Merge pull request #1 from bids-standard/bep022

Bep022

.pre-commit-config.yaml

@@ -38,7 +38,7 @@ repos:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.2
+    rev: v3.0.3
     hooks:
       - id: prettier
         files: src/schema/.*/.*\.yaml

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

@@ -210,7 +210,7 @@ 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

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"

src/schema/rules/checks/dataset.yaml

@@ -43,7 +43,8 @@ SamplesTSVMissing:
   issue:
     code: SAMPLES_TSV_MISSING
     message: |
-      The compulsory file /samples.tsv is missing. See Modality agnostic files section of the BIDS specification.
+      The compulsory file '/samples.tsv' is missing.
+      See 'Modality agnostic files' section of the BIDS specification.
     level: error
   selectors:
     - path == 'dataset_description.json'
@@ -55,7 +56,7 @@ UnknownVersion:
   issue:
     code: UNKNOWN_BIDS_VERSION
     message: |
-      The BIDSVersion field of dataset_description.json does not match a known release.
+      The BIDSVersion field of 'dataset_description.json' does not match a known release.
       The BIDS Schema used for validation may be out of date.
     level: warning
   selectors:
@@ -68,7 +69,7 @@ SingleSourceAuthors:
     code: AUTHORS_AND_CITATION_FILE_MUTUALLY_EXCLUSIVE
     level: error
     message: |
-      CITATION.cff file found. The "Authors" field of dataset_description.json
+      'CITATION.cff' file found. The "Authors" field of 'dataset_description.json'
       must be removed to avoid inconsistency.
   selectors:
     - path == 'CITATION.cff'
@@ -80,9 +81,9 @@ SingleSourceCitationFields:
     code: SINGLE_SOURCE_CITATION_FIELDS
     level: warning
     message: |
-      CITATION.cff file found. The "HowToAckowledge", "License",
-      and "ReferencesAndLinks" fields of dataset_description.json
-      should be removed to avoid inconsistency.
+      CITATION.cff file found.
+      The "HowToAckowledge", "License", and "ReferencesAndLinks" fields of
+      'dataset_description.json' should be removed to avoid inconsistency.
   selectors:
     - path == 'CITATION.cff'
   checks:

src/schema/rules/checks/dwi.yaml

@@ -6,7 +6,7 @@ DWIVolumeCount:
     code: VOLUME_COUNT_MISMATCH
     message: |
       The number of volumes in this scan does not match the number of volumes in the
-      corresponding .bvec and .bval files.
+      associated '.bvec' and '.bval' files.
     level: error
   selectors:
     - suffix == "dwi"
@@ -22,7 +22,7 @@ DWIBvalRows:
   issue:
     code: BVAL_MULTIPLE_ROWS
     message: |
-      '.bval' files should contain exactly one row of volumes.
+      '.bval' files should contain exactly one row of values.
     level: error
   selectors:
     - extension == ".bval"
@@ -34,7 +34,7 @@ DWIBvecRows:
   issue:
     code: BVEC_NUMBER_ROWS
     message: |
-      '.bvec' files should contain exactly three rows of volumes.
+      '.bvec' files should contain exactly three rows of values.
     level: error
   selectors:
     - extension == ".bvec"
@@ -46,7 +46,7 @@ DWIMissingBvec:
   issue:
     code: DWI_MISSING_BVEC
     message: |
-      DWI scans must have a corresponding .bvec file.
+      DWI scans must have a corresponding '.bvec' file.
     level: error
   selectors:
     - suffix == "dwi"
@@ -59,7 +59,7 @@ DWIMissingBval:
   issue:
     code: DWI_MISSING_BVAL
     message: |
-      DWI scans must have a corresponding .bval file.
+      DWI scans must have a corresponding '.bval' file.
     level: error
   selectors:
     - suffix == "dwi"

src/schema/rules/checks/events.yaml

@@ -5,7 +5,7 @@ EventsMissing:
   issue:
     code: EVENTS_TSV_MISSING
     message: |
-      Task scans should have a corresponding events.tsv file.
+      Task scans should have a corresponding 'events.tsv' file.
       If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".
     level: warning # could be an error with the proper selectors, I think
   selectors:

src/schema/rules/checks/fmap.yaml

@@ -18,7 +18,7 @@ FmapFieldmapWithoutMagnitude:
   issue:
     code: FIELDMAP_WITHOUT_MAGNITUDE_FILE
     message: |
-      '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
+      'fieldmap.nii[.gz]' file does not have an associated 'magnitude.nii[.gz]' file.
     level: error
   selectors:
     - suffix == "fieldmap"
@@ -30,7 +30,7 @@ FmapPhasediffWithoutMagnitude:
   issue:
     code: MISSING_MAGNITUDE1_FILE
     message: |
-      Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
+      'phasediff.nii[.gz]' file does not have an associated 'magnitude1.nii[.gz]' file.
     level: warning
   selectors:
     - suffix == "phasediff"
@@ -42,7 +42,7 @@ MagnitudeFileWithTooManyDimensions:
   issue:
     code: MAGNITUDE_FILE_WITH_TOO_MANY_DIMENSIONS
     message: |
-      _magnitude1.nii[.gz] and _magnitude2.nii[.gz] files must have exactly three dimensions.
+      'magnitude1.nii[.gz]' and 'magnitude2.nii[.gz]' files must have exactly three dimensions.
     level: error
   selectors:
     - intersects([suffix], ['magnitude1', 'magnitude2'])

src/schema/rules/checks/func.yaml

@@ -5,10 +5,10 @@ PhaseSuffixDeprecated:
     code: PHASE_SUFFIX_DEPRECATED
     message: |
       DEPRECATED. Phase information associated with magnitude information stored in BOLD contrast.
-      This suffix should be replaced by the part-phase in conjunction with the bold suffix.
-      For backwards compatibility, _phase is considered equivalent to _part-phase_bold.
-      When the _phase suffix is not used, each file shares the same name with the exception of the
-      part-<mag|phase> or part-<real|imag> key/value.
+      This suffix should be replaced by the 'part-phase' entity in conjunction with the 'bold' suffix.
+      For backwards compatibility, 'phase' is considered equivalent to 'part-phase_bold'.
+      When the 'phase' suffix is not used, each file shares the same name with the exception of the
+      'part-<mag|phase>' or 'part-<real|imag>' key/value.
     level: warning
   selectors:
     - datatype == "func"
@@ -20,7 +20,7 @@ RepetitionTimeGreaterThan:
   issue:
     code: REPETITION_TIME_GREATER_THAN
     message: |
-      'RepetitionTime' is greater than 100 are you sure it's expressed in seconds?
+      'RepetitionTime' is greater than 100. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - suffix == "bold"
@@ -47,7 +47,7 @@ BoldNot4d:
   issue:
     code: BOLD_NOT_4D
     message: |
-      Bold scans must be 4 dimensional.
+      BOLD scans must be 4 dimensional.
     level: error
   selectors:
     - suffix == "bold"
@@ -60,8 +60,8 @@ SliceTimingGreaterThanRepetitionTime:
   issue:
     code: SLICETIMING_VALUES_GREATER_THAN_REPETITION_TIME
     message: |
-      SliceTiming values contains invalid value as it is greater than RepetitionTime.
-      SliceTiming values should be in seconds not milliseconds (common mistake).
+      'SliceTiming' contains invalid value(s) greater than 'RepetitionTime'.
+      'SliceTiming' values should be in seconds, not milliseconds (common mistake).
     level: error
   selectors:
     - suffix == "bold"

src/schema/rules/checks/general.yaml

@@ -5,7 +5,7 @@ DuplicateFiles:
   issue:
     code: DUPLICATE_FILES
     message: |
-      File exists with and without `.gz` extension
+      File exists with and without `.gz` extension.
     level: error
   selectors:
     - match(extension, '\.gz$')
@@ -16,8 +16,8 @@ ReadmeFileSmall:
   issue:
     code: README_FILE_SMALL
     message: |
-      The recommended file /README is very small. Please consider expanding it
-      with additional information about the dataset.
+      The recommended file '/README' is very small.
+      Please consider expanding it with additional information about the dataset.
     level: warning
   selectors:
     - match(path, '^README')

src/schema/rules/checks/hints.yaml

@@ -9,9 +9,10 @@ TooFewAuthors:
   issue:
     code: TOO_FEW_AUTHORS
     message: |
-      The Authors field of dataset_description.json should contain an array of fields -
-      with one author per field. This was triggered based on the presence of only one
-      author field. Please ignore if all contributors are already properly listed.
+      The 'Authors' field of 'dataset_description.json' should contain an array of values -
+      with one author per value.
+      This was triggered based on the presence of only one author field.
+      Please ignore if all contributors are already properly listed.
     level: warning
   selectors:
     - path == '/dataset_description.json'

src/schema/rules/checks/micr.yaml

@@ -4,7 +4,8 @@ PixelSizeInconsistent:
   issue:
     code: PIXEL_SIZE_INCONSISTENT
     message: |
-      PixelSize need to be consistent with PhysicalSizeX, PhysicalSizeY and PhysicalSizeZ OME metadata fields
+      'PixelSize' need to be consistent with the 'PhysicalSizeX', 'PhysicalSizeY' and 'PhysicalSizeZ'
+      OME metadata fields.
     level: error
   selectors:
     - ome != null