Merge branch 'master' into mikkel-dev

Author: effigies

.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: v1.17.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

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-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/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

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/sidecars/anat.yaml

@@ -19,7 +19,7 @@ MRIAnatomyCommonMetadataFields:
 TaskMetadata:
   selectors:
     - datatype == "anat"
-    - entity.task != null
+    - entities.task != null
     - match(extension, "^\.nii(\.gz)?$")
   fields:
     TaskName:

src/schema/rules/sidecars/func.yaml

@@ -44,7 +44,7 @@ MRIFuncVolumeTiming:
       description_addendum: |
         This field is mutually exclusive with `"DelayTime"`.
         If defined, this requires acquisition time (TA) be defined via either
-        `"SliceTiming"` or `"AcquisitionDuration"`.
+        `"SliceTiming"` or `"FrameAcquisitionDuration"`.
 
 # Timing Parameters
 MRIFuncTimingParameters:
@@ -56,13 +56,18 @@ MRIFuncTimingParameters:
     NumberOfVolumesDiscardedByScanner: optional
     NumberOfVolumesDiscardedByUser: optional
     DelayTime: optional
-    AcquisitionDuration:
+    FrameAcquisitionDuration:
       level: optional
       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: optional
+    AcquisitionDuration:
+      level: deprecated
+      description_addendum: |
+        This field was previously used to indicate volume acquisition duration
+        for BOLD data. The `FrameAcquisitionDuration` field should be used instead.
 
 # fMRI task information
 MRIFuncTaskInformation:

src/schema/rules/sidecars/mri.yaml

@@ -262,6 +262,7 @@ MRITimingParameters:
       level: optional
       level_addendum: required if `inv` entity is present
     DwellTime: recommended
+    AcquisitionDuration: optional
 
 EchoTimeRequiredASL:
   selectors:

tools/schemacode/src/bidsschematools/utils.py

@@ -148,4 +148,4 @@ def jsonschema_validator(
 
     validator_kwargs: ValidatorKwargs
     validator_kwargs = {"format_checker": validator_cls.FORMAT_CHECKER} if check_format else {}
-    return validator_cls(schema, **validator_kwargs)
+    return validator_cls(schema, **validator_kwargs)  # type: ignore[call-arg]