Merge branch 'bids-standard:master' into master

Author: markmikkelsen

.circleci/config.yml

@@ -35,7 +35,7 @@ jobs:
               uvx linkchecker -t 1 ~/project/site/
               # check external separately by pointing to all *html so no
               # failures for local file:/// -- yoh found no better way,
-              linkchecker -t 1 --check-extern \
+              uvx linkchecker -t 1 --check-extern \
                 --ignore-url 'file:///.*' \
                 --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
                 --ignore-url 'https://doi.org/.*' \
@@ -45,6 +45,7 @@ jobs:
                 --ignore-url 'https://www.incf.org' \
                 --ignore-url 'https://dicomlookup.com/dicomtags/.*' \
                 --ignore-url 'https://www.instagram.com/bidsstandard/' \
+                --ignore-url 'https://jsoneditoronline.org' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.0
+    rev: 0.33.2
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -49,7 +49,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -68,6 +68,6 @@ repos:
         args: ["tools/schemacode/src"]
         pass_filenames: false
   - repo: https://github.com/koalaman/shellcheck-precommit
-    rev: v0.10.0
+    rev: v0.11.0
     hooks:
       - id: shellcheck

src/appendices/contributors.md

@@ -1,7 +1,7 @@
 # Contributors
 
 Legend (source:
-<https://allcontributors.org/docs/en/emoji-key>)
+<https://github.com/all-contributors/all-contributors/blob/master/docs/emoji-key.md>)
 
 | **Emoji** | **Represents**                                                                         |
 | --------- | -------------------------------------------------------------------------------------- |

src/modality-agnostic-files/dataset-description.md

@@ -33,6 +33,7 @@ and a guide for using macros can be found at
       "DatasetType": "RECOMMENDED",
       "License": "RECOMMENDED",
       "Authors": "RECOMMENDED if CITATION.cff is not present",
+      "Keywords": "OPTIONAL",
       "Acknowledgements": "OPTIONAL",
       "HowToAcknowledge": "OPTIONAL",
       "Funding": "OPTIONAL",
@@ -67,6 +68,11 @@ Example:
     "Paul Broca",
     "Carl Wernicke"
   ],
+  "Keywords": [
+    "neuroscience",
+    "language",
+    "brain"
+  ],
   "Acknowledgements": "Special thanks to Korbinian Brodmann for help in formatting this dataset in BIDS. We thank Alan Lloyd Hodgkin and Andrew Huxley for helpful comments and discussions about the experiment and manuscript; Hermann Ludwig Helmholtz for administrative support; and Claudius Galenus for providing data for the medial-to-lateral index analysis.",
   "HowToAcknowledge": "Please cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
   "Funding": [

src/modality-specific-files/magnetic-resonance-imaging-data.md

@@ -600,13 +600,13 @@ to be populated for functional sequences. Note that all these options can be
 used for non sparse sequences but that only options B, D and E are valid for
 sparse sequences.
 
-|          | **`RepetitionTime`** | **`SliceTiming`** | **`AcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
-| -------- | -------------------- | ----------------- | ------------------------- | --------------- | ------------------ |
-| option A | \[ X ]               |                   | \[ ]                      |                 | \[ ]               |
-| option B | \[ ]                 | \[ X ]            |                           | \[ ]            | \[ X ]             |
-| option C | \[ ]                 |                   | \[ X ]                    | \[ ]            | \[ X ]             |
-| option D | \[ X ]               | \[ X ]            | \[ ]                      |                 | \[ ]               |
-| option E | \[ X ]               |                   | \[ ]                      | \[ X ]          | \[ ]               |
+|          | **`RepetitionTime`** | **`SliceTiming`** | **`FrameAcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
+| -------- | -------------------- | ----------------- | ------------------------------ | --------------- | ------------------ |
+| option A | \[ X ]               |                   | \[ ]                           |                 | \[ ]               |
+| option B | \[ ]                 | \[ X ]            |                                | \[ ]            | \[ X ]             |
+| option C | \[ ]                 |                   | \[ X ]                         | \[ ]            | \[ X ]             |
+| option D | \[ X ]               | \[ X ]            | \[ ]                           |                 | \[ ]               |
+| option E | \[ X ]               |                   | \[ ]                           | \[ X ]          | \[ ]               |
 
 **Legend**
 

src/schema/meta/associations.yaml

@@ -14,7 +14,7 @@
 ---
 events:
   selectors:
-    - 'task in entities'
+    - '"task" in entities'
     - extension != '.json'
   target:
     suffix: events

src/schema/objects/metadata.yaml

@@ -20,9 +20,8 @@ AcquisitionDuration:
   name: AcquisitionDuration
   display_name: Acquisition Duration
   description: |
-    Duration (in seconds) of volume acquisition.
+    Duration (in seconds) of scan acquisition, including all volumes for multi-volume scans.
     Corresponds to [DICOM Tag 0018, 9073](https://dicomlookup.com/dicomtags/(0018,9073)) `Acquisition Duration`.
-    This field is mutually exclusive with `"RepetitionTime"`.
   type: number
   exclusiveMinimum: 0
   unit: s
@@ -1200,6 +1199,15 @@ FlipAngle:
         unit: degree
         exclusiveMinimum: 0
         maximum: 360
+FrameAcquisitionDuration:
+  name: FrameAcquisitionDuration
+  display_name: Frame Acquisition Duration
+  description: |
+    Duration (in seconds) of volume acquisition.
+    Corresponds to DICOM Tag 0018, 9220 `Frame Acquisition Duration`.
+  type: number
+  exclusiveMinimum: 0
+  unit: s
 FrameDuration:
   name: FrameDuration
   display_name: Frame Duration
@@ -1728,6 +1736,15 @@ JNTANGChannelCount:
     Number of joint angle channels.
   type: integer
   minimum: 0
+Keywords:
+  name: Keywords
+  display_name: Keywords
+  description: |
+    A list of keywords that describe the content or subject matter of the dataset.
+    These may be used to enhance the findability of the dataset on public archives.
+  type: array
+  items:
+    type: string
 LabelingDistance:
   name: LabelingDistance
   display_name: Labeling Distance

src/schema/rules/checks/events.yaml

@@ -13,7 +13,7 @@ EventsMissing:
     - datatype != "beh"
     - '"task" in entities'
     - '!match(entities.task, "rest")'
-    - '!intersects([suffix], ["events", "beh"])'
+    - '!intersects([suffix], ["events", "beh", "channels", "electrodes", "optodes"])'
     - extension != ".json"
     - datatype != "meg" || entities.subject != "emptyroom" && entities.task != "noise"
   checks:

src/schema/rules/checks/func.yaml

@@ -12,6 +12,7 @@ PhaseSuffixDeprecated:
     level: warning
   selectors:
     - datatype == "func"
+    - match(extension, "^\.nii(\.gz)?$")
   checks:
     - suffix != "phase"
 
@@ -67,6 +68,7 @@ SliceTimingGreaterThanRepetitionTime:
     level: error
   selectors:
     - suffix == "bold"
+    - match(extension, "^\.nii(\.gz)?$")
     - type(sidecar.SliceTiming) != "null"
     - type(sidecar.RepetitionTime) != "null"
   checks:
@@ -88,24 +90,24 @@ VolumeTimingRepetitionTimeMutex:
       or 'VolumeTiming' when variable times are used.
     level: error
   selectors:
-    - type(nifti_header) != "null"
     - intersects([suffix], ["asl", "bold"])
+    - match(extension, "^\.nii(\.gz)?$")
     - type(sidecar.VolumeTiming) != "null"
   checks:
     - type(sidecar.RepetitionTime) == "null"
 
-RepetitionTimeAcquisitionDurationMutex:
+RepetitionTimeFrameAcquisitionDurationMutex:
   issue:
     code: REPETITION_TIME_AND_ACQUISITION_DURATION_MUTUALLY_EXCLUSIVE
     message: |
-      The fields 'RepetitionTime' and 'AcquisitionDuration' for this file are mutually exclusive.
+      The fields 'RepetitionTime' and 'FrameAcquisitionDuration' for this file are mutually exclusive.
       To specify acquisition duration, use 'SliceTiming' or 'DelayTime'
-      (RepetitionTime - AcquisitionDuration).
+      (RepetitionTime - FrameAcquisitionDuration).
     level: error
   selectors:
-    - type(nifti_header) != "null"
     - intersects([suffix], ["asl", "bold"])
-    - type(sidecar.AcquisitionDuration) != "null"
+    - match(extension, "^\.nii(\.gz)?$")
+    - type(sidecar.FrameAcquisitionDuration) != "null"
   checks:
     - type(sidecar.RepetitionTime) == "null"
 
@@ -114,24 +116,44 @@ VolumeTimingDelayTimeMutex:
     code: VOLUME_TIMING_AND_DELAY_TIME_MUTUALLY_EXCLUSIVE
     message: |
       The fields 'VolumeTiming' and 'DelayTime' for this file are mutually exclusive.
-      To specify acquisition duration, use 'AcquisitionDuration' or 'SliceTiming'.
+      To specify acquisition duration, use 'FrameAcquisitionDuration' or 'SliceTiming'.
     level: error
   selectors:
-    - type(nifti_header) != "null"
     - intersects([suffix], ["asl", "bold"])
+    - match(extension, "^\.nii(\.gz)?$")
     - type(sidecar.VolumeTiming) != "null"
+    - type(sidecar.RepetitionTime) == "null"
   checks:
     - type(sidecar.DelayTime) == "null"
 
-VolumeTimingMissingAcquisitionDuration:
+VolumeTimingMissingFrameAcquisitionDuration:
   issue:
     code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
     message: |
-      The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
+      The field 'VolumeTiming' requires 'FrameAcquisitionDuration' or 'SliceTiming' to be defined.
     level: error
   selectors:
-    - type(nifti_header) != "null"
     - intersects([suffix], ["asl", "bold"])
+    - match(extension, "^\.nii(\.gz)?$")
+    - type(sidecar.VolumeTiming) != "null"
+    - type(sidecar.RepetitionTime) == "null"
+  checks:
+    - |
+      "SliceTiming" in sidecar ||
+      "FrameAcquisitionDuration" in sidecar ||
+      "AcquisitionDuration" in sidecar
+
+DeprecatedAcquisitionDuration:
+  issue:
+    code: DEPRECATED_ACQUISITION_DURATION
+    message: |
+      The 'AcquisitionDuration' field has been replaced with 'FrameAcquisitionDuration'
+      to indicate the duration of volume acquisition in sparse acquisition sequences.
+    level: warning
+  selectors:
+    - intersects([suffix], ["asl", "bold"])
+    - match(extension, "^\.nii(\.gz)?$")
     - type(sidecar.VolumeTiming) != "null"
+    - type(sidecar.FrameAcquisitionDuration) == "null"
   checks:
-    - '"SliceTiming" in sidecar || "AcquisitionDuration" in sidecar'
+    - '!("AcquisitionDuration" in sidecar)'

src/schema/rules/dataset_metadata.yaml

@@ -10,6 +10,7 @@ dataset_description:
     Authors:
       level: optional
       level_addendum: recommended if no CITATION.cff file is present
+    Keywords: optional
     Acknowledgements: optional
     HowToAcknowledge: optional
     Funding: optional