Merge branch 'master' into master

.github/workflows/schemacode_ci.yml

@@ -26,7 +26,7 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -64,7 +64,7 @@ jobs:
             python-version: 3
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: "Set up Python"
         uses: actions/setup-python@v4
@@ -129,7 +129,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate schema
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set Up Python environment
         uses: actions/setup-python@v4
@@ -157,7 +157,7 @@ jobs:
     needs: [test, validate_schema]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Download artifacts
         uses: actions/download-artifact@v3

.github/workflows/validation.yml

@@ -16,14 +16,14 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: codespell-project/actions-codespell@master
 
   # Markdown formatting
   remark:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-node@v3
         with:
           node-version: 14
@@ -36,7 +36,7 @@ jobs:
   yamllint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -49,7 +49,7 @@ jobs:
   python-style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -63,7 +63,7 @@ jobs:
   latin-phrases:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -86,7 +86,7 @@ jobs:
   validate_cff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v4
       with:
         python-version: 3

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -38,7 +38,7 @@ repos:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.1
+    rev: v3.0.3
     hooks:
       - id: prettier
         files: src/schema/.*/.*\.yaml
@@ -48,7 +48,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.0
+    rev: v1.5.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

README.md

@@ -1,5 +1,6 @@
 [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml)
 [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification)
+[![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
 [![@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)
 

src/common-principles.md

@@ -513,6 +513,29 @@ Example:
 }
 ```
 
+Each level can be described with a string as in the example above,
+or with an object containing the fields [`Description`](./glossary.md#description-metadata)
+and [`TermURL`](./glossary.md#termurl-metadata)
+like in the example below.
+
+```JSON
+{
+    "sex": {
+        "Description": "sex of the participant as reported by the participant",
+        "Levels": {
+            "M": {
+                "Description": "Male",
+                "TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68008297"
+            },
+            "F": {
+                "Description": "Female",
+                "TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68005260"
+            },
+        }
+    }
+}
+```
+
 ### Key-value files (dictionaries)
 
 JavaScript Object Notation (JSON) files MUST be used for storing key-value

src/modality-specific-files/magnetoencephalography.md

@@ -89,17 +89,20 @@ which some installations impose to be run on raw data prior to analysis.
 Such processing steps are needed for example because of active shielding software corrections
 that have to be performed to before the MEG data can actually be exploited.
 
-### Recording EEG simultaneously with MEG
+### Recording (i)EEG simultaneously with MEG
 
-Note that if EEG is recorded with a separate amplifier,
+Note that if (i)EEG is recorded with a separate amplifier,
 it SHOULD be stored separately under a new `/eeg` data type
-(see [the EEG specification](electroencephalography.md)).
+(see the [EEG](electroencephalography.md) and
+[iEEG](intracranial-electroencephalography.md) specifications).
 
-If however EEG is recorded simultaneously **with the same MEG system**,
+If however (i)EEG is recorded simultaneously **with the same MEG system**,
 it MAY be stored under the `/meg` data type.
 In that case, it SHOULD have the same sampling frequency as MEG (see `SamplingFrequency` field below).
-Furthermore, the EEG sensor coordinates SHOULD be specified using MEG-specific coordinate
-systems (see [coordinates section](#coordinate-system-json-_coordsystemjson) below and
+Furthermore, (i)EEG sensor coordinates MAY be recorded in an
+[`electrodes.tsv`](electroencephalography.md#electrodes-description-_electrodestsv)
+file using MEG-specific coordinate systems
+(see [Coordinate System JSON](#coordinate-system-json-_coordsystemjson) below and
 the [Coordinate Systems Appendix](../appendices/coordinate-systems.md)).
 
 ### Sidecar JSON (`*_meg.json`)

src/schema/objects/columns.yaml

@@ -37,6 +37,9 @@ age:
   display_name: Subject age
   description: |
     Numeric value in years (float or integer value).
+
+    It is recommended to tag participant ages that are 89 or higher as 89+,
+    for privacy purposes.
   type: number
   unit: year
 cardiac:

src/schema/objects/entities.yaml

@@ -189,7 +189,7 @@ part:
     `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 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` entity MAY be
@@ -356,7 +356,7 @@ stain:
     although the label may be different.
 
     Descriptions of antibodies SHOULD also be indicated in the `"SamplePrimaryAntibodies"`
-    and/or `"SampleSecondaryAntobodies"` metadata fields, as appropriate.
+    and/or `"SampleSecondaryAntibodies"` metadata fields, as appropriate.
   type: string
   format: label
 subject:

src/schema/objects/metadata.yaml

@@ -3365,9 +3365,10 @@ TermURL:
   name: TermURL
   display_name: TermURL
   description: |
-    URL pointing to a formal definition of this type of data in an ontology
-    available on the web.
+    URL pointing to a formal definition of this type of data in an ontology available on the web.
+    For example: https://www.ncbi.nlm.nih.gov/mesh/68008297 for "male".
   type: string
+  format: uri
 TimeZero:
   name: TimeZero
   display_name: Time Zero

src/schema/rules/checks/asl.yaml

@@ -15,7 +15,7 @@ ASLLabelingDurationNiftiLength:
       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`.
+      the associated `aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
   selectors:
     - suffix == "asl"
@@ -30,7 +30,7 @@ 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
+      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:
@@ -68,7 +68,7 @@ ASLFlipAngleASLContextLength:
     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'.
+      associated '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,
@@ -114,7 +114,7 @@ ASLPostLabelingDelayASLContextLength:
     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'.
+      in the associated '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).
@@ -138,7 +138,7 @@ ASLLabelingDurationASLContextLength:
     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'.
+      in the associated '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`,
@@ -147,7 +147,7 @@ ASLLabelingDurationASLContextLength:
       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`.
+      specified in the associated `aslcontext.tsv`.
       Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
   selectors:
@@ -163,7 +163,7 @@ ASLRepetitionTimePreparationASLContextLength:
     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'.
+      volumes in the associated '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.
@@ -201,9 +201,9 @@ ASLTotalAcquiredVolumesASLContextLength:
     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'.
+      volumes in the associated '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'.
+      associated 'aslcontext.tsv'.
     level: warning
   selectors:
     - suffix == "asl"
@@ -217,7 +217,7 @@ PostLabelingDelayGreater:
   issue:
     code: POST_LABELING_DELAY_GREATER
     message: |
-      'PostLabelingDelay' is greater than 10, are you sure it's expressed in seconds?
+      'PostLabelingDelay' is greater than 10. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - suffix == "asl"
@@ -230,7 +230,7 @@ BolusCutOffDelayTimeGreater:
   issue:
     code: BOLUS_CUT_OFF_DELAY_TIME_GREATER
     message: |
-      'BolusCutOffDelayTime' is greater than 10, are you sure it's expressed in seconds?
+      'BolusCutOffDelayTime' is greater than 10. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - sidecar.BolusCutOffDelayTime != null
@@ -242,7 +242,7 @@ LabelingDurationGreater:
   issue:
     code: LABELING_DURATION_GREATER
     message: |
-      'LabelingDuration' is greater than 10, are you sure it's expressed in seconds?
+      'LabelingDuration' is greater than 10. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - sidecar.LabelingDuration != null
@@ -255,7 +255,7 @@ ASLEchoTimeASLContextLength:
     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'.
+      associated 'aslcontext.tsv'.
       'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
     level: warning
   selectors:
@@ -272,8 +272,8 @@ 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.
+      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:
@@ -289,7 +289,8 @@ 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'.
+      You defined M0Type as 'absent' while including an m0scan volume within the associated
+      'aslcontext.tsv'.
       This is not allowed, please check that this field are filled correctly.
     level: error
   selectors:
@@ -306,7 +307,8 @@ ASLM0TypeIncorrect:
     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.
+      If 'M0Type' is equal to 'separate', the dataset should include an associated
+      'm0scan.nii[.gz]' and 'm0scan.json' file.
     level: error
   selectors:
     - suffix == "asl"