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fix: uprank the warning about dir-<label> to common principles
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as this important principle was buried in the bottom of the fieldmaps
section.
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oesteban committed Oct 24, 2020
1 parent 6e05ad6 commit b28e76a
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17 changes: 11 additions & 6 deletions src/02-common-principles.md
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Expand Up @@ -149,6 +149,11 @@ 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.

Key-value pairs SHOULD NOT be used to encode scanning parameters of the
corresponding data.
For instance, in echo-planar imaging MRI, the [`dir-<label>`](../99-appendices/09-entities.md#dir)
MAY NOT be used as a replacement for the `PhaseEncodingDirection` metadata.

A summary of all entities in BIDS and the order in which they MUST be
specified is available in the [entity table](./99-appendices/04-entity-table.md)
in the appendix.
Expand Down Expand Up @@ -552,16 +557,16 @@ 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).

## Uniform Resource Indicator
## Uniform Resource Indicator

A Uniform Resource Indicator (URI) is a string referring to a resource and SHOULD
have the form `<scheme>:[//<authority>]<path>[?<query>][#<fragment>]`, as specified
in [RFC 3986](https://tools.ietf.org/html/rfc3986).
This applies to URLs and other common URIs, including Digital Object Identifiers (DOIs),
which may be fully specified as `doi:<path>`,
have the form `<scheme>:[//<authority>]<path>[?<query>][#<fragment>]`, as specified
in [RFC 3986](https://tools.ietf.org/html/rfc3986).
This applies to URLs and other common URIs, including Digital Object Identifiers (DOIs),
which may be fully specified as `doi:<path>`,
for example, [doi:10.5281/zenodo.3686061](https://doi.org/10.5281/zenodo.3686061).
A given resource may have multiple URIs.
When selecting URIs to add to dataset metadata, it is important to consider
When selecting URIs to add to dataset metadata, it is important to consider
specificity and persistence.

Several fields are designated for DOIs, for example, `DatasetDOI` in `dataset_description.json`.
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Expand Up @@ -710,13 +710,11 @@ sub-<label>/[ses-<label>/]
sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.json
```

The REQUIRED [`dir-<label>`](../99-appendices/09-entities.md#dir) key/value pair
can be set to arbitrary alphanumeric label (`[a-zA-Z0-9]+` for
example `dir-LR` or `dir-AP`) that can help users to distinguish between different
files, but should not be used to infer any scanning parameters (such as phase
encoding directions) of the corresponding sequence.
It is RECOMMENDED to only rely on the JSON sidecar metadata described in the following
to obtain the scanning parameters.
The [`dir-<label>`](../99-appendices/09-entities.md#dir) key/value pair is
distinguish between different phase-encoding directions is REQUIRED for these
files, and SHOULD NOT be used to replace the required `PhaseEncodingDirection`
(nor any other acquisition parameter, as prescribed by the
[common principles](../02-common-principles.md#file-name-structure).)

Required fields:

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4 changes: 2 additions & 2 deletions src/99-appendices/09-entities.md
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Expand Up @@ -103,8 +103,8 @@ Full name: Phase-Encoding Direction

Format: `dir-<label>`

Definition: The `dir-<label>` key/value can be used to distinguish
different phase-encoding directions.
Definition: 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.

## run

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