema.rules.datatypes.pet.events
+  _ref: schema.rules.datatypes.pet.events
   entities:
-    $ref: schema.rules.datatypes.pet.events.entities
+    _ref: schema.rules.datatypes.pet.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_timeseries_common:
-  $ref: schema.rules.datatypes.pet.timeseries
+  _ref: schema.rules.datatypes.pet.timeseries
   entities:
-    $ref: schema.rules.datatypes.pet.timeseries.entities
+    _ref: schema.rules.datatypes.pet.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
diff --git a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index 796449fa74..7ab10f001c 100644
--- a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -1,48 +1,48 @@
 ---
 anat_parametric_volumetric:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_nonparametric_volumetric:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 dwi_volumetric:
-  $ref: schema.rules.datatypes.dwi.dwi
+  _ref: schema.rules.datatypes.dwi.dwi
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    _ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 func_volumetric:
-  $ref: schema.rules.datatypes.func.func
+  _ref: schema.rules.datatypes.func.func
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    _ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_mask:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -50,13 +50,13 @@ anat_parametric_mask:
     desc: OPTIONAL
 
 anat_nonparametric_mask:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -64,13 +64,13 @@ anat_nonparametric_mask:
     desc: OPTIONAL
 
 dwi_mask:
-  $ref: schema.rules.datatypes.dwi.dwi
+  _ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    _ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -78,13 +78,13 @@ dwi_mask:
     desc: OPTIONAL
 
 func_mask:
-  $ref: schema.rules.datatypes.func.func
+  _ref: schema.rules.datatypes.func.func
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    _ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -92,128 +92,128 @@ func_mask:
     desc: OPTIONAL
 
 anat_parametric_discrete_segmentation:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 func_discrete_segmentation:
-  $ref: schema.rules.datatypes.func.func
+  _ref: schema.rules.datatypes.func.func
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    _ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 dwi_discrete_segmentation:
-  $ref: schema.rules.datatypes.dwi.dwi
+  _ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    _ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 func_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.func.func
+  _ref: schema.rules.datatypes.func.func
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    _ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.dwi.dwi
+  _ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    _ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_parametic_discrete_surface:
-  $ref: schema.rules.datatypes.anat.parametric
+  _ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    _ref: schema.rules.datatypes.anat.parametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametic_discrete_surface:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  _ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    _ref: schema.rules.datatypes.anat.nonparametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL

From dca1564f0be4318ebe49ad8ee8d00bba857653d3 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 19 Apr 2022 10:35:42 -0500
Subject: [PATCH 337/347] remove excessive commas and add missing underscore
 (#1083)

---
 src/schema/README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/schema/README.md b/src/schema/README.md
index 15218a1720..aaa365db47 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -1,9 +1,9 @@
 # BIDS-schema
 
-Portions of the BIDS specification are defined using YAML files, in order to
+Portions of the BIDS specification are defined using YAML files in order to
 make the specification machine-readable.
 
-Currently, the portions of the specification that rely on this schema are
+Currently the portions of the specification that rely on this schema are
 the entity tables, entity definitions, filename templates, and metadata tables.
 Any changes to the specification should be mirrored in the schema.
 
@@ -73,7 +73,7 @@ For objects with `snake_case` names, two underscores must be used.
 There should also be a comment near the object definition in the YAML file describing the nature of the different objects.
 
 For example, the TSV column `"reference"` means different things when used for EEG data, as compared to iEEG data.
-As such, there are two definitions in `columns.yaml` for the `"reference"` column: `"reference__eeg"` and `"reference_ieeg"`.
+As such, there are two definitions in `columns.yaml` for the `"reference"` column: `"reference__eeg"` and `"reference__ieeg"`.
 
 ```yaml
 # reference column for channels.tsv files for EEG data

From f51869b24f605c04536031a681553ec19d9d3479 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 20 Apr 2022 12:07:10 -0500
Subject: [PATCH 338/347] Revert "change  to _ref in schema"

This reverts commit d9e38fa9b45f1d39528bf10baeab30196e6b86e5.
---
 .../derivatives/common_derivatives.yaml       | 236 +++++++++---------
 .../common_imaging_derivatives.yaml           |  72 +++---
 2 files changed, 154 insertions(+), 154 deletions(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
index ef5e726473..48c3744f8d 100644
--- a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
@@ -1,413 +1,413 @@
 ---
 anat_nonparametric_common:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_common:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_defacemask_common:
-  _ref: schema.rules.datatypes.anat.defacemask
+  $ref: schema.rules.datatypes.anat.defacemask
   entities:
-    _ref: schema.rules.datatypes.anat.defacemask.entities
+    $ref: schema.rules.datatypes.anat.defacemask.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiecho_common:
-  _ref: schema.rules.datatypes.anat.multiecho
+  $ref: schema.rules.datatypes.anat.multiecho
   entities:
-    _ref: schema.rules.datatypes.anat.multiecho.entities
+    $ref: schema.rules.datatypes.anat.multiecho.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiflip_common:
-  _ref: schema.rules.datatypes.anat.multiflip
+  $ref: schema.rules.datatypes.anat.multiflip
   entities:
-    _ref: schema.rules.datatypes.anat.multiflip.entities
+    $ref: schema.rules.datatypes.anat.multiflip.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiinversion_common:
-  _ref: schema.rules.datatypes.anat.multiinversion
+  $ref: schema.rules.datatypes.anat.multiinversion
   entities:
-    _ref: schema.rules.datatypes.anat.multiinversion.entities
+    $ref: schema.rules.datatypes.anat.multiinversion.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mp2rage_common:
-  _ref: schema.rules.datatypes.anat.mp2rage
+  $ref: schema.rules.datatypes.anat.mp2rage
   entities:
-    _ref: schema.rules.datatypes.anat.mp2rage.entities
+    $ref: schema.rules.datatypes.anat.mp2rage.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_vfamt_common:
-  _ref: schema.rules.datatypes.anat.vfamt
+  $ref: schema.rules.datatypes.anat.vfamt
   entities:
-    _ref: schema.rules.datatypes.anat.vfamt.entities
+    $ref: schema.rules.datatypes.anat.vfamt.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mtr_common:
-  _ref: schema.rules.datatypes.anat.mtr
+  $ref: schema.rules.datatypes.anat.mtr
   entities:
-    _ref: schema.rules.datatypes.anat.mtr.entities
+    $ref: schema.rules.datatypes.anat.mtr.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_timeseries_common:
-  _ref: schema.rules.datatypes.beh.timeseries
+  $ref: schema.rules.datatypes.beh.timeseries
   entities:
-    _ref: schema.rules.datatypes.beh.timeseries.entities
+    $ref: schema.rules.datatypes.beh.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_noncontinuous_common:
-  _ref: schema.rules.datatypes.beh.noncontinuous
+  $ref: schema.rules.datatypes.beh.noncontinuous
   entities:
-    _ref: schema.rules.datatypes.beh.noncontinuous.entities
+    $ref: schema.rules.datatypes.beh.noncontinuous.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_dwi_common:
-  _ref: schema.rules.datatypes.dwi.dwi
+  $ref: schema.rules.datatypes.dwi.dwi
   entities:
-    _ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_sbref_common:
-  _ref: schema.rules.datatypes.dwi.sbref
+  $ref: schema.rules.datatypes.dwi.sbref
   entities:
-    _ref: schema.rules.datatypes.dwi.sbref.entities
+    $ref: schema.rules.datatypes.dwi.sbref.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_timeseries_common:
-  _ref: schema.rules.datatypes.dwi.timeseries
+  $ref: schema.rules.datatypes.dwi.timeseries
   entities:
-    _ref: schema.rules.datatypes.dwi.timeseries.entities
+    $ref: schema.rules.datatypes.dwi.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_eeg_common:
-  _ref: schema.rules.datatypes.eeg.eeg
+  $ref: schema.rules.datatypes.eeg.eeg
   entities:
-    _ref: schema.rules.datatypes.eeg.eeg.entities
+    $ref: schema.rules.datatypes.eeg.eeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_channels_common:
-  _ref: schema.rules.datatypes.eeg.channels
+  $ref: schema.rules.datatypes.eeg.channels
   entities:
-    _ref: schema.rules.datatypes.eeg.channels.entities
+    $ref: schema.rules.datatypes.eeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_coordsystem_common:
-  _ref: schema.rules.datatypes.eeg.coordsystem
+  $ref: schema.rules.datatypes.eeg.coordsystem
   entities:
-    _ref: schema.rules.datatypes.eeg.coordsystem.entities
+    $ref: schema.rules.datatypes.eeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_electrodes_common:
-  _ref: schema.rules.datatypes.eeg.electrodes
+  $ref: schema.rules.datatypes.eeg.electrodes
   entities:
-    _ref: schema.rules.datatypes.eeg.electrodes.entities
+    $ref: schema.rules.datatypes.eeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_events_common:
-  _ref: schema.rules.datatypes.eeg.events
+  $ref: schema.rules.datatypes.eeg.events
   entities:
-    _ref: schema.rules.datatypes.eeg.events.entities
+    $ref: schema.rules.datatypes.eeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_photo_common:
-  _ref: schema.rules.datatypes.eeg.photo
+  $ref: schema.rules.datatypes.eeg.photo
   entities:
-    _ref: schema.rules.datatypes.eeg.photo.entities
+    $ref: schema.rules.datatypes.eeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_timeseries_common:
-  _ref: schema.rules.datatypes.eeg.timeseries
+  $ref: schema.rules.datatypes.eeg.timeseries
   entities:
-    _ref: schema.rules.datatypes.eeg.timeseries.entities
+    $ref: schema.rules.datatypes.eeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_fieldmaps_common:
-  _ref: schema.rules.datatypes.fmap.fieldmaps
+  $ref: schema.rules.datatypes.fmap.fieldmaps
   entities:
-    _ref: schema.rules.datatypes.fmap.fieldmaps.entities
+    $ref: schema.rules.datatypes.fmap.fieldmaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_pepolar_common:
-  _ref: schema.rules.datatypes.fmap.pepolar
+  $ref: schema.rules.datatypes.fmap.pepolar
   entities:
-    _ref: schema.rules.datatypes.fmap.pepolar.entities
+    $ref: schema.rules.datatypes.fmap.pepolar.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1DAM_common:
-  _ref: schema.rules.datatypes.fmap.TB1DAM
+  $ref: schema.rules.datatypes.fmap.TB1DAM
   entities:
-    _ref: schema.rules.datatypes.fmap.TB1DAM.entities
+    $ref: schema.rules.datatypes.fmap.TB1DAM.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1EPI_common:
-  _ref: schema.rules.datatypes.fmap.TB1EPI
+  $ref: schema.rules.datatypes.fmap.TB1EPI
   entities:
-    _ref: schema.rules.datatypes.fmap.TB1EPI.entities
+    $ref: schema.rules.datatypes.fmap.TB1EPI.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_RFFieldMaps_common:
-  _ref: schema.rules.datatypes.fmap.RFFieldMaps
+  $ref: schema.rules.datatypes.fmap.RFFieldMaps
   entities:
-    _ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
+    $ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1SRGE_common:
-  _ref: schema.rules.datatypes.fmap.TB1SRGE
+  $ref: schema.rules.datatypes.fmap.TB1SRGE
   entities:
-    _ref: schema.rules.datatypes.fmap.TB1SRGE.entities
+    $ref: schema.rules.datatypes.fmap.TB1SRGE.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_parametric_common:
-  _ref: schema.rules.datatypes.fmap.parametric
+  $ref: schema.rules.datatypes.fmap.parametric
   entities:
-    _ref: schema.rules.datatypes.fmap.parametric.entities
+    $ref: schema.rules.datatypes.fmap.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_func_common:
-  _ref: schema.rules.datatypes.func.func
+  $ref: schema.rules.datatypes.func.func
   entities:
-    _ref: schema.rules.datatypes.func.func.entities
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_phase_common:
-  _ref: schema.rules.datatypes.func.phase
+  $ref: schema.rules.datatypes.func.phase
   entities:
-    _ref: schema.rules.datatypes.func.phase.entities
+    $ref: schema.rules.datatypes.func.phase.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_events_common:
-  _ref: schema.rules.datatypes.func.events
+  $ref: schema.rules.datatypes.func.events
   entities:
-    _ref: schema.rules.datatypes.func.events.entities
+    $ref: schema.rules.datatypes.func.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_timeseries_common:
-  _ref: schema.rules.datatypes.func.timeseries
+  $ref: schema.rules.datatypes.func.timeseries
   entities:
-    _ref: schema.rules.datatypes.func.timeseries.entities
+    $ref: schema.rules.datatypes.func.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_ieeg_common:
-  _ref: schema.rules.datatypes.ieeg.ieeg
+  $ref: schema.rules.datatypes.ieeg.ieeg
   entities:
-    _ref: schema.rules.datatypes.ieeg.ieeg.entities
+    $ref: schema.rules.datatypes.ieeg.ieeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_channels_common:
-  _ref: schema.rules.datatypes.ieeg.channels
+  $ref: schema.rules.datatypes.ieeg.channels
   entities:
-    _ref: schema.rules.datatypes.ieeg.channels.entities
+    $ref: schema.rules.datatypes.ieeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_coordsystem_common:
-  _ref: schema.rules.datatypes.ieeg.coordsystem
+  $ref: schema.rules.datatypes.ieeg.coordsystem
   entities:
-    _ref: schema.rules.datatypes.ieeg.coordsystem.entities
+    $ref: schema.rules.datatypes.ieeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_electrodes_common:
-  _ref: schema.rules.datatypes.ieeg.electrodes
+  $ref: schema.rules.datatypes.ieeg.electrodes
   entities:
-    _ref: schema.rules.datatypes.ieeg.electrodes.entities
+    $ref: schema.rules.datatypes.ieeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_events_common:
-  _ref: schema.rules.datatypes.ieeg.events
+  $ref: schema.rules.datatypes.ieeg.events
   entities:
-    _ref: schema.rules.datatypes.ieeg.events.entities
+    $ref: schema.rules.datatypes.ieeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_photo_common:
-  _ref: schema.rules.datatypes.ieeg.photo
+  $ref: schema.rules.datatypes.ieeg.photo
   entities:
-    _ref: schema.rules.datatypes.ieeg.photo.entities
+    $ref: schema.rules.datatypes.ieeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_timeseries_common:
-  _ref: schema.rules.datatypes.ieeg.timeseries
+  $ref: schema.rules.datatypes.ieeg.timeseries
   entities:
-    _ref: schema.rules.datatypes.ieeg.timeseries.entities
+    $ref: schema.rules.datatypes.ieeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_meg_common:
-  _ref: schema.rules.datatypes.meg.meg
+  $ref: schema.rules.datatypes.meg.meg
   entities:
-    _ref: schema.rules.datatypes.meg.meg.entities
+    $ref: schema.rules.datatypes.meg.meg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_calibration_common:
-  _ref: schema.rules.datatypes.meg.calibration
+  $ref: schema.rules.datatypes.meg.calibration
   entities:
-    _ref: schema.rules.datatypes.meg.calibration.entities
+    $ref: schema.rules.datatypes.meg.calibration.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_crosstalk_common:
-  _ref: schema.rules.datatypes.meg.crosstalk
+  $ref: schema.rules.datatypes.meg.crosstalk
   entities:
-    _ref: schema.rules.datatypes.meg.crosstalk.entities
+    $ref: schema.rules.datatypes.meg.crosstalk.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_headshape_common:
-  _ref: schema.rules.datatypes.meg.headshape
+  $ref: schema.rules.datatypes.meg.headshape
   entities:
-    _ref: schema.rules.datatypes.meg.headshape.entities
+    $ref: schema.rules.datatypes.meg.headshape.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_markers_common:
-  _ref: schema.rules.datatypes.meg.markers
+  $ref: schema.rules.datatypes.meg.markers
   entities:
-    _ref: schema.rules.datatypes.meg.markers.entities
+    $ref: schema.rules.datatypes.meg.markers.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_coordsystem_common:
-  _ref: schema.rules.datatypes.meg.coordsystem
+  $ref: schema.rules.datatypes.meg.coordsystem
   entities:
-    _ref: schema.rules.datatypes.meg.coordsystem.entities
+    $ref: schema.rules.datatypes.meg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_channels_common:
-  _ref: schema.rules.datatypes.meg.channels
+  $ref: schema.rules.datatypes.meg.channels
   entities:
-    _ref: schema.rules.datatypes.meg.channels.entities
+    $ref: schema.rules.datatypes.meg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_events_common:
-  _ref: schema.rules.datatypes.meg.events
+  $ref: schema.rules.datatypes.meg.events
   entities:
-    _ref: schema.rules.datatypes.meg.events.entities
+    $ref: schema.rules.datatypes.meg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_photo_common:
-  _ref: schema.rules.datatypes.meg.photo
+  $ref: schema.rules.datatypes.meg.photo
   entities:
-    _ref: schema.rules.datatypes.meg.photo.entities
+    $ref: schema.rules.datatypes.meg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_timeseries_common:
-  _ref: schema.rules.datatypes.meg.timeseries
+  $ref: schema.rules.datatypes.meg.timeseries
   entities:
-    _ref: schema.rules.datatypes.meg.timeseries.entities
+    $ref: schema.rules.datatypes.meg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_microscopy_common:
-  _ref: schema.rules.datatypes.micr.microscopy
+  $ref: schema.rules.datatypes.micr.microscopy
   entities:
-    _ref: schema.rules.datatypes.micr.microscopy.entities
+    $ref: schema.rules.datatypes.micr.microscopy.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_photo_common:
-  _ref: schema.rules.datatypes.micr.photo
+  $ref: schema.rules.datatypes.micr.photo
   entities:
-    _ref: schema.rules.datatypes.micr.photo.entities
+    $ref: schema.rules.datatypes.micr.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asl_common:
-  _ref: schema.rules.datatypes.perf.asl
+  $ref: schema.rules.datatypes.perf.asl
   entities:
-    _ref: schema.rules.datatypes.perf.asl.entities
+    $ref: schema.rules.datatypes.perf.asl.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_aslcontext_common:
-  _ref: schema.rules.datatypes.perf.aslcontext
+  $ref: schema.rules.datatypes.perf.aslcontext
   entities:
-    _ref: schema.rules.datatypes.perf.aslcontext.entities
+    $ref: schema.rules.datatypes.perf.aslcontext.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asllabeling_common:
-  _ref: schema.rules.datatypes.perf.asllabeling
+  $ref: schema.rules.datatypes.perf.asllabeling
   entities:
-    _ref: schema.rules.datatypes.perf.asllabeling.entities
+    $ref: schema.rules.datatypes.perf.asllabeling.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_timeseries_common:
-  _ref: schema.rules.datatypes.perf.timeseries
+  $ref: schema.rules.datatypes.perf.timeseries
   entities:
-    _ref: schema.rules.datatypes.perf.timeseries.entities
+    $ref: schema.rules.datatypes.perf.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_pet_common:
-  _ref: schema.rules.datatypes.pet.pet
+  $ref: schema.rules.datatypes.pet.pet
   entities:
-    _ref: schema.rules.datatypes.pet.pet.entities
+    $ref: schema.rules.datatypes.pet.pet.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_blood_common:
-  _ref: schema.rules.datatypes.pet.blood
+  $ref: schema.rules.datatypes.pet.blood
   entities:
-    _ref: schema.rules.datatypes.pet.blood.entities
+    $ref: schema.rules.datatypes.pet.blood.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_events_common:
-  _ref: schema.rules.datatypes.pet.events
+  $ref: schema.rules.datatypes.pet.events
   entities:
-    _ref: schema.rules.datatypes.pet.events.entities
+    $ref: schema.rules.datatypes.pet.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_timeseries_common:
-  _ref: schema.rules.datatypes.pet.timeseries
+  $ref: schema.rules.datatypes.pet.timeseries
   entities:
-    _ref: schema.rules.datatypes.pet.timeseries.entities
+    $ref: schema.rules.datatypes.pet.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
diff --git a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index 7ab10f001c..796449fa74 100644
--- a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -1,48 +1,48 @@
 ---
 anat_parametric_volumetric:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_nonparametric_volumetric:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 dwi_volumetric:
-  _ref: schema.rules.datatypes.dwi.dwi
+  $ref: schema.rules.datatypes.dwi.dwi
   entities:
-    _ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 func_volumetric:
-  _ref: schema.rules.datatypes.func.func
+  $ref: schema.rules.datatypes.func.func
   entities:
-    _ref: schema.rules.datatypes.func.func.entities
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_mask:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -50,13 +50,13 @@ anat_parametric_mask:
     desc: OPTIONAL
 
 anat_nonparametric_mask:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -64,13 +64,13 @@ anat_nonparametric_mask:
     desc: OPTIONAL
 
 dwi_mask:
-  _ref: schema.rules.datatypes.dwi.dwi
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -78,13 +78,13 @@ dwi_mask:
     desc: OPTIONAL
 
 func_mask:
-  _ref: schema.rules.datatypes.func.func
+  $ref: schema.rules.datatypes.func.func
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.func.func.entities
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -92,128 +92,128 @@ func_mask:
     desc: OPTIONAL
 
 anat_parametric_discrete_segmentation:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 func_discrete_segmentation:
-  _ref: schema.rules.datatypes.func.func
+  $ref: schema.rules.datatypes.func.func
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.func.func.entities
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 dwi_discrete_segmentation:
-  _ref: schema.rules.datatypes.dwi.dwi
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 func_probabilistic_segmentation:
-  _ref: schema.rules.datatypes.func.func
+  $ref: schema.rules.datatypes.func.func
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.func.func.entities
+    $ref: schema.rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
-  _ref: schema.rules.datatypes.dwi.dwi
+  $ref: schema.rules.datatypes.dwi.dwi
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    _ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: schema.rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_parametic_discrete_surface:
-  _ref: schema.rules.datatypes.anat.parametric
+  $ref: schema.rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    _ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: schema.rules.datatypes.anat.parametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametic_discrete_surface:
-  _ref: schema.rules.datatypes.anat.nonparametric
+  $ref: schema.rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    _ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: schema.rules.datatypes.anat.nonparametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL

From cdbd725274b631c3f5de5c7b585a84b9a149af52 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Anibal=20S=C3=B3lon?= <anibalsolon@gmail.com>
Date: Wed, 20 Apr 2022 12:10:06 -0500
Subject: [PATCH 339/347] [MNT] Set light and dark mode image for logo in
 README (#1085)

* fix: set image for light and dark mode

* fix: set image height
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3ac31ba5ed..5bf0f2b55b 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,8 @@
 [![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/BIDSstandard)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061)
 
-<img src="./BIDS_logo/BIDS_logo_black_transparent_background_crop.png" alt="bids-logo" width="600"/>
+<img src="./BIDS_logo/BIDS_logo_white_transparent_background_crop.png#gh-dark-mode-only" alt="bids-logo" width="600"/>
+<img src="./BIDS_logo/BIDS_logo_black_transparent_background_crop.png#gh-light-mode-only" alt="bids-logo" width="600"/>
 
 The [Brain Imaging Data Structure (BIDS)](https://bids.neuroimaging.io) is an emerging standard for the
 organisation of neuroimaging data.

From bb2285cbcd5a7b619af8605bb93c2928c7a955c7 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 20 Apr 2022 13:12:26 -0500
Subject: [PATCH 340/347] remove 'schema' at root of references in derivative
 schema

---
 .../derivatives/common_derivatives.yaml       | 236 +++++++++---------
 .../common_imaging_derivatives.yaml           |  72 +++---
 2 files changed, 154 insertions(+), 154 deletions(-)

diff --git a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
index 48c3744f8d..adddf62f37 100644
--- a/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_derivatives.yaml
@@ -1,413 +1,413 @@
 ---
 anat_nonparametric_common:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_common:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_defacemask_common:
-  $ref: schema.rules.datatypes.anat.defacemask
+  $ref: rules.datatypes.anat.defacemask
   entities:
-    $ref: schema.rules.datatypes.anat.defacemask.entities
+    $ref: rules.datatypes.anat.defacemask.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiecho_common:
-  $ref: schema.rules.datatypes.anat.multiecho
+  $ref: rules.datatypes.anat.multiecho
   entities:
-    $ref: schema.rules.datatypes.anat.multiecho.entities
+    $ref: rules.datatypes.anat.multiecho.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiflip_common:
-  $ref: schema.rules.datatypes.anat.multiflip
+  $ref: rules.datatypes.anat.multiflip
   entities:
-    $ref: schema.rules.datatypes.anat.multiflip.entities
+    $ref: rules.datatypes.anat.multiflip.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_multiinversion_common:
-  $ref: schema.rules.datatypes.anat.multiinversion
+  $ref: rules.datatypes.anat.multiinversion
   entities:
-    $ref: schema.rules.datatypes.anat.multiinversion.entities
+    $ref: rules.datatypes.anat.multiinversion.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mp2rage_common:
-  $ref: schema.rules.datatypes.anat.mp2rage
+  $ref: rules.datatypes.anat.mp2rage
   entities:
-    $ref: schema.rules.datatypes.anat.mp2rage.entities
+    $ref: rules.datatypes.anat.mp2rage.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_vfamt_common:
-  $ref: schema.rules.datatypes.anat.vfamt
+  $ref: rules.datatypes.anat.vfamt
   entities:
-    $ref: schema.rules.datatypes.anat.vfamt.entities
+    $ref: rules.datatypes.anat.vfamt.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 anat_mtr_common:
-  $ref: schema.rules.datatypes.anat.mtr
+  $ref: rules.datatypes.anat.mtr
   entities:
-    $ref: schema.rules.datatypes.anat.mtr.entities
+    $ref: rules.datatypes.anat.mtr.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_timeseries_common:
-  $ref: schema.rules.datatypes.beh.timeseries
+  $ref: rules.datatypes.beh.timeseries
   entities:
-    $ref: schema.rules.datatypes.beh.timeseries.entities
+    $ref: rules.datatypes.beh.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 beh_noncontinuous_common:
-  $ref: schema.rules.datatypes.beh.noncontinuous
+  $ref: rules.datatypes.beh.noncontinuous
   entities:
-    $ref: schema.rules.datatypes.beh.noncontinuous.entities
+    $ref: rules.datatypes.beh.noncontinuous.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_dwi_common:
-  $ref: schema.rules.datatypes.dwi.dwi
+  $ref: rules.datatypes.dwi.dwi
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_sbref_common:
-  $ref: schema.rules.datatypes.dwi.sbref
+  $ref: rules.datatypes.dwi.sbref
   entities:
-    $ref: schema.rules.datatypes.dwi.sbref.entities
+    $ref: rules.datatypes.dwi.sbref.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 dwi_timeseries_common:
-  $ref: schema.rules.datatypes.dwi.timeseries
+  $ref: rules.datatypes.dwi.timeseries
   entities:
-    $ref: schema.rules.datatypes.dwi.timeseries.entities
+    $ref: rules.datatypes.dwi.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_eeg_common:
-  $ref: schema.rules.datatypes.eeg.eeg
+  $ref: rules.datatypes.eeg.eeg
   entities:
-    $ref: schema.rules.datatypes.eeg.eeg.entities
+    $ref: rules.datatypes.eeg.eeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_channels_common:
-  $ref: schema.rules.datatypes.eeg.channels
+  $ref: rules.datatypes.eeg.channels
   entities:
-    $ref: schema.rules.datatypes.eeg.channels.entities
+    $ref: rules.datatypes.eeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_coordsystem_common:
-  $ref: schema.rules.datatypes.eeg.coordsystem
+  $ref: rules.datatypes.eeg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.eeg.coordsystem.entities
+    $ref: rules.datatypes.eeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_electrodes_common:
-  $ref: schema.rules.datatypes.eeg.electrodes
+  $ref: rules.datatypes.eeg.electrodes
   entities:
-    $ref: schema.rules.datatypes.eeg.electrodes.entities
+    $ref: rules.datatypes.eeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_events_common:
-  $ref: schema.rules.datatypes.eeg.events
+  $ref: rules.datatypes.eeg.events
   entities:
-    $ref: schema.rules.datatypes.eeg.events.entities
+    $ref: rules.datatypes.eeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_photo_common:
-  $ref: schema.rules.datatypes.eeg.photo
+  $ref: rules.datatypes.eeg.photo
   entities:
-    $ref: schema.rules.datatypes.eeg.photo.entities
+    $ref: rules.datatypes.eeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 eeg_timeseries_common:
-  $ref: schema.rules.datatypes.eeg.timeseries
+  $ref: rules.datatypes.eeg.timeseries
   entities:
-    $ref: schema.rules.datatypes.eeg.timeseries.entities
+    $ref: rules.datatypes.eeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_fieldmaps_common:
-  $ref: schema.rules.datatypes.fmap.fieldmaps
+  $ref: rules.datatypes.fmap.fieldmaps
   entities:
-    $ref: schema.rules.datatypes.fmap.fieldmaps.entities
+    $ref: rules.datatypes.fmap.fieldmaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_pepolar_common:
-  $ref: schema.rules.datatypes.fmap.pepolar
+  $ref: rules.datatypes.fmap.pepolar
   entities:
-    $ref: schema.rules.datatypes.fmap.pepolar.entities
+    $ref: rules.datatypes.fmap.pepolar.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1DAM_common:
-  $ref: schema.rules.datatypes.fmap.TB1DAM
+  $ref: rules.datatypes.fmap.TB1DAM
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1DAM.entities
+    $ref: rules.datatypes.fmap.TB1DAM.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1EPI_common:
-  $ref: schema.rules.datatypes.fmap.TB1EPI
+  $ref: rules.datatypes.fmap.TB1EPI
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1EPI.entities
+    $ref: rules.datatypes.fmap.TB1EPI.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_RFFieldMaps_common:
-  $ref: schema.rules.datatypes.fmap.RFFieldMaps
+  $ref: rules.datatypes.fmap.RFFieldMaps
   entities:
-    $ref: schema.rules.datatypes.fmap.RFFieldMaps.entities
+    $ref: rules.datatypes.fmap.RFFieldMaps.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_TB1SRGE_common:
-  $ref: schema.rules.datatypes.fmap.TB1SRGE
+  $ref: rules.datatypes.fmap.TB1SRGE
   entities:
-    $ref: schema.rules.datatypes.fmap.TB1SRGE.entities
+    $ref: rules.datatypes.fmap.TB1SRGE.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 fmap_parametric_common:
-  $ref: schema.rules.datatypes.fmap.parametric
+  $ref: rules.datatypes.fmap.parametric
   entities:
-    $ref: schema.rules.datatypes.fmap.parametric.entities
+    $ref: rules.datatypes.fmap.parametric.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_func_common:
-  $ref: schema.rules.datatypes.func.func
+  $ref: rules.datatypes.func.func
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    $ref: rules.datatypes.func.func.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_phase_common:
-  $ref: schema.rules.datatypes.func.phase
+  $ref: rules.datatypes.func.phase
   entities:
-    $ref: schema.rules.datatypes.func.phase.entities
+    $ref: rules.datatypes.func.phase.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_events_common:
-  $ref: schema.rules.datatypes.func.events
+  $ref: rules.datatypes.func.events
   entities:
-    $ref: schema.rules.datatypes.func.events.entities
+    $ref: rules.datatypes.func.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 func_timeseries_common:
-  $ref: schema.rules.datatypes.func.timeseries
+  $ref: rules.datatypes.func.timeseries
   entities:
-    $ref: schema.rules.datatypes.func.timeseries.entities
+    $ref: rules.datatypes.func.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_ieeg_common:
-  $ref: schema.rules.datatypes.ieeg.ieeg
+  $ref: rules.datatypes.ieeg.ieeg
   entities:
-    $ref: schema.rules.datatypes.ieeg.ieeg.entities
+    $ref: rules.datatypes.ieeg.ieeg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_channels_common:
-  $ref: schema.rules.datatypes.ieeg.channels
+  $ref: rules.datatypes.ieeg.channels
   entities:
-    $ref: schema.rules.datatypes.ieeg.channels.entities
+    $ref: rules.datatypes.ieeg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_coordsystem_common:
-  $ref: schema.rules.datatypes.ieeg.coordsystem
+  $ref: rules.datatypes.ieeg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.ieeg.coordsystem.entities
+    $ref: rules.datatypes.ieeg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_electrodes_common:
-  $ref: schema.rules.datatypes.ieeg.electrodes
+  $ref: rules.datatypes.ieeg.electrodes
   entities:
-    $ref: schema.rules.datatypes.ieeg.electrodes.entities
+    $ref: rules.datatypes.ieeg.electrodes.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_events_common:
-  $ref: schema.rules.datatypes.ieeg.events
+  $ref: rules.datatypes.ieeg.events
   entities:
-    $ref: schema.rules.datatypes.ieeg.events.entities
+    $ref: rules.datatypes.ieeg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_photo_common:
-  $ref: schema.rules.datatypes.ieeg.photo
+  $ref: rules.datatypes.ieeg.photo
   entities:
-    $ref: schema.rules.datatypes.ieeg.photo.entities
+    $ref: rules.datatypes.ieeg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 ieeg_timeseries_common:
-  $ref: schema.rules.datatypes.ieeg.timeseries
+  $ref: rules.datatypes.ieeg.timeseries
   entities:
-    $ref: schema.rules.datatypes.ieeg.timeseries.entities
+    $ref: rules.datatypes.ieeg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_meg_common:
-  $ref: schema.rules.datatypes.meg.meg
+  $ref: rules.datatypes.meg.meg
   entities:
-    $ref: schema.rules.datatypes.meg.meg.entities
+    $ref: rules.datatypes.meg.meg.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_calibration_common:
-  $ref: schema.rules.datatypes.meg.calibration
+  $ref: rules.datatypes.meg.calibration
   entities:
-    $ref: schema.rules.datatypes.meg.calibration.entities
+    $ref: rules.datatypes.meg.calibration.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_crosstalk_common:
-  $ref: schema.rules.datatypes.meg.crosstalk
+  $ref: rules.datatypes.meg.crosstalk
   entities:
-    $ref: schema.rules.datatypes.meg.crosstalk.entities
+    $ref: rules.datatypes.meg.crosstalk.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_headshape_common:
-  $ref: schema.rules.datatypes.meg.headshape
+  $ref: rules.datatypes.meg.headshape
   entities:
-    $ref: schema.rules.datatypes.meg.headshape.entities
+    $ref: rules.datatypes.meg.headshape.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_markers_common:
-  $ref: schema.rules.datatypes.meg.markers
+  $ref: rules.datatypes.meg.markers
   entities:
-    $ref: schema.rules.datatypes.meg.markers.entities
+    $ref: rules.datatypes.meg.markers.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_coordsystem_common:
-  $ref: schema.rules.datatypes.meg.coordsystem
+  $ref: rules.datatypes.meg.coordsystem
   entities:
-    $ref: schema.rules.datatypes.meg.coordsystem.entities
+    $ref: rules.datatypes.meg.coordsystem.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_channels_common:
-  $ref: schema.rules.datatypes.meg.channels
+  $ref: rules.datatypes.meg.channels
   entities:
-    $ref: schema.rules.datatypes.meg.channels.entities
+    $ref: rules.datatypes.meg.channels.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_events_common:
-  $ref: schema.rules.datatypes.meg.events
+  $ref: rules.datatypes.meg.events
   entities:
-    $ref: schema.rules.datatypes.meg.events.entities
+    $ref: rules.datatypes.meg.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_photo_common:
-  $ref: schema.rules.datatypes.meg.photo
+  $ref: rules.datatypes.meg.photo
   entities:
-    $ref: schema.rules.datatypes.meg.photo.entities
+    $ref: rules.datatypes.meg.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 meg_timeseries_common:
-  $ref: schema.rules.datatypes.meg.timeseries
+  $ref: rules.datatypes.meg.timeseries
   entities:
-    $ref: schema.rules.datatypes.meg.timeseries.entities
+    $ref: rules.datatypes.meg.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_microscopy_common:
-  $ref: schema.rules.datatypes.micr.microscopy
+  $ref: rules.datatypes.micr.microscopy
   entities:
-    $ref: schema.rules.datatypes.micr.microscopy.entities
+    $ref: rules.datatypes.micr.microscopy.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 micr_photo_common:
-  $ref: schema.rules.datatypes.micr.photo
+  $ref: rules.datatypes.micr.photo
   entities:
-    $ref: schema.rules.datatypes.micr.photo.entities
+    $ref: rules.datatypes.micr.photo.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asl_common:
-  $ref: schema.rules.datatypes.perf.asl
+  $ref: rules.datatypes.perf.asl
   entities:
-    $ref: schema.rules.datatypes.perf.asl.entities
+    $ref: rules.datatypes.perf.asl.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_aslcontext_common:
-  $ref: schema.rules.datatypes.perf.aslcontext
+  $ref: rules.datatypes.perf.aslcontext
   entities:
-    $ref: schema.rules.datatypes.perf.aslcontext.entities
+    $ref: rules.datatypes.perf.aslcontext.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_asllabeling_common:
-  $ref: schema.rules.datatypes.perf.asllabeling
+  $ref: rules.datatypes.perf.asllabeling
   entities:
-    $ref: schema.rules.datatypes.perf.asllabeling.entities
+    $ref: rules.datatypes.perf.asllabeling.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 perf_timeseries_common:
-  $ref: schema.rules.datatypes.perf.timeseries
+  $ref: rules.datatypes.perf.timeseries
   entities:
-    $ref: schema.rules.datatypes.perf.timeseries.entities
+    $ref: rules.datatypes.perf.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_pet_common:
-  $ref: schema.rules.datatypes.pet.pet
+  $ref: rules.datatypes.pet.pet
   entities:
-    $ref: schema.rules.datatypes.pet.pet.entities
+    $ref: rules.datatypes.pet.pet.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_blood_common:
-  $ref: schema.rules.datatypes.pet.blood
+  $ref: rules.datatypes.pet.blood
   entities:
-    $ref: schema.rules.datatypes.pet.blood.entities
+    $ref: rules.datatypes.pet.blood.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_events_common:
-  $ref: schema.rules.datatypes.pet.events
+  $ref: rules.datatypes.pet.events
   entities:
-    $ref: schema.rules.datatypes.pet.events.entities
+    $ref: rules.datatypes.pet.events.entities
     space: OPTIONAL
     desc: OPTIONAL
 
 pet_timeseries_common:
-  $ref: schema.rules.datatypes.pet.timeseries
+  $ref: rules.datatypes.pet.timeseries
   entities:
-    $ref: schema.rules.datatypes.pet.timeseries.entities
+    $ref: rules.datatypes.pet.timeseries.entities
     space: OPTIONAL
     desc: OPTIONAL
diff --git a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
index 796449fa74..b41a438081 100644
--- a/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
+++ b/src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
@@ -1,48 +1,48 @@
 ---
 anat_parametric_volumetric:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_nonparametric_volumetric:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 dwi_volumetric:
-  $ref: schema.rules.datatypes.dwi.dwi
+  $ref: rules.datatypes.dwi.dwi
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 func_volumetric:
-  $ref: schema.rules.datatypes.func.func
+  $ref: rules.datatypes.func.func
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    $ref: rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     desc: OPTIONAL
 
 anat_parametric_mask:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -50,13 +50,13 @@ anat_parametric_mask:
     desc: OPTIONAL
 
 anat_nonparametric_mask:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -64,13 +64,13 @@ anat_nonparametric_mask:
     desc: OPTIONAL
 
 dwi_mask:
-  $ref: schema.rules.datatypes.dwi.dwi
+  $ref: rules.datatypes.dwi.dwi
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -78,13 +78,13 @@ dwi_mask:
     desc: OPTIONAL
 
 func_mask:
-  $ref: schema.rules.datatypes.func.func
+  $ref: rules.datatypes.func.func
   suffixes:
   - mask
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    $ref: rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
@@ -92,128 +92,128 @@ func_mask:
     desc: OPTIONAL
 
 anat_parametric_discrete_segmentation:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametric_discrete_segmentation:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 func_discrete_segmentation:
-  $ref: schema.rules.datatypes.func.func
+  $ref: rules.datatypes.func.func
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    $ref: rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 dwi_discrete_segmentation:
-  $ref: schema.rules.datatypes.dwi.dwi
+  $ref: rules.datatypes.dwi.dwi
   suffixes:
   - dseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_parametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_nonparametric_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 func_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.func.func
+  $ref: rules.datatypes.func.func
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.func.func.entities
+    $ref: rules.datatypes.func.func.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 dwi_probabilistic_segmentation:
-  $ref: schema.rules.datatypes.dwi.dwi
+  $ref: rules.datatypes.dwi.dwi
   suffixes:
   - probseg
   extensions:
   - .nii.gz
   entities:
-    $ref: schema.rules.datatypes.dwi.dwi.entities
+    $ref: rules.datatypes.dwi.dwi.entities
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
     label: OPTIONAL
 
 anat_parametic_discrete_surface:
-  $ref: schema.rules.datatypes.anat.parametric
+  $ref: rules.datatypes.anat.parametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    $ref: schema.rules.datatypes.anat.parametric.entities
+    $ref: rules.datatypes.anat.parametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL
     density: OPTIONAL
 
 anat_nonparametic_discrete_surface:
-  $ref: schema.rules.datatypes.anat.nonparametric
+  $ref: rules.datatypes.anat.nonparametric
   suffixes:
   - dseg
   extensions:
   - .label.gii
   - .dlabel.nii
   entities:
-    $ref: schema.rules.datatypes.anat.nonparametric.entities
+    $ref: rules.datatypes.anat.nonparametric.entities
     hemisphere:: OPTIONAL
     space: OPTIONAL
     resolution: OPTIONAL

From 43a42888baad941fe7ee3aeb69164bfd015220f6 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 20 Apr 2022 16:01:14 -0500
Subject: [PATCH 341/347] correct for derivative files found in test_render.py
 datatypes count check

---
 tools/schemacode/schemacode/tests/test_render.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/schemacode/schemacode/tests/test_render.py b/tools/schemacode/schemacode/tests/test_render.py
index 1a05e5b188..b7c45fa34f 100644
--- a/tools/schemacode/schemacode/tests/test_render.py
+++ b/tools/schemacode/schemacode/tests/test_render.py
@@ -104,7 +104,8 @@ def test_make_filename_template(schema_obj, schema_dir):
             datatype_level = True
             datatype_bases_found += 1
     # Are all datatypes listed?
-    assert datatype_bases_found == datatype_count
+    # correct for derivatives files in count
+    assert datatype_bases_found == datatype_count - 2
 
 
 def test_make_entity_table(schema_obj):

From b16a746ae6117d03959b61c0f0224c222df0bdc0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 20 Apr 2022 16:10:08 -0500
Subject: [PATCH 342/347] yamllint asl_validation

---
 src/schema/rules/sidecars/asl_validation.yaml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 3f461396de..8039f78577 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -6,8 +6,8 @@ ASLLabelingDurationNiftiLength:
     issue:
         code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
         message: |
-            The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
-            'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+            The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI
+            header. 'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
             corresponding to the temporal width of the labeling bolus for `(P)CASL`.
             In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
             specified.
@@ -49,7 +49,8 @@ ASLFlipAngleNiftiLength:
             The data type number may apply to files from any MRI modality concerned with a single value for this field,
             or to the files in a file collection where the value of this field is iterated using the flip entity.
             The data type array provides a value for each volume in a 4D dataset and should only be used when the
-            volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
+            volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI
+            sequences.
         level: error
     selectors:
     - suffix == "asl"
@@ -91,7 +92,8 @@ ASLPostLabelingDelayNiftiLength:
             labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
             (for 3D acquisition) or first slice (for 2D acquisition).
             Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
+            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and
+            'label')
             in the acquisition order. Any image within the time-series without a PLD (for example, an 'm0scan') is
             indicated by a zero.
             Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
@@ -114,7 +116,8 @@ ASLPostLabelingDelayASLContextLength:
             middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
             the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
             Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and 'label')
+            In the latter case, the array of numbers contains the PLD of each volume (that is, each 'control' and
+            'label')
             in the acquisition order.
             Any image within the time-series without a PLD (for example, an 'm0scan') is indicated by a zero.
             Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.

From 4beb22d83db908ee1f1f7b3f87c9d9e5a401d6c2 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 25 Apr 2022 12:11:13 -0500
Subject: [PATCH 343/347] convert exisiting schema selectors and checks to be
 more js like

---
 src/schema/rules/checks/asl.yaml              | 89 +++++++++----------
 src/schema/rules/checks/dwi.yaml              |  8 +-
 src/schema/rules/checks/events.yaml           |  6 +-
 src/schema/rules/checks/fmap.yaml             |  4 +-
 .../rules/common_derivatives_validation.yaml  | 16 ++--
 src/schema/rules/dataset_metadata.yaml        |  2 +-
 src/schema/rules/sidecars/asl.yaml            | 26 +++---
 src/schema/rules/sidecars/beh.yaml            |  2 +-
 src/schema/rules/sidecars/continuous.yaml     |  2 +-
 .../derivatives/common_derivatives.yaml       | 22 ++---
 src/schema/rules/sidecars/eeg.yaml            |  4 +-
 src/schema/rules/sidecars/entities.yaml       | 22 ++---
 src/schema/rules/sidecars/fmap.yaml           |  4 +-
 src/schema/rules/sidecars/func.yaml           | 18 ++--
 src/schema/rules/sidecars/ieeg.yaml           |  2 +-
 src/schema/rules/sidecars/meg.yaml            | 14 +--
 src/schema/rules/sidecars/micr.yaml           |  6 +-
 src/schema/rules/sidecars/mri.yaml            | 22 ++---
 .../derivatives/common_derivatives.yaml       |  2 +-
 src/schema/rules/tabular_data/pet.yaml        |  8 +-
 src/schema/rules/tabular_data/task.yaml       |  2 +-
 21 files changed, 140 insertions(+), 141 deletions(-)

diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml
index 47d6d3c110..4e73a513cd 100644
--- a/src/schema/rules/checks/asl.yaml
+++ b/src/schema/rules/checks/asl.yaml
@@ -20,10 +20,10 @@ ASLLabelingDurationNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - sidecar contains "LabelingDuration"
-  - type(sidecar.LabelingDuration) == "array"
+  - 'sidecar'.includes('"LabelingDuration")'
+  - sidecar.LabelingDuration.constructor.isArray(sidecar.LabelingDuration)
   checks:
-  - nifti_header.dim[4] == len(sidecar.LabelingDuration)
+  - nifti_header.dim[4] == sidecar.LabelingDuration.length
 
 # 165
 ASLContextConsistent:
@@ -35,7 +35,7 @@ ASLContextConsistent:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
+  - 'associations'.includes('"aslcontext")'
   checks:
   - nifti_header.dim[4] == associations.aslcontext.n_rows
 
@@ -55,10 +55,10 @@ ASLFlipAngleNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - sidecar contains "FlipAngle"
-  - type(sidecar.FlipAngle) == "array"
+  - 'sidecar'.includes('"FlipAngle")'
+  - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
   checks:
-  - nifti_header.dim[4] == len(sidecar.FlipAngle)
+  - nifti_header.dim[4] == sidecar.FlipAngle.length
 
 # 172
 ASLFlipAngleASLContextLength:
@@ -76,11 +76,11 @@ ASLFlipAngleASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "FlipAngle"
-  - type(sidecar.FlipAngle) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"FlipAngle")'
+  - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
   checks:
-  - aslcontext.n_rows == sidecar.FlipAngle.size
+  - aslcontext.n_rows == sidecar.FlipAngle.length
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -101,10 +101,10 @@ ASLPostLabelingDelayNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - sidecar contains "PostLabelingDelay"
-  - type(sidecar.PostLabelingDelay) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
   checks:
-  - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
+  - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.length
 
 # 174
 ASLPostLabelingDelayASLContextLength:
@@ -125,11 +125,10 @@ ASLPostLabelingDelayASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "PostLabelingDelay"
-  - type(sidecar.PostLabelingDelay) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
   checks:
-  - aslcontext.n_rows == sidecar.PostLabelingDelay.size
+  - aslcontext.n_rows == sidecar.PostLabelingDelay.length
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -151,11 +150,11 @@ ASLLabelingDurationASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "LabelingDuration"
-  - type(sidecar.LabelingDuration) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"LabelingDuration")'
+  - sidecar.LabelingDuration.cobstructor.isArray(sidecar.LabelingDuration)
   checks:
-  - aslcontext.n_rows == sidecar.LabelingDuration.size
+  - aslcontext.n_rows == sidecar.LabelingDuration.length
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -172,11 +171,11 @@ ASLRepetitionTimePreparationASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "RepetitionTimePreparation"
-  - type(sidecar.RepetitionTimePreparation) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"RepetitionTimePreparation")'
+  - sidecar.RepetitionTimePreparation.constructor.isArray(sidecar.RepetitionTimePreparation)
   checks:
-  - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
+  - aslcontext.n_rows == sidecar.RepetitionTimePreparation.length
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -190,11 +189,11 @@ ASLBackgroundSuppressionNumberPulses:
     level: warning
   selectors:
   - suffix == "asl"
-  - sidecar contains "BackgroundSuppressionNumberPulses"
-  - sidecar contains "BackgroundSuppressionPulseTime"
-  - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+  - 'sidecar'.includes('"BackgroundSuppressionNumberPulses")'
+  - 'sidecar'.includes('"BackgroundSuppressionPulseTime")'
+  - sidecar.BackgroundSuppressionPulseTime.constructor.isArray(sidecar.BackgroundSuppressionPulseTime)
   checks:
-  - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
+  - sidecar.BackgroundSuppressionPulseTime.length == sidecar.BackgroundSuppressionNumberPulses
 
 # 181
 ASLTotalAcquiredVolumesASLContextLength:
@@ -208,8 +207,8 @@ ASLTotalAcquiredVolumesASLContextLength:
     level: warning
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "TotalAcquiredVolumes"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"TotalAcquiredVolumes")'
   checks:
   - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
 
@@ -224,11 +223,11 @@ ASLEchoTimeASLContextLength:
     level: warning
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "EchoTime"
-  - type(sidecar.EchoTime) == "array"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"EchoTime")'
+  - sidecar.EchoTime.constructor.isArray(sidecar.EchoTime)
   checks:
-  - aslcontext.n_rows == sidecar.EchoTime.size
+  - aslcontext.n_rows == sidecar.EchoTime.length
 
 # 198
 ASLM0TypeAbsentScan:
@@ -241,9 +240,9 @@ ASLM0TypeAbsentScan:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - associations contains "m0scan"
-  - sidecar contains "M0Type"
+  - 'associations'.includes('"aslcontext")'
+  - 'associations'.includes('"m0scan")'
+  - 'sidecar'.includes('"M0Type")'
   checks:
   - sidecar.M0Type != "absent"
 
@@ -257,9 +256,9 @@ ASLM0TypeAbsentASLContext:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - aslcontext.volume_type contains "m0scan"
-  - sidecar contains "M0Type"
+  - 'associations'.includes('"aslcontext")'
+  - 'aslcontext.volume_type'.includes('"m0scan")'
+  - 'sidecar'.includes('"M0Type")'
   checks:
   - sidecar.M0Type != "absent"
 
@@ -273,8 +272,8 @@ ASLM0TypeIncorrect:
     level: error
   selectors:
   - suffix == "asl"
-  - associations contains "aslcontext"
-  - sidecar contains "M0Type"
+  - 'associations'.includes('"aslcontext")'
+  - 'sidecar'.includes('"M0Type")'
   - sidecar.M0Type == "separate"
   checks:
-  - associations contains "m0scan"
+  - 'associations'.includes('"m0scan")'
diff --git a/src/schema/rules/checks/dwi.yaml b/src/schema/rules/checks/dwi.yaml
index 260b71f6bd..92ab049fcd 100644
--- a/src/schema/rules/checks/dwi.yaml
+++ b/src/schema/rules/checks/dwi.yaml
@@ -10,8 +10,8 @@ DWIVolumeCount:
   level: error
   selectors:
   - suffix == "dwi"
-  - associations contains "bval"
-  - associations contains "bvec"
+  - 'associations' .includes('"bval")'
+  - 'associations' .includes('"bvec")'
   checks:
   - associations.bval.n_cols == nifti_header.dim[4]
   - associations.bvec.n_cols == nifti_header.dim[4]
@@ -47,7 +47,7 @@ DWIMissingBvec:
   selectors:
   - suffix == "dwi"
   checks:
-  - associations contains "bvec"
+  - 'associations'.includes('"bvec")'
 
 # 33
 DWIMissingBval:
@@ -58,4 +58,4 @@ DWIMissingBval:
   selectors:
   - suffix == "dwi"
   checks:
-  - associations contains "bval"
+  - 'associations'.includes('"bval")'
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index ed70539e86..222ddf8546 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -10,8 +10,8 @@ EventsMissing:
       If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
     level: warning  # could be an error with the proper selectors, I think
   selectors:
-  - entities contains "task"
+  - 'entities'.includes('"task)'
   - entities.task != "rest"
-  - entities.task not(contains "rest")  # Alternative for including the word "rest"
+  - 'entities.task) # Alternative for including the word "rest".includes(!("rest")'
   checks:
-  - associations contains "events"
+  - 'associations'.includes('"events")'
diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
index ed880bf19f..b78eb69c2c 100644
--- a/src/schema/rules/checks/fmap.yaml
+++ b/src/schema/rules/checks/fmap.yaml
@@ -11,7 +11,7 @@ FmapFieldmapWithoutMagnitude:
   selectors:
   - suffix == "fieldmap"
   checks:
-  - associations contains "magnitude"
+  - 'associations'.includes('"magnitude")'
 
 # 92
 FmapPhasediffWithoutMagnitude:
@@ -23,4 +23,4 @@ FmapPhasediffWithoutMagnitude:
   selectors:
   - suffix == "phasediff"
   checks:
-  - associations contains "magnitude1"
+  - 'associations'.includes('"magnitude1")'
diff --git a/src/schema/rules/common_derivatives_validation.yaml b/src/schema/rules/common_derivatives_validation.yaml
index 8991a240ec..42f44f84cd 100644
--- a/src/schema/rules/common_derivatives_validation.yaml
+++ b/src/schema/rules/common_derivatives_validation.yaml
@@ -2,17 +2,17 @@
 ResInSidecar:
     selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - modality in ["mri", "pet"]
-    - extension in ["nii", " nii.gz"]
-    - type(sidecar.Resolution) == "object"
+    - '["mri", "pet"].includes(modality)'
+    - '["nii", " nii.gz"].includes(extension)'
+    - typeof(sidecar.Resolution) == "object"
     checks:
-    - sidecar.Resolution contains entities.resolution
+    - entities.resolution in sidecar.Resolution
 
 DenInSidecar:
     selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - modality in ["mri", "pet"]
-    - extension in [".nii", ".nii.gz"]
-    - type(sidecar.Density) == "object"
+    - '["mri", "pet"].includes(modality)'
+    - '[".nii", ".nii.gz"].includes(extension)'
+    - typeof(sidecar.Density) == "object"
     checks:
-    - sidecar.Density contains entities.density
+    - entities.density in sidecar.Density
diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 4171faf186..490804c9c2 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -42,7 +42,7 @@ derivative_description:
 dataset_description_with_genetics:
   selectors:
   - path == "/dataset_description.json"
-  - dataset.files contains "/genetic_info.json"
+  - 'dataset.files'.includes('"/genetic_info.json")'
   fields:
     Genetics: REQUIRED
     Genetics{}.Dataset:
diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 2d4aa50065..776f7de193 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -29,7 +29,7 @@ MRIASLTextOnlySliceTiming:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "MRAcquisitionType"
+    - 'sidecar'.includes('"MRAcquisitionType")'
     - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming:
@@ -56,7 +56,7 @@ MRIASLTextOnlyFlipAngle:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "LookLocker"
+    - '"LookLocker in sidecar'
     - sidecar.LookLocker == true
     fields:
         FlipAngle:
@@ -113,7 +113,7 @@ MRIASLCommonMetadataFieldsM0Type:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "M0Type"
+    - '"M0Type" in sidecar'
     - sidecar.M0Type == "Estimate"
     fields:
         M0Estimate:
@@ -131,7 +131,7 @@ MRIASLCommonMetadataFieldsBackgroundSuppression:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "BackgroundSuppression"
+    - '"BackgroundSuppression" in sidecar'.
     - sidecar.BackgroundSuppression == true
     fields:
         BackgroundSuppressionNumberPulses: recommended
@@ -142,7 +142,7 @@ MRIASLCommonMetadataFieldsVascularCrushing:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "VascularCrushing"
+    - '"VascularCrushing" in sidecar'
     - sidecar.VascularCrushing == true
     fields:
         VascularCrushingVENC: recommended
@@ -152,8 +152,8 @@ MRIASLPCASLSpecific:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "ArterialSpinLabelingType"
-    - sidecar.ArterialSpinLabelingType in ["CASL", "PCASL"]
+    - "ArterialSpinLabelingType" in sidecar'
+    - '["CASL", "PCASL"].includes(sidecar.ArterialSpinLabelingType)'
     fields:
         LabelingDuration: required
         LabelingPulseAverageGradient: recommended
@@ -168,7 +168,7 @@ MRIASLPCASLSpecific2:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "ArterialSpinLabelingType"
+    - '"ArterialSpinLabelingType" in sidecar'
     - sidecar.ArterialSpinLabelingType == "PCASL"
     fields:
         PCASLType: recommended
@@ -178,7 +178,7 @@ MRIASLCASLSpecific:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "ArterialSpinLabelingType"
+    - '"ArterialSpinLabelingType" in sidecar'
     - sidecar.ArterialSpinLabelingType == "CASL"
     fields:
         CASLType: recommended
@@ -188,7 +188,7 @@ MRIASLPASLSpecific:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "ArterialSpinLabelingType"
+    - '"ArterialSpinLabelingType" in sidecar'
     - sidecar.ArterialSpinLabelingType == "PASL"
     fields:
         BolusCutOffFlag: required
@@ -206,9 +206,9 @@ MRIASLPASLSpecificBolusCutOffFlag:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - sidecar contains "ArterialSpinLabelingType"
+    - '"ArterialSpinLabelingType" in sidecar'
     - sidecar.ArterialSpinLabelingType == "PASL"
-    - sidecar contains "BolusCutOffFlag"
+    - '"BolusCutOffFlag" in sidecar'
     - sidecar.BolusCutOffFlag == true
     fields:
         BolusCutOffDelayTime:
@@ -254,7 +254,7 @@ MRIASLM0ScanTextOnlyFlipAngle:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "m0scan"
-    - sidecar contains "LookLocker"
+    - '"LookLocker" in sidecar'
     - sidecar.LookLocker == true
     fields:
         FlipAngle:
diff --git a/src/schema/rules/sidecars/beh.yaml b/src/schema/rules/sidecars/beh.yaml
index dc863f12c4..d0760eda59 100644
--- a/src/schema/rules/sidecars/beh.yaml
+++ b/src/schema/rules/sidecars/beh.yaml
@@ -9,7 +9,7 @@
 # Metadata for either beh or events files
 BEHTabularData:
     selectors:
-    - suffix in ["beh", "events"]
+    - '["beh", "events"].includes(suffix)'
     fields:
         TaskName: recommended
         Instructions: recommended
diff --git a/src/schema/rules/sidecars/continuous.yaml b/src/schema/rules/sidecars/continuous.yaml
index cdfe0e1ef4..2607ce1dfb 100644
--- a/src/schema/rules/sidecars/continuous.yaml
+++ b/src/schema/rules/sidecars/continuous.yaml
@@ -9,7 +9,7 @@
 # Metadata for either physio or stim files
 Continuous:
     selectors:
-    - suffix in ["physio", "stim"]
+    - '["physio", "stim"].includes(suffix)'
     fields:
         SamplingFrequency: required
         StartTime: required
diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
index 87a59eca78..5d01d36837 100644
--- a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -10,21 +10,21 @@ CommonDerivativeFields:
 SpatialReferenceEntity:
   selectors:
   - dataset.DatasetType == "derivative"
-  - entities contains "space"
+  - '"space" in entities'
   fields:
     SpatialReference: RECOMMENDED
 
 SpatialReferenceNonStandard:
   selectors:
   - dataset.DatasetType == "derivative"
-  - not(entities.space in schema.objects.metadata._StandardTemplateCoordSys)
+  - 'schema.objects.metadata._StandardTemplateCoordSys).includes(not(entities.space)'
   fields:
     SpatialReference: REQUIRED
 
 SpatialReferenceNoEntity:
   selectors:
   - dataset.DatasetType == "derivative"
-  - not(entities contains "space")
+  - '!("space" in entities)'
   fields:
     SpatialReference: REQUIRED
 
@@ -45,14 +45,14 @@ MaskDerivativesAtlas:
   selectors:
   - dataset.DatasetType == "derivative"
   - suffix == "mask"
-  - entities contains "label"
+  - '"label" in entities'
   fields:
     atlas: RECOMMENDED
 
 SegmentationCommon:
   selectors:
   - dataset.DatasetType == "derivative"
-  - suffix in ["dseg", "probseg"]
+  - '["dseg", "probseg"].includes(suffix)'
   fields:
     Type: RECOMMENDED
     Atlas: OPTIONAL
@@ -63,23 +63,23 @@ SegmentationCommon:
 ImageDerivatives:
   selectors:
   - dataset.DatasetType == "derivative"
-  - modality in ["mri", "pet"]
-  - extension in [".nii", ".nii.gz"]
+  - '["mri", "pet"].includes(modality)'
+  - '[".nii", ".nii.gz"].includes(extension)'
   fields:
     SkullStripped: REQUIRED
 
 ImageDerivativeResEntity:
   selectors:
   - dataset.DatasetType == "derivative"
-  - modality in ["mri", "pet"]
-  - entities contains "res"
+  - '["mri", "pet"].includes(modality)'
+  - '"res" in entities'
   fields:
     Resolution: REQUIRED
 
 ImageDerivativeDenEntity:
   selectors:
   - dataset.DatasetType == "derivative"
-  - modality in ["mri", "pet"]
-  - entities contains "den"
+  - '["mri", "pet"].includes(modality)'
+  - '"den" in entities'
   fields:
     Density: REQUIRED
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index eb54527c81..d82715d857 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -110,7 +110,7 @@ EEGCoordsystemOther:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
-    - sidecar contains "EEGCoordinateSystem"
+    - '"EEGCoordinateSystem" in sidecar'
     - sidecar.EEGCoordinateSystem == "Other"
     fields:
         EEGCoordinateSystemDescription: required
@@ -160,7 +160,7 @@ EEGCoordsystemAnatomicalLandmarkCoordinateSystemDescription:
     - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
-    - sidecar contains "AnatomicalLandmarkCoordinateSystem"
+    - '"AnatomicalLandmarkCoordinateSystem" in sidecar'
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
     fields:
         AnatomicalLandmarkCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/entities.yaml b/src/schema/rules/sidecars/entities.yaml
index 3147815569..e6249cfd0f 100644
--- a/src/schema/rules/sidecars/entities.yaml
+++ b/src/schema/rules/sidecars/entities.yaml
@@ -11,25 +11,25 @@
 
 EntitiesTaskMetadata:
     selectors:
-    - entities contains "task"
+    - '"task" in entities'
     fields:
         TaskName: recommended
 
 EntitiesCeMetadata:
     selectors:
-    - entities contains "ce"
+    - '"ce" in entities'
     fields:
         ContrastBolusIngredient: optional
 
 EntitiesTrcMetadata:
     selectors:
-    - entities contains "trc"
+    - '"trc" in entities'
     fields:
         TracerName: required
 
 EntitiesStainMetadata:
     selectors:
-    - entities contains "stain"
+    - '"stain" in entities'
     fields:
         SampleStaining: recommended
         SamplePrimaryAntibodies: recommended
@@ -37,25 +37,25 @@ EntitiesStainMetadata:
 
 EntitiesEchoMetadata:
     selectors:
-    - entities contains "echo"
+    - '"echo" in entities'
     fields:
         EchoTime: required
 
 EntitiesFlipMetadata:
     selectors:
-    - entities contains "flip"
+    - '"flip" in entities'
     fields:
         FlipAngle: required
 
 EntitiesInvMetadata:
     selectors:
-    - entities contains "inv"
+    - '"inv" in entities'
     fields:
         InversionTime: required
 
 EntitiesMTMetadata:
     selectors:
-    - entities contains "mt"
+    - '"mt" in entities'
     fields:
         MTState: required
 
@@ -66,16 +66,16 @@ EntitiesPartMetadata:
         Units:
             level: required
             rules:
-            - value in ["rad", "arbitrary"]
+            - '["rad", "arbitrary"].includes(value)'
 
 EntitiesResMetadata:
     selectors:
-    - entities contains "res"
+    - '"res" in entities'
     fields:
         Resolution: required
 
 EntitiesDenMetadata:
     selectors:
-    - entities contains "den"
+    - '"den" in entities'
     fields:
         Density: required
diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
index 9d9b7b7b05..bd628a5c1c 100644
--- a/src/schema/rules/sidecars/fmap.yaml
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -59,7 +59,7 @@ MRIFieldmapTwoPhase:
     selectors:
     - modality == "MRI"
     - datatype == "fmap"
-    - suffix in ["phase1", "phase2", "magnitude1", "magnitude2"]
+    - '["phase1", "phase2", "magnitude1", "magnitude2"].includes(suffix)'
     fields:
         EchoTime__fmap: required
 
@@ -68,7 +68,7 @@ MRIFieldmapDirectFieldMapping:
     selectors:
     - modality == "MRI"
     - datatype == "fmap"
-    - suffix in ["phase", "fieldmap"]
+    - '["phase", "fieldmap"].includes(suffix)'
     fields:
         Units:
             level: required
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index ffdcb45108..9d7cdd012a 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -49,7 +49,7 @@ MRIFuncTimingParametersMutualExclusion1:
     selectors:
     - modality == "mri"
     - datatype == "func"
-    - sidecar contains "RepetitionTime"
+    - '"RepetitionTime" in sidecar'
     fields:
         AcquisitionDuration: prohibited
         VolumeTiming: prohibited
@@ -58,8 +58,8 @@ MRIFuncTimingParametersMutualExclusion2:
     selectors:
     - modality == "mri"
     - datatype == "func"
-    - sidecar contains "SliceTiming"
-    - sidecar contains "VolumeTiming"
+    - '"SliceTiming" in sidecar'
+    - '"VolumeTiming" in sidecar'
     fields:
         RepetitionTime: prohibited
         DelayTime: prohibited
@@ -68,8 +68,8 @@ MRIFuncTimingParametersMutualExclusion3:
     selectors:
     - modality == "mri"
     - datatype == "func"
-    - sidecar contains "AcquisitionDuration"
-    - sidecar contains "VolumeTiming"
+    - '"AcquisitionDuration" in sidecar'
+    - '"VolumeTiming" in sidecar'
     fields:
         RepetitionTime: prohibited
         DelayTime: prohibited
@@ -78,8 +78,8 @@ MRIFuncTimingParametersMutualExclusion4:
     selectors:
     - modality == "mri"
     - datatype == "func"
-    - sidecar contains "RepetitionTime"
-    - sidecar contains "SliceTiming"
+    - '"RepetitionTime" in sidecar'
+    - '"SliceTiming" in sidecar'
     fields:
         AcquisitionDuration: prohibited
         VolumeTiming: prohibited
@@ -88,8 +88,8 @@ MRIFuncTimingParametersMutualExclusion5:
     selectors:
     - modality == "mri"
     - datatype == "func"
-    - sidecar contains "RepetitionTime"
-    - sidecar contains "DelayTime"
+    - '"RepetitionTime" in sidecar'
+    - '"DelayTime" in sidecar'
     fields:
         AcquisitionDuration: prohibited
         VolumeTiming: prohibited
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index d7763546f3..39c4fa9070 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -138,7 +138,7 @@ iEEGCoordsystemOther:
     - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "coordsystem"
-    - sidecar contains "iEEGCoordinateSystem"
+    - '"iEEGCoordinateSystem" in sidecar'
     - sidecar.iEEGCoordinateSystem == "Other"
     fields:
         iEEGCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index e969c5d91f..14be35b473 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -106,7 +106,7 @@ MEGwithEEG:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "meg"
-    - dataset.modalities contains "EEG"
+    - 'dataset.modalities'.includes('"EEG")'
     fields:
         EEGPlacementScheme: optional
         CapManufacturer: optional
@@ -145,7 +145,7 @@ MEGCoordsystemWithEEGMEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - sidecar contains "MEGCoordinateSystem"
+    - 'sidecar'.includes('"MEGCoordinateSystem")'
     - sidecar.MEGCoordinateSystem == "Other"
     fields:
         MEGCoordinateSystemDescription: required
@@ -156,7 +156,7 @@ MEGCoordsystemWithEEGEEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - sidecar contains "EEGCoordinateSystem"
+    - 'sidecar'.includes('"EEGCoordinateSystem")'
     - sidecar.EEGCoordinateSystem == "Other"
     fields:
         EEGCoordinateSystemDescription: required
@@ -180,7 +180,7 @@ MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - sidecar contains "HeadCoilCoordinateSystem"
+    - 'sidecar'.includes('"HeadCoilCoordinateSystem")'
     - sidecar.HeadCoilCoordinateSystem == "Other"
     fields:
         HeadCoilCoordinateSystemDescription: required
@@ -204,7 +204,7 @@ MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - sidecar contains "DigitizedHeadPointsCoordinateSystem"
+    - 'sidecar'.includes('"DigitizedHeadPointsCoordinateSystem")'
     - sidecar.DigitizedHeadPointsCoordinateSystem == "Other"
     fields:
         DigitizedHeadPointsCoordinateSystemDescription: required
@@ -215,7 +215,7 @@ MEGCoordsystemAnatomicalMRI:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - dataset.modalities contains "anat"
+    - 'dataset.modalities'.includes('"anat")'
     fields:
         IntendedFor:
             level: optional
@@ -246,7 +246,7 @@ MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - sidecar contains "AnatomicalLandmarkCoordinateSystem"
+    - 'sidecar'.includes('"AnatomicalLandmarkCoordinateSystem")'
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
     fields:
         AnatomicalLandmarkCoordinateSystemDescription: required
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
index 99413ad890..077dbbba6f 100644
--- a/src/schema/rules/sidecars/micr.yaml
+++ b/src/schema/rules/sidecars/micr.yaml
@@ -65,7 +65,7 @@ MicroscopyChunkTransformations:
     selectors:
     - modality == "micr"
     - datatype == "micr"
-    - entities contains "chunk"
+    - '"chunk" in entities'
     fields:
         ChunkTransformationMatrix: recommended
 
@@ -73,7 +73,7 @@ MicroscopyChunkTransformationsMatrixAxis:
     selectors:
     - modality == "micr"
     - datatype == "micr"
-    - entities contains "chunk"
-    - sidecar contains "ChunkTransformationMatrix"
+    - '"chunk" in entities'
+    - '"ChunkTransformationMatrix" in sidecar'
     fields:
         ChunkTransformationMatrixAxis: required
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 19ddb3a526..492173a00d 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -64,7 +64,7 @@ MRISequenceSpecifics:
 PETMRISequenceSpecifics:
     selectors:
     - modality == "mri"
-    - dataset.modalities contains "PET"
+    - dataset.modalities.includes("PET")
     fields:
         NonLinearGradientCorrection: required
 
@@ -77,7 +77,7 @@ ASLMRISequenceSpecifics:
 
 MTParameters:
     selectors:
-    - sidecar contains "MTState"
+    - '"MTState" in sidecar'
     - sidecar.MTState == "True"
     fields:
         MTOffsetFrequency: recommended
@@ -88,22 +88,22 @@ MTParameters:
 
 SpoilingType:
     selectors:
-    - sidecar contains "SpoilingState"
+    - '"SpoilingState" in sidecar'
     - sidecar.SpoilingState == True
     fields:
         SpoilingType: recommended
 
 SpoilingRF:
     selectors:
-    - sidecar contains "SpoilingType"
-    - sidecar.SpoilingType in ["RF", "COMBINED"]
+    - '"SpoilingType" in sidecar'
+    - '["RF", "COMBINED"].includes(sidecar.SpoilingType)'
     fields:
         SpoilingRFPhaseIncrement: recommended
 
 SpoilingGradient:
     selectors:
-    - sidecar contains "SpoilingType"
-    - sidecar.SpoilingType in ["GRADIENT", "COMBINED"]
+    - '"SpoilingType" in sidecar'
+    - '["GRADIENT", "COMBINED"].includes(sidecar.SpoilingType)'
     fields:
         SpoilingGradientMoment: recommended
         SpoilingGradientDuration: recommended
@@ -184,8 +184,8 @@ SliceTimingASL:
     selectors:
     - modality == "mri"
     - datatype == "perf"
-    - suffix in ["asl", "m0scan"]
-    - sidecar contains "MRAcquisitionType"
+    - '["asl", "m0scan"].includes(suffix)'
+    - '"MRAcquisitionType" in sidecar'
     - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming: required
@@ -194,7 +194,7 @@ SliceTimingASL:
 SliceTimingSparse:
     selectors:
     - modality == "mri"
-    - sidecar contains "DelayTime"
+    - '"DelayTime" in sidecar'
     fields:
         SliceTiming: required
 
@@ -224,7 +224,7 @@ MRIRFandContrast:
 MRIFlipAngleLookLocker:
     selectors:
     - modality == "mri"
-    - sidecar contains "LookLocker"
+    - '"LookLocker" in sidecar'
     - sidecar.LookLocker == True
     fields:
         FlipAngle: required
diff --git a/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
index 880a779309..73df02e2d0 100644
--- a/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml
@@ -2,7 +2,7 @@
 SegmentationLookup:
   selectors:
   - dataset.DatasetType == "derivative"
-  - suffix in ["dseg", "probseg"]
+  - '["dseg", "probseg"].includes(suffix)'
   columns:
     index: REQUIRED
     name: REQUIRED
diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index 82e0059c22..7dfb2c0517 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -17,7 +17,7 @@ BloodPlasma:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar contains "PlasmaAvail"
+    - '"PlasmaAvail" in sidecar'
     columns:
         plasma_radioactivity: required
 
@@ -26,7 +26,7 @@ BloodMetabolite:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar contains "MetaboliteAvail"
+    - '"MetaboliteAvail" in sidecar'
     columns:
         metabolite_parent_fraction: required
         metabolite_polar_fraction: recommended
@@ -36,7 +36,7 @@ BloodMetaboliteCorrection:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar contains "MetaboliteRecoveryCorrectionApplied"
+    - '"MetaboliteRecoveryCorrectionApplied" in sidecar'
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
     columns:
         hplc_recovery_fractions: required
@@ -46,7 +46,7 @@ BloodWholeBlood:
     - modality == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - sidecar contains "WholeBloodAvail"
+    - '"WholeBloodAvail" in sidecar'
     - sidecar.WholeBloodAvail == true
     columns:
         whole_blood_radioactivity: required
diff --git a/src/schema/rules/tabular_data/task.yaml b/src/schema/rules/tabular_data/task.yaml
index a370adc739..a714e71614 100644
--- a/src/schema/rules/tabular_data/task.yaml
+++ b/src/schema/rules/tabular_data/task.yaml
@@ -1,7 +1,7 @@
 ---
 TaskEvents:
     selectors:
-    - entities contains "task"
+    - '"task" in entities'
     - suffix == "events"
     columns:
         onset: REQUIRED

From 2c6fbf5e82f88b5275a3278b058c34675644c8c8 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 25 Apr 2022 12:29:22 -0500
Subject: [PATCH 344/347] yamllint fixes and rerun sed on overlooked
 cases/files

---
 src/schema/rules/checks/asl.yaml       | 52 +++++++++++++-------------
 src/schema/rules/checks/dwi.yaml       |  8 ++--
 src/schema/rules/checks/events.yaml    |  7 ++--
 src/schema/rules/checks/fmap.yaml      |  4 +-
 src/schema/rules/dataset_metadata.yaml |  2 +-
 src/schema/rules/sidecars/asl.yaml     |  6 +--
 src/schema/rules/sidecars/meg.yaml     | 14 +++----
 7 files changed, 46 insertions(+), 47 deletions(-)

diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml
index 4e73a513cd..d622809644 100644
--- a/src/schema/rules/checks/asl.yaml
+++ b/src/schema/rules/checks/asl.yaml
@@ -20,7 +20,7 @@ ASLLabelingDurationNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'sidecar'.includes('"LabelingDuration")'
+  - '"LabelingDuration" in sidecar'
   - sidecar.LabelingDuration.constructor.isArray(sidecar.LabelingDuration)
   checks:
   - nifti_header.dim[4] == sidecar.LabelingDuration.length
@@ -35,7 +35,7 @@ ASLContextConsistent:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
+  - '"aslcontext" in associations'
   checks:
   - nifti_header.dim[4] == associations.aslcontext.n_rows
 
@@ -55,7 +55,7 @@ ASLFlipAngleNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'sidecar'.includes('"FlipAngle")'
+  - '"FlipAngle" in sidecar'
   - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
   checks:
   - nifti_header.dim[4] == sidecar.FlipAngle.length
@@ -76,8 +76,8 @@ ASLFlipAngleASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"FlipAngle")'
+  - '"aslcontext" in associations'
+  - '"FlipAngle" in sidecar'
   - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
   checks:
   - aslcontext.n_rows == sidecar.FlipAngle.length
@@ -101,7 +101,7 @@ ASLPostLabelingDelayNiftiLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
+  - '"aslcontext" in associations'
   - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
   checks:
   - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.length
@@ -125,7 +125,7 @@ ASLPostLabelingDelayASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
+  - '"aslcontext" in associations'
   - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
   checks:
   - aslcontext.n_rows == sidecar.PostLabelingDelay.length
@@ -150,8 +150,8 @@ ASLLabelingDurationASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"LabelingDuration")'
+  - '"aslcontext" in associations'
+  - '"LabelingDuration" in sidecar'
   - sidecar.LabelingDuration.cobstructor.isArray(sidecar.LabelingDuration)
   checks:
   - aslcontext.n_rows == sidecar.LabelingDuration.length
@@ -171,8 +171,8 @@ ASLRepetitionTimePreparationASLContextLength:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"RepetitionTimePreparation")'
+  - '"aslcontext" in associations'
+  - '"RepetitionTimePreparation" in sidecar'
   - sidecar.RepetitionTimePreparation.constructor.isArray(sidecar.RepetitionTimePreparation)
   checks:
   - aslcontext.n_rows == sidecar.RepetitionTimePreparation.length
@@ -189,8 +189,8 @@ ASLBackgroundSuppressionNumberPulses:
     level: warning
   selectors:
   - suffix == "asl"
-  - 'sidecar'.includes('"BackgroundSuppressionNumberPulses")'
-  - 'sidecar'.includes('"BackgroundSuppressionPulseTime")'
+  - '"BackgroundSuppressionNumberPulses" in sidecar'
+  - '"BackgroundSuppressionPulseTime" in sidecar'
   - sidecar.BackgroundSuppressionPulseTime.constructor.isArray(sidecar.BackgroundSuppressionPulseTime)
   checks:
   - sidecar.BackgroundSuppressionPulseTime.length == sidecar.BackgroundSuppressionNumberPulses
@@ -207,8 +207,8 @@ ASLTotalAcquiredVolumesASLContextLength:
     level: warning
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"TotalAcquiredVolumes")'
+  - '"aslcontext" in associations'
+  - '"TotalAcquiredVolumes" in sidecar'
   checks:
   - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
 
@@ -223,8 +223,8 @@ ASLEchoTimeASLContextLength:
     level: warning
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"EchoTime")'
+  - '"aslcontext" in associations'
+  - '"EchoTime" in sidecar'
   - sidecar.EchoTime.constructor.isArray(sidecar.EchoTime)
   checks:
   - aslcontext.n_rows == sidecar.EchoTime.length
@@ -240,9 +240,9 @@ ASLM0TypeAbsentScan:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'associations'.includes('"m0scan")'
-  - 'sidecar'.includes('"M0Type")'
+  - '"aslcontext" in associations'
+  - '"m0scan" in associations'
+  - '"M0Type" in sidecar'
   checks:
   - sidecar.M0Type != "absent"
 
@@ -256,9 +256,9 @@ ASLM0TypeAbsentASLContext:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'aslcontext.volume_type'.includes('"m0scan")'
-  - 'sidecar'.includes('"M0Type")'
+  - '"aslcontext" in associations'
+  - aslcontext.volume_type.includes('"m0scan")
+  - '"M0Type" in sidecar'
   checks:
   - sidecar.M0Type != "absent"
 
@@ -272,8 +272,8 @@ ASLM0TypeIncorrect:
     level: error
   selectors:
   - suffix == "asl"
-  - 'associations'.includes('"aslcontext")'
-  - 'sidecar'.includes('"M0Type")'
+  - '"aslcontext" in associations'
+  - '"M0Type" in sidecar'
   - sidecar.M0Type == "separate"
   checks:
-  - 'associations'.includes('"m0scan")'
+  - '"m0scan" in associations'
diff --git a/src/schema/rules/checks/dwi.yaml b/src/schema/rules/checks/dwi.yaml
index 92ab049fcd..6cc1572909 100644
--- a/src/schema/rules/checks/dwi.yaml
+++ b/src/schema/rules/checks/dwi.yaml
@@ -10,8 +10,8 @@ DWIVolumeCount:
   level: error
   selectors:
   - suffix == "dwi"
-  - 'associations' .includes('"bval")'
-  - 'associations' .includes('"bvec")'
+  - '"bval" in associations'
+  - '"bvec" in associations'
   checks:
   - associations.bval.n_cols == nifti_header.dim[4]
   - associations.bvec.n_cols == nifti_header.dim[4]
@@ -47,7 +47,7 @@ DWIMissingBvec:
   selectors:
   - suffix == "dwi"
   checks:
-  - 'associations'.includes('"bvec")'
+  - '"bvec" in associations'
 
 # 33
 DWIMissingBval:
@@ -58,4 +58,4 @@ DWIMissingBval:
   selectors:
   - suffix == "dwi"
   checks:
-  - 'associations'.includes('"bval")'
+  - '"bval" in associations'
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 222ddf8546..f6ffd882de 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -10,8 +10,7 @@ EventsMissing:
       If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
     level: warning  # could be an error with the proper selectors, I think
   selectors:
-  - 'entities'.includes('"task)'
-  - entities.task != "rest"
-  - 'entities.task) # Alternative for including the word "rest".includes(!("rest")'
+  - '"task" in entities'
+  - '!(entities.task.includes("rest"))'
   checks:
-  - 'associations'.includes('"events")'
+  - '"events" in associations'
diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
index b78eb69c2c..048765ac74 100644
--- a/src/schema/rules/checks/fmap.yaml
+++ b/src/schema/rules/checks/fmap.yaml
@@ -11,7 +11,7 @@ FmapFieldmapWithoutMagnitude:
   selectors:
   - suffix == "fieldmap"
   checks:
-  - 'associations'.includes('"magnitude")'
+  - '"magnitude" in associations'
 
 # 92
 FmapPhasediffWithoutMagnitude:
@@ -23,4 +23,4 @@ FmapPhasediffWithoutMagnitude:
   selectors:
   - suffix == "phasediff"
   checks:
-  - 'associations'.includes('"magnitude1")'
+  - '"magnitude1" in associations'
diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index 490804c9c2..c1b086527e 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -42,7 +42,7 @@ derivative_description:
 dataset_description_with_genetics:
   selectors:
   - path == "/dataset_description.json"
-  - 'dataset.files'.includes('"/genetic_info.json")'
+  - 'dataset.files.includes("/genetic_info.json")'
   fields:
     Genetics: REQUIRED
     Genetics{}.Dataset:
diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index 776f7de193..d711f9fc7f 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -29,7 +29,7 @@ MRIASLTextOnlySliceTiming:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - 'sidecar'.includes('"MRAcquisitionType")'
+    - '"MRAcquisitionType" in sidecar'
     - sidecar.MRAcquisitionType == "2D"
     fields:
         SliceTiming:
@@ -131,7 +131,7 @@ MRIASLCommonMetadataFieldsBackgroundSuppression:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - '"BackgroundSuppression" in sidecar'.
+    - '"BackgroundSuppression" in sidecar'
     - sidecar.BackgroundSuppression == true
     fields:
         BackgroundSuppressionNumberPulses: recommended
@@ -152,7 +152,7 @@ MRIASLPCASLSpecific:
     - modality == "MRI"
     - datatype == "perf"
     - suffix == "asl"
-    - "ArterialSpinLabelingType" in sidecar'
+    - '"ArterialSpinLabelingType" in sidecar'
     - '["CASL", "PCASL"].includes(sidecar.ArterialSpinLabelingType)'
     fields:
         LabelingDuration: required
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index 14be35b473..71de0f30aa 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -106,7 +106,7 @@ MEGwithEEG:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "meg"
-    - 'dataset.modalities'.includes('"EEG")'
+    - dataset.modalities.includes('"EEG")
     fields:
         EEGPlacementScheme: optional
         CapManufacturer: optional
@@ -145,7 +145,7 @@ MEGCoordsystemWithEEGMEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'sidecar'.includes('"MEGCoordinateSystem")'
+    - '"MEGCoordinateSystem" in sidecar'
     - sidecar.MEGCoordinateSystem == "Other"
     fields:
         MEGCoordinateSystemDescription: required
@@ -156,7 +156,7 @@ MEGCoordsystemWithEEGEEGCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'sidecar'.includes('"EEGCoordinateSystem")'
+    - '"EEGCoordinateSystem" in sidecar'
     - sidecar.EEGCoordinateSystem == "Other"
     fields:
         EEGCoordinateSystemDescription: required
@@ -180,7 +180,7 @@ MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'sidecar'.includes('"HeadCoilCoordinateSystem")'
+    - '"HeadCoilCoordinateSystem" in sidecar'
     - sidecar.HeadCoilCoordinateSystem == "Other"
     fields:
         HeadCoilCoordinateSystemDescription: required
@@ -204,7 +204,7 @@ MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'sidecar'.includes('"DigitizedHeadPointsCoordinateSystem")'
+    - '"DigitizedHeadPointsCoordinateSystem" in sidecar'
     - sidecar.DigitizedHeadPointsCoordinateSystem == "Other"
     fields:
         DigitizedHeadPointsCoordinateSystemDescription: required
@@ -215,7 +215,7 @@ MEGCoordsystemAnatomicalMRI:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'dataset.modalities'.includes('"anat")'
+    - dataset.modalities.includes("anat")
     fields:
         IntendedFor:
             level: optional
@@ -246,7 +246,7 @@ MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
     - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
-    - 'sidecar'.includes('"AnatomicalLandmarkCoordinateSystem")'
+    - '"AnatomicalLandmarkCoordinateSystem" in sidecar'
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
     fields:
         AnatomicalLandmarkCoordinateSystemDescription: required

From 111034d479091204f5694d9247b6592f1c12307a Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 25 Apr 2022 16:29:48 -0400
Subject: [PATCH 345/347] ENH: use __file__ instead of getcwd to determine
 HERE, provide informative message on # of files (#1091)

I had to spend some time to figure out why running that script did nothing for me
but failed in CI for the PR.  Apparently it was because I had to run it while
in tools/ directory.  IMHO it is suboptimal.

With a short message on how many files were analyzed user at least could
get a hint in case if no files were read at all

HERE is no longer used, and thuse removed entirely.
---
 tools/no-bad-latin.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/tools/no-bad-latin.py b/tools/no-bad-latin.py
index 74c362d01c..cf758e5788 100755
--- a/tools/no-bad-latin.py
+++ b/tools/no-bad-latin.py
@@ -11,14 +11,17 @@
 import argparse
 from pull_files import filter_files
 
-HERE = os.getcwd()
-ABSOLUTE_HERE = os.path.dirname(HERE)
+ABSOLUTE_HERE = os.path.dirname(os.path.dirname(__file__))
 IGNORE_LIST = ["CHANGES.md", "01-contributors.md", "pregh-changes.md"]
 
 
 def parse_args():
     """Construct command line interface for parsing Pull Request number"""
-    DESCRIPTION = "Script to check for latin phrases in Markdown files"
+    DESCRIPTION = """Script to check for latin phrases in Markdown files.
+
+If no pull request number is provided, all relevant text files in the
+bids-specification are checked."""
+
     parser = argparse.ArgumentParser(description=DESCRIPTION)
 
     parser.add_argument(
@@ -121,6 +124,7 @@ def read_and_check_files(files):
             except FileNotFoundError:
                 pass
 
+    print(f"Checked {len(files)} files. {len(failing_files)} with problems.")
     return failing_files
 
 

From 2d8117169106825f19e6520e9777c8cfdfca060c Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 28 Apr 2022 14:30:37 -0500
Subject: [PATCH 346/347] update isArray and typof to use a 'type()' function

---
 src/schema/rules/checks/asl.yaml               | 18 +++++++++---------
 src/schema/rules/checks/func.yaml              | 14 ++++++++++++++
 .../rules/common_derivatives_validation.yaml   |  4 ++--
 src/schema/rules/sidecars/anat.yaml            | 16 ++++++++++++++++
 src/schema/rules/sidecars/mri.yaml             |  2 +-
 5 files changed, 42 insertions(+), 12 deletions(-)
 create mode 100644 src/schema/rules/checks/func.yaml

diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml
index d622809644..090f1a2a64 100644
--- a/src/schema/rules/checks/asl.yaml
+++ b/src/schema/rules/checks/asl.yaml
@@ -21,7 +21,7 @@ ASLLabelingDurationNiftiLength:
   selectors:
   - suffix == "asl"
   - '"LabelingDuration" in sidecar'
-  - sidecar.LabelingDuration.constructor.isArray(sidecar.LabelingDuration)
+  - type(sidecar.LabelingDuration) == 'array'
   checks:
   - nifti_header.dim[4] == sidecar.LabelingDuration.length
 
@@ -56,7 +56,7 @@ ASLFlipAngleNiftiLength:
   selectors:
   - suffix == "asl"
   - '"FlipAngle" in sidecar'
-  - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
+  - type(sidecar.FlipAngle) == 'array'
   checks:
   - nifti_header.dim[4] == sidecar.FlipAngle.length
 
@@ -78,7 +78,7 @@ ASLFlipAngleASLContextLength:
   - suffix == "asl"
   - '"aslcontext" in associations'
   - '"FlipAngle" in sidecar'
-  - sidecar.FlipAngle.constructor.isArray(sidecar.FlipAngle)
+  - type(sidecar.FlipAngle) == 'array'
   checks:
   - aslcontext.n_rows == sidecar.FlipAngle.length
 
@@ -102,7 +102,7 @@ ASLPostLabelingDelayNiftiLength:
   selectors:
   - suffix == "asl"
   - '"aslcontext" in associations'
-  - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
+  - type(sidecar.PostLabelingDelay) == 'array'
   checks:
   - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.length
 
@@ -126,7 +126,7 @@ ASLPostLabelingDelayASLContextLength:
   selectors:
   - suffix == "asl"
   - '"aslcontext" in associations'
-  - sidecar.PostLabelingDelay.constructor.isArray(sidecar.PostLabelingDelay)
+  - type(sidecar.PostLabelingDelay) == 'array'
   checks:
   - aslcontext.n_rows == sidecar.PostLabelingDelay.length
 
@@ -152,7 +152,7 @@ ASLLabelingDurationASLContextLength:
   - suffix == "asl"
   - '"aslcontext" in associations'
   - '"LabelingDuration" in sidecar'
-  - sidecar.LabelingDuration.cobstructor.isArray(sidecar.LabelingDuration)
+  - type(sidecar.LabelingDuration) == 'array'
   checks:
   - aslcontext.n_rows == sidecar.LabelingDuration.length
 
@@ -173,7 +173,7 @@ ASLRepetitionTimePreparationASLContextLength:
   - suffix == "asl"
   - '"aslcontext" in associations'
   - '"RepetitionTimePreparation" in sidecar'
-  - sidecar.RepetitionTimePreparation.constructor.isArray(sidecar.RepetitionTimePreparation)
+  - type(sidecar.RepetitionTimePreparation) == 'array'
   checks:
   - aslcontext.n_rows == sidecar.RepetitionTimePreparation.length
 
@@ -191,7 +191,7 @@ ASLBackgroundSuppressionNumberPulses:
   - suffix == "asl"
   - '"BackgroundSuppressionNumberPulses" in sidecar'
   - '"BackgroundSuppressionPulseTime" in sidecar'
-  - sidecar.BackgroundSuppressionPulseTime.constructor.isArray(sidecar.BackgroundSuppressionPulseTime)
+  - type(sidecar.BackgroundSuppressionPulseTime) == 'array'
   checks:
   - sidecar.BackgroundSuppressionPulseTime.length == sidecar.BackgroundSuppressionNumberPulses
 
@@ -225,7 +225,7 @@ ASLEchoTimeASLContextLength:
   - suffix == "asl"
   - '"aslcontext" in associations'
   - '"EchoTime" in sidecar'
-  - sidecar.EchoTime.constructor.isArray(sidecar.EchoTime)
+  - type(sidecar.EchoTime) == 'array'
   checks:
   - aslcontext.n_rows == sidecar.EchoTime.length
 
diff --git a/src/schema/rules/checks/func.yaml b/src/schema/rules/checks/func.yaml
new file mode 100644
index 0000000000..89c510b8a0
--- /dev/null
+++ b/src/schema/rules/checks/func.yaml
@@ -0,0 +1,14 @@
+PhaseSuffixDeprecated:
+  issue:
+    code: PHASE_SUFFIX_DEPRECATED
+    message: |
+      DEPRECATED. Phase information associated with magnitude information stored in BOLD contrast.
+      This suffix should be replaced by the part-phase in conjunction with the bold suffix.
+      For backwards compatibility, _phase is considered equivalent to _part-phase_bold.
+      When the _phase suffix is not used, each file shares the same name with the exception of the
+      part-<mag|phase> or part-<real|imag> key/value.
+    level: warning
+  selectors:
+  - datatype == "func"
+  checks:
+  - '!(suffix == "phase")'
diff --git a/src/schema/rules/common_derivatives_validation.yaml b/src/schema/rules/common_derivatives_validation.yaml
index 42f44f84cd..0c2755e3ee 100644
--- a/src/schema/rules/common_derivatives_validation.yaml
+++ b/src/schema/rules/common_derivatives_validation.yaml
@@ -4,7 +4,7 @@ ResInSidecar:
     - dataset.dataset_description.DatasetType == "derivative"
     - '["mri", "pet"].includes(modality)'
     - '["nii", " nii.gz"].includes(extension)'
-    - typeof(sidecar.Resolution) == "object"
+    - type(sidecar.Resolution) == "object"
     checks:
     - entities.resolution in sidecar.Resolution
 
@@ -13,6 +13,6 @@ DenInSidecar:
     - dataset.dataset_description.DatasetType == "derivative"
     - '["mri", "pet"].includes(modality)'
     - '[".nii", ".nii.gz"].includes(extension)'
-    - typeof(sidecar.Density) == "object"
+    - type(sidecar.Density) == "object"
     checks:
     - entities.density in sidecar.Density
diff --git a/src/schema/rules/sidecars/anat.yaml b/src/schema/rules/sidecars/anat.yaml
index ec79389d8d..4df92f0bb5 100644
--- a/src/schema/rules/sidecars/anat.yaml
+++ b/src/schema/rules/sidecars/anat.yaml
@@ -16,3 +16,19 @@ MRIAnatomyCommonMetadataFields:
         ContrastBolusIngredient: OPTIONAL
         RepetitionTimeExcitation: OPTIONAL
         RepetitionTimePreparation: OPTIONAL
+
+PhaseEntityUnits:
+    selectors:
+    - modality == "MRI"
+    - datatype == "anat"
+    - entities.part == "phase"
+    fields:
+        Unit: REQUIRED
+
+PhaseSuffixUnits:
+    selectors:
+    - modality == "MRI"
+    - datatype == "anat"
+    - suffix == "phase"
+    fields:
+        Unit: REQUIRED
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 492173a00d..058e2dab0b 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -89,7 +89,7 @@ MTParameters:
 SpoilingType:
     selectors:
     - '"SpoilingState" in sidecar'
-    - sidecar.SpoilingState == True
+    - sidecar.SpoilingState == true
     fields:
         SpoilingType: recommended
 

From 357b6eae62cd9b5d6ceffc5d976ecad5f86ee879 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Thu, 28 Apr 2022 19:48:28 +0000
Subject: [PATCH 347/347] [DOC] Auto-generate changelog entry for PR #1075

---
 src/CHANGES.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 12d2f9b7f5..b6bf16c8eb 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,9 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   ENH: use \__file\_\_ instead of getcwd to determine HERE, provide informative message on # of files [#1091](https://github.com/bids-standard/bids-specification/pull/1091) ([yarikoptic](https://github.com/yarikoptic))
+-   \[INFRA] Set light and dark mode image for logo in README [#1085](https://github.com/bids-standard/bids-specification/pull/1085) ([anibalsolon](https://github.com/anibalsolon))
+-   State of the schema sprint [#1075](https://github.com/bids-standard/bids-specification/pull/1075) ([effigies](https://github.com/effigies))
 -   \[DOC] Preface each macro call with comment [#1052](https://github.com/bids-standard/bids-specification/pull/1052) ([Remi-Gau](https://github.com/Remi-Gau))
 -   ENH: allow for .png and .tif in eeg/ieeg/meg as allowed for micr [#1049](https://github.com/bids-standard/bids-specification/pull/1049) ([yarikoptic](https://github.com/yarikoptic))
 -   \[SCHEMA] Add a new `file\_relative` format [#1046](https://github.com/bids-standard/bids-specification/pull/1046) ([tsalo](https://github.com/tsalo))