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[FIX] Typos discovered by codespell #784

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[FIX] Typos discovered by codespell #784

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d91bf0a
[DATALAD RUNCMD] Fix some typos detected by codespell src
yarikoptic Apr 21, 2021
43faa0e
STY: Fix table alignment
effigies Apr 22, 2021
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2 changes: 1 addition & 1 deletion src/02-common-principles.md
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Expand Up @@ -254,7 +254,7 @@ 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.
The above example is just a convention that can be useful for organizing raw,
source, and derived data while maintaining BIDS compliancy of the raw data
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:

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4 changes: 2 additions & 2 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -151,7 +151,7 @@ non-parametric structural MR images include:
| Inplane T1 | inplaneT1 | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image. |
| Inplane T2 | inplaneT2 | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image. |
| PD and T2 weighted images | PDT2 | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)). |
| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1 | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information. |
| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1 | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Please see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information. |

If the structural images included in the dataset were defaced (to protect
identity of participants) one MAY provide the binary mask that was used to
Expand Down Expand Up @@ -954,7 +954,7 @@ are REQUIRED for these field mapping sequences.
Fieldmaps are typically acquired with the purpose of correcting one or more EPI
scans under `func/` or `dwi/` for distortions derived from *B<sub>0</sub>*
nonuniformity.
This linking between fieldmaps and their targetted data MAY be encoded with the
This linking between fieldmaps and their targeted data MAY be encoded with the
`IntendedFor` metadata.

#### Using `IntendedFor` metadata
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2 changes: 1 addition & 1 deletion src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -47,7 +47,7 @@ remember to list all files separately in `scans.tsv` and that the entries for th
`acq_time` column in `scans.tsv` MUST all be identical, as described in
[Scans file](../03-modality-agnostic-files.md#scans-file).

Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh sytem,
Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh system,
which saves the MEG sensor coil positions in a separate file with two possible filename extensions (`.sqd`, `.mrk`).
For these files, the `markers` suffix MUST be used.
For example: `sub-01_task-nback_markers.sqd`
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2 changes: 1 addition & 1 deletion src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -198,7 +198,7 @@ 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 auxilliary, non-electrode device.
of two electrodes, or a data channel originating from an auxiliary, non-electrode device.
That is, in most cases `*_electrodes.tsv` will have more entries than `*_channels.tsv`.
See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in
["Electrodes description"](./03-electroencephalography.md#electrodes-description-_electrodestsv).
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4 changes: 2 additions & 2 deletions src/04-modality-specific-files/05-task-events.md
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Expand Up @@ -158,7 +158,7 @@ in the accompanying JSON sidecar as follows:
{
"trial_type": {
"LongName": "Emotion image type",
"Descripton": "Type of emotional face from Karolinska database that is displayed",
"Description": "Type of emotional face from Karolinska database that is displayed",
"Levels": {
"afraid": "A face showing fear is displayed",
"angry": "A face showing anger is displayed",
Expand Down Expand Up @@ -216,7 +216,7 @@ in the accompanying JSON sidecar as follows (based on the example of the previou
{
"trial_type": {
"LongName": "Emotion image type",
"Descripton": "Type of emotional face from Karolinska database that is displayed",
"Description": "Type of emotional face from Karolinska database that is displayed",
"Levels": {
"afraid": "A face showing fear is displayed",
"angry": "A face showing anger is displayed",
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2 changes: 1 addition & 1 deletion src/99-appendices/07-meg-systems.md
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@@ -1,6 +1,6 @@
# Appendix VII: MEG systems

Perferred names of MEG systems comprise restricted keywords for Manufacturer field in the `*_meg.json` file:
Preferred names of MEG systems comprise restricted keywords for Manufacturer field in the `*_meg.json` file:

- [`CTF`](06-meg-file-formats.md#ctf)
- [`Neuromag/Elekta/Megin`](06-meg-file-formats.md#neuromagelektamegin)
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2 changes: 1 addition & 1 deletion src/99-appendices/08-coordinate-systems.md
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Expand Up @@ -205,7 +205,7 @@ In the case of multiple study templates, additional names may need to be defined

| Coordinate System | Description |
| ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| individual | Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been refered to as `fsnative`. |
| individual | Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been referred to as `fsnative`. |
| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. |

### Non-template coordinate system identifiers
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2 changes: 1 addition & 1 deletion src/99-appendices/10-file-collections.md
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Expand Up @@ -5,7 +5,7 @@ Here, some concrete use-cases of [entity-linked file collections](../02-common-p
The tables in this appendix catalog applications where the use of
a file collection is REQUIRED.

Certain entitites interlink the files in a file collection through a metadata field.
Certain entities interlink the files in a file collection through a metadata field.
Unlike other common entities (for example `run`), they require an iteration over different
values of the metadata fields they represent.
Please keep the following list of linking entities up-to-date with the file collections
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8 changes: 4 additions & 4 deletions src/99-appendices/11-qmri.md
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Expand Up @@ -236,7 +236,7 @@ For example, without the information of `MagneticFieldStrength`, white-matter T1
| ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
| `BasedOn` | List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing. |
| `EstimationReference` | Reference to the study/studies on which the implementation is based. |
| `EstimationAlgorithm` | Type of algoritm used to perform fitting (for example, linear, non-linear, LM and such) |
| `EstimationAlgorithm` | Type of algorithm used to perform fitting (for example, linear, non-linear, LM and such) |
| `Units` | Units of the maps, in accordance with the BIDS specification. |

Example:
Expand Down Expand Up @@ -307,15 +307,15 @@ This approach aims at:
| MPM | | `EchoTime` (`echo`) | MPM-ME |

In this table, (`entity`/`fixed`) denotes whether the OPTIONAL metadata that forms a new
flavor of qMRI applicaiton for the respective suffix varies across files of a file collection
flavor of qMRI application for the respective suffix varies across files of a file collection
(which calls for using a linking entity) or fixed. If former is the case, the entity is to be
added to the files in that file collection. Note that this addition MUST be allowed by the
priority levels given for that suffix in the [`entity table`](./04-entity-table.md). If latter (`fixed`) is the case,
filenames will remain the same; however, the optional metadata (third column) may
define the flavor of the application (fourth column) along with the conditional value of a
required metadata field (second column).

A derived qMRI application becomes avaiable if all the optional metadata fields
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
for the description of a derived qMRI application. Note that the value of this
Expand Down Expand Up @@ -382,7 +382,7 @@ 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 neccesary provenance information.
`derivatives` folder with necessary provenance information.

##### `NumberShots` metadata field

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