From 94105cb9c2c77562df498bf0cbc4e4d35f6b120f Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 24 Aug 2023 16:48:04 -0500
Subject: [PATCH 1/6] Update pet.yaml PlasmaAvail check. (#1595)

BloodPlasma requirement in tabular data didn't check if the corresponding json was true. All jsons are required to have the PlasmaAvail field, so any dataset with PlasmaAvail false would fail this check.
---
 src/schema/rules/tabular_data/pet.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index b00d9f1e88..7c72b028ea 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -28,6 +28,7 @@ BloodPlasma:
     - suffix == "blood"
     - extension == ".tsv"
     - '"PlasmaAvail" in sidecar'
+    - sidecar.PlasmaAvail == true
   columns:
     plasma_radioactivity: required
 

From 60c173d3a576f45a4241f1185a5819de892ec10f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 25 Aug 2023 11:32:30 -0400
Subject: [PATCH 2/6] Improve check messages (#1599)

* Remove redundant phase entity rule.

* Add missing newline.

* Adjust check messages.

* Add note about 89+ to age column description.
---
 src/schema/objects/columns.yaml      |  3 +++
 src/schema/rules/checks/asl.yaml     | 36 +++++++++++++++-------------
 src/schema/rules/checks/dataset.yaml | 13 +++++-----
 src/schema/rules/checks/dwi.yaml     | 10 ++++----
 src/schema/rules/checks/events.yaml  |  2 +-
 src/schema/rules/checks/fmap.yaml    |  6 ++---
 src/schema/rules/checks/func.yaml    | 16 ++++++-------
 src/schema/rules/checks/general.yaml |  6 ++---
 src/schema/rules/checks/hints.yaml   |  7 +++---
 src/schema/rules/checks/micr.yaml    |  3 ++-
 src/schema/rules/checks/mri.yaml     | 11 ++++-----
 src/schema/rules/checks/nifti.yaml   |  6 ++---
 src/schema/rules/checks/privacy.yaml |  7 +++---
 src/schema/rules/sidecars/anat.yaml  |  8 -------
 src/schema/rules/sidecars/mri.yaml   |  1 +
 15 files changed, 67 insertions(+), 68 deletions(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index bd1ab1478e..65fbde5a6c 100644
--- a/src/schema/objects/columns.yaml
+++ b/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:
diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml
index cda02f4325..1b42593212 100644
--- a/src/schema/rules/checks/asl.yaml
+++ b/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"
diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
index 999de949cf..b0f0aba634 100644
--- a/src/schema/rules/checks/dataset.yaml
+++ b/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:
diff --git a/src/schema/rules/checks/dwi.yaml b/src/schema/rules/checks/dwi.yaml
index 8f22ab6aae..d331775030 100644
--- a/src/schema/rules/checks/dwi.yaml
+++ b/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"
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 1492c03e2d..458e60d408 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/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:
diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
index debddd03ea..af042351d8 100644
--- a/src/schema/rules/checks/fmap.yaml
+++ b/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'])
diff --git a/src/schema/rules/checks/func.yaml b/src/schema/rules/checks/func.yaml
index b17ea7a422..cce740a1ec 100644
--- a/src/schema/rules/checks/func.yaml
+++ b/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"
diff --git a/src/schema/rules/checks/general.yaml b/src/schema/rules/checks/general.yaml
index 054090b61f..b0505250b3 100644
--- a/src/schema/rules/checks/general.yaml
+++ b/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')
diff --git a/src/schema/rules/checks/hints.yaml b/src/schema/rules/checks/hints.yaml
index fe0fc7561e..7c733d8d51 100644
--- a/src/schema/rules/checks/hints.yaml
+++ b/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'
diff --git a/src/schema/rules/checks/micr.yaml b/src/schema/rules/checks/micr.yaml
index 1476a0abb7..bf2f4c55c3 100644
--- a/src/schema/rules/checks/micr.yaml
+++ b/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
diff --git a/src/schema/rules/checks/mri.yaml b/src/schema/rules/checks/mri.yaml
index 983ccd686e..5887f0e95f 100644
--- a/src/schema/rules/checks/mri.yaml
+++ b/src/schema/rules/checks/mri.yaml
@@ -3,8 +3,7 @@ PhasePartUnits:
   issue:
     code: PHASE_UNITS
     message: |
-      Phase images (with the `part-phase` entity) must have units
-      "rad" or "arbitrary".
+      Phase images (with the `part-phase` entity) must have units "rad" or "arbitrary".
     level: error
   selectors:
     - modality == "mri"
@@ -18,7 +17,7 @@ EchoTimeGreaterThan:
   issue:
     code: ECHO_TIME_GREATER_THAN
     message: |
-      'EchoTime' is greater than 1 are you sure it's expressed in seconds?
+      'EchoTime' is greater than 1. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - modality == "MRI"
@@ -31,7 +30,7 @@ TotalReadoutTimeGreaterThan:
   issue:
     code: TOTAL_READOUT_TIME_GREATER_THAN
     message: |
-      'TotalReadoutTime' is greater than 10 are you sure it's expressed in seconds?
+      'TotalReadoutTime' is greater than 10. Are you sure it's expressed in seconds?
     level: warning
   selectors:
     - modality == "MRI"
@@ -64,7 +63,7 @@ SliceTimingElements:
   issue:
     code: SLICETIMING_ELEMENTS
     message: |
-      The number of elements in the SliceTiming array should match the 'k'
+      The number of elements in the 'SliceTiming' array should match the 'k'
       dimension of the corresponding NIfTI volume.
     level: warning
   selectors:
@@ -79,7 +78,7 @@ EESGreaterThanTRT:
   issue:
     code: EFFECTIVEECHOSPACING_LARGER_THAN_TOTALREADOUTTIME
     message: |
-      EffectiveEchoSpacing should always be smaller than TotalReadoutTime.
+      'EffectiveEchoSpacing' should always be smaller than 'TotalReadoutTime'.
     level: error
   selectors:
     - modality == "MRI"
diff --git a/src/schema/rules/checks/nifti.yaml b/src/schema/rules/checks/nifti.yaml
index 9fdae953cc..eb160f2047 100644
--- a/src/schema/rules/checks/nifti.yaml
+++ b/src/schema/rules/checks/nifti.yaml
@@ -4,7 +4,7 @@ NiftiDimension:
   issue:
     code: NIFTI_DIMENSION
     message: |
-      NIfTI file's header field for dimension information blank or too short.
+      NIfTI file's header field for dimension information is blank or too short.
     level: warning
   selectors:
     - type(nifti_header) != "null"
@@ -17,7 +17,7 @@ NiftiUnit:
   issue:
     code: NIFTI_UNIT
     message: |
-      NIfTI file's header field for unit information for x, y, z, and t dimensions empty or too short
+      NIfTI file's header field for unit information for x, y, z, and t dimensions is empty or too short.
     level: warning
   selectors:
     - type(nifti_header) != "null"
@@ -30,7 +30,7 @@ NiftiPixdim:
   issue:
     code: NIFTI_PIXDIM
     message: |
-      NIfTI file's header field for pixel dimension information empty or too short.
+      NIfTI file's header field for pixel dimension information is empty or too short.
     level: warning
   selectors:
     - type(nifti_header) != "null"
diff --git a/src/schema/rules/checks/privacy.yaml b/src/schema/rules/checks/privacy.yaml
index dd58320c0a..c9e2ecf0cb 100644
--- a/src/schema/rules/checks/privacy.yaml
+++ b/src/schema/rules/checks/privacy.yaml
@@ -3,9 +3,8 @@ GzipHeaderFields:
   issue:
     code: GZIP_HEADER_DATA
     message: |
-      The gzip header contains a non-zero timestamp or a non-empty filename
-      and/or comment field. These may leak sensitive information or indicate
-      a non-reproducible conversion process.
+      The gzip header contains a non-zero timestamp or a non-empty filename and/or comment field.
+      These may leak sensitive information or indicate a non-reproducible conversion process.
     level: warning
   selectors:
     - match(extension, ".gz$")
@@ -21,7 +20,7 @@ CheckAge89:
     message: |
       As per section 164.514(C) of "The De-identification Standard" under HIPAA guidelines,
       participants with age 89 or higher should be tagged as 89+. More information can be found at
-      https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/#standard
+      https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/#standard.
     level: warning
   selectors:
     - path == 'participants.tsv'
diff --git a/src/schema/rules/sidecars/anat.yaml b/src/schema/rules/sidecars/anat.yaml
index 0bd1527d80..78255dc338 100644
--- a/src/schema/rules/sidecars/anat.yaml
+++ b/src/schema/rules/sidecars/anat.yaml
@@ -16,14 +16,6 @@ MRIAnatomyCommonMetadataFields:
     RepetitionTimeExcitation: optional
     RepetitionTimePreparation: optional
 
-PhaseEntityUnits:
-  selectors:
-    - modality == "mri"
-    - datatype == "anat"
-    - entities.part == "phase"
-  fields:
-    Units: required
-
 PhaseSuffixUnits:
   selectors:
     - modality == "mri"
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 63e4a900df..d95714de6b 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -146,6 +146,7 @@ PhaseEncodingDirectionRec:
         acquired with opposing phase encoding directions are present
         (see [Case 4: Multiple phase encoded
         directions](#case-4-multiple-phase-encoded-directions-pepolar))
+
 PhaseEncodingDirectionReq:
   selectors:
     - modality == "mri"

From 6246705f4b77316f240584f5481ea4baa8e4a2e8 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Aug 2023 11:44:22 -0400
Subject: [PATCH 3/6] [ENH] Add optional low_cutoff and high_cutoff columns for
 fnirs channels.tsv (#1597)

---
 src/schema/rules/tabular_data/nirs.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/schema/rules/tabular_data/nirs.yaml b/src/schema/rules/tabular_data/nirs.yaml
index 117116abd3..996b5bc585 100644
--- a/src/schema/rules/tabular_data/nirs.yaml
+++ b/src/schema/rules/tabular_data/nirs.yaml
@@ -25,6 +25,8 @@ nirsChannels:
       level: optional
       level_addendum: required if `type` is `ACCEL`, `GYRO` or `MAGN`
     wavelength_actual: optional
+    low_cutoff: optional
+    high_cutoff: optional
     description: optional
     wavelength_emission_actual: optional
     short_channel: optional

From 9ea418ba0408a4f9c70dd146f1ed54da49757216 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 25 Aug 2023 12:15:46 -0400
Subject: [PATCH 4/6] [SCHEMA] Various fixes on selectors and expressions
 (#1600)

* [schema][fix] intersect() -> intersects()

* [schema][fix] Identify MEG data files with task entity

Closes bids-standard/bids-examples#398

* [schema][fix] Remove redundant modality checks

* [schema][fix] modalities are lowercase

* [schema][fix] Better selectors for MRI images

* [schema][fix] More modality/datatype cleanups

* [schema] Clarify name of Units metadata field

* [schema] Typo: Antobodies -> Antibodies

* FIX: metabolite_polar_fraction is recommended at most in 1.6.0

* FIX: Drop redundant check for fields in sidecar

* SCHEMA: Reorder IntendedFor/B0FieldIdentifier rules

* FIX: Move "anat" rule for _phase images to proper location, update selectors
---
 src/schema/objects/entities.yaml       |  4 ++--
 src/schema/rules/checks/mri.yaml       | 16 ++++++++--------
 src/schema/rules/checks/nirs.yaml      |  8 ++++----
 src/schema/rules/sidecars/anat.yaml    | 11 ++---------
 src/schema/rules/sidecars/asl.yaml     | 15 ---------------
 src/schema/rules/sidecars/dwi.yaml     |  6 ++++--
 src/schema/rules/sidecars/eeg.yaml     | 13 -------------
 src/schema/rules/sidecars/fmap.yaml    | 25 +++++++++++++------------
 src/schema/rules/sidecars/func.yaml    |  9 +++++++++
 src/schema/rules/sidecars/ieeg.yaml    |  9 ---------
 src/schema/rules/sidecars/meg.yaml     | 24 +++++++-----------------
 src/schema/rules/sidecars/micr.yaml    |  9 ++-------
 src/schema/rules/sidecars/motion.yaml  |  5 -----
 src/schema/rules/sidecars/mri.yaml     |  2 --
 src/schema/rules/sidecars/nirs.yaml    |  3 +--
 src/schema/rules/sidecars/pet.yaml     | 26 +++++++++++++-------------
 src/schema/rules/tabular_data/pet.yaml | 16 ++++++----------
 17 files changed, 71 insertions(+), 130 deletions(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 3260b4a3d4..74740444f1 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -199,7 +199,7 @@ 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:
diff --git a/src/schema/rules/checks/mri.yaml b/src/schema/rules/checks/mri.yaml
index 5887f0e95f..8837f5faa9 100644
--- a/src/schema/rules/checks/mri.yaml
+++ b/src/schema/rules/checks/mri.yaml
@@ -20,7 +20,7 @@ EchoTimeGreaterThan:
       'EchoTime' is greater than 1. Are you sure it's expressed in seconds?
     level: warning
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar.EchoTime
   checks:
     - sidecar.EchoTime <= 1
@@ -33,7 +33,7 @@ TotalReadoutTimeGreaterThan:
       'TotalReadoutTime' is greater than 10. Are you sure it's expressed in seconds?
     level: warning
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar.TotalReadoutTime
   checks:
     - sidecar.TotalReadoutTime <= 10
@@ -46,7 +46,7 @@ EffectiveEchoSpacingTooLarge:
       Abnormally high value of 'EffectiveEchoSpacing'.
     level: error
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - type(sidecar.RepetitionTime) != "null"
     - type(sidecar.EffectiveEchoSpacing) != "null"
     - type(sidecar.PhaseEncodingDirection) != "null"
@@ -67,7 +67,7 @@ SliceTimingElements:
       dimension of the corresponding NIfTI volume.
     level: warning
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - type(sidecar.SliceTiming) != "null"
     - type(nifti_header) != "null"
   checks:
@@ -81,7 +81,7 @@ EESGreaterThanTRT:
       'EffectiveEchoSpacing' should always be smaller than 'TotalReadoutTime'.
     level: error
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar.EffectiveEchoSpacing != null
     - sidecar.TotalReadoutTime != null
   checks:
@@ -95,7 +95,7 @@ VolumeTimingNotMonotonicallyIncreasing:
       'VolumeTiming' is not monotonically increasing.
     level: error
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar.VolumeTiming != null
   checks:
     - sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming
@@ -108,7 +108,7 @@ BolusCutOffDelayTimeNotMonotonicallyIncreasing:
       'BolusCutOffDelayTime' is not monotonically increasing.
     level: error
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - sidecar.BolusCutoffDelayTime != null
   checks:
     - sorted(sidecar.BolusCutoffDelayTime) == sidecar.BolusCutoffDelayTime
@@ -122,7 +122,7 @@ RepetitionTimePreparationNotConsistent:
       not match the 4th dimension of the NIfTI header.
     level: error
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - type(sidecar.RepetitionTimePreparation) == "array"
     - type(nifti_header) != "null"
   checks:
diff --git a/src/schema/rules/checks/nirs.yaml b/src/schema/rules/checks/nirs.yaml
index db9299eb07..29cd2f1b9b 100644
--- a/src/schema/rules/checks/nirs.yaml
+++ b/src/schema/rules/checks/nirs.yaml
@@ -49,7 +49,7 @@ Component:
     - datatype == "nirs"
     - suffix == "channels"
     - extension == ".tsv"
-    - intersect(columns.type, ["ACCEL", "GYRO", "MAGN"])
+    - intersects(columns.type, ["ACCEL", "GYRO", "MAGN"])
   checks:
     - columns.component != null
 
@@ -66,7 +66,7 @@ RequiredTemplateX:
     - datatype == "nirs"
     - suffix == "optodes"
     - extension == ".tsv"
-    - intersect(columns.x, ["n/a"])
+    - intersects(columns.x, ["n/a"])
   checks:
     - columns.template_x != null
 
@@ -75,7 +75,7 @@ RequiredTemplateY:
     - datatype == "nirs"
     - suffix == "optodes"
     - extension == ".tsv"
-    - intersect(columns.y, ["n/a"])
+    - intersects(columns.y, ["n/a"])
   checks:
     - columns.template_y != null
 
@@ -84,7 +84,7 @@ RequiredTemplateZ:
     - datatype == "nirs"
     - suffix == "optodes"
     - extension == ".tsv"
-    - intersect(columns.z, ["n/a"])
+    - intersects(columns.z, ["n/a"])
   checks:
     - columns.template_z != null
 
diff --git a/src/schema/rules/sidecars/anat.yaml b/src/schema/rules/sidecars/anat.yaml
index 78255dc338..70a18cae3a 100644
--- a/src/schema/rules/sidecars/anat.yaml
+++ b/src/schema/rules/sidecars/anat.yaml
@@ -9,25 +9,18 @@
 
 MRIAnatomyCommonMetadataFields:
   selectors:
-    - modality == "mri"
     - datatype == "anat"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     ContrastBolusIngredient: optional
     RepetitionTimeExcitation: optional
     RepetitionTimePreparation: optional
 
-PhaseSuffixUnits:
-  selectors:
-    - modality == "mri"
-    - datatype == "anat"
-    - suffix == "phase"
-  fields:
-    Units: required
-
 TaskMetadata:
   selectors:
     - datatype == "anat"
     - entity.task != null
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     TaskName:
       level: recommended
diff --git a/src/schema/rules/sidecars/asl.yaml b/src/schema/rules/sidecars/asl.yaml
index f0b91e10d4..ab540b537c 100644
--- a/src/schema/rules/sidecars/asl.yaml
+++ b/src/schema/rules/sidecars/asl.yaml
@@ -8,7 +8,6 @@
 # Fields described in text, but not in tables
 MRIASLTextOnly:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - intersects([suffix], ["asl", "m0scan"])
   fields:
@@ -17,7 +16,6 @@ MRIASLTextOnly:
 # Common metadata fields applicable to both (P)CASL and PASL
 MRIASLCommonMetadataFields:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
   fields:
@@ -36,7 +34,6 @@ MRIASLCommonMetadataFields:
 
 MRIASLCommonMetadataFieldsM0TypeRec:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.M0Type != "Estimate"
@@ -47,7 +44,6 @@ MRIASLCommonMetadataFieldsM0TypeRec:
 
 MRIASLCommonMetadataFieldsM0TypeReq:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.M0Type == "Estimate"
@@ -64,7 +60,6 @@ MRIASLCommonMetadataFieldsM0TypeReq:
 
 MRIASLCommonMetadataFieldsBackgroundSuppressionOpt:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.BackgroundSuppression == false
@@ -78,7 +73,6 @@ MRIASLCommonMetadataFieldsBackgroundSuppressionOpt:
 
 MRIASLCommonMetadataFieldsBackgroundSuppressionReq:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.BackgroundSuppression == true
@@ -88,7 +82,6 @@ MRIASLCommonMetadataFieldsBackgroundSuppressionReq:
 
 MRIASLCommonMetadataFieldsVascularCrushingOpt:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.VascularCrushing == false
@@ -99,7 +92,6 @@ MRIASLCommonMetadataFieldsVascularCrushingOpt:
 
 MRIASLCommonMetadataFieldsVascularCrushingRec:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.VascularCrushing == true
@@ -108,7 +100,6 @@ MRIASLCommonMetadataFieldsVascularCrushingRec:
 
 MRIASLCaslPcaslSpecific:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - intersects([sidecar.ArterialSpinLabelingType], ["CASL", "PCASL"])
@@ -123,7 +114,6 @@ MRIASLCaslPcaslSpecific:
 
 MRIASLPcaslSpecific:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.ArterialSpinLabelingType == "PCASL"
@@ -134,7 +124,6 @@ MRIASLPcaslSpecific:
 
 MRIASLCaslSpecific:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.ArterialSpinLabelingType == "CASL"
@@ -145,7 +134,6 @@ MRIASLCaslSpecific:
 
 MRIASLPaslSpecific:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.ArterialSpinLabelingType == "PASL"
@@ -156,7 +144,6 @@ MRIASLPaslSpecific:
 
 MRIASLPASLSpecificBolusCutOffFlagFalse:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.ArterialSpinLabelingType == "PASL"
@@ -171,7 +158,6 @@ MRIASLPASLSpecificBolusCutOffFlagFalse:
 
 MRIASLPaslSpecificBolusCutOffFlagTrue:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
     - sidecar.ArterialSpinLabelingType == "PASL"
@@ -205,7 +191,6 @@ MRIASLPaslSpecificBolusCutOffFlagTrue:
 # m0scan metadata fields
 MRIASLM0Scan:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "m0scan"
   fields:
diff --git a/src/schema/rules/sidecars/dwi.yaml b/src/schema/rules/sidecars/dwi.yaml
index 381f5db039..51ae4b336a 100644
--- a/src/schema/rules/sidecars/dwi.yaml
+++ b/src/schema/rules/sidecars/dwi.yaml
@@ -3,16 +3,18 @@
 # NOTE: I don't think this can be schemafied, since it depends on owner intent.
 MRIDiffusionMultipart:
   selectors:
-    - modality == "mri"
     - datatype == "dwi"
+    - suffix == "dwi"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     MultipartID: optional
 
 # Other recommended metadata
 MRIDiffusionOtherMetadata:
   selectors:
-    - modality == "mri"
     - datatype == "dwi"
+    - suffix == "dwi"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     PhaseEncodingDirection: recommended
     TotalReadoutTime: recommended
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 793bd38000..f74da26f7b 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -7,7 +7,6 @@
 ---
 EEGHardware:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
   fields:
@@ -18,7 +17,6 @@ EEGHardware:
 
 EEGTaskInformation:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
   fields:
@@ -38,7 +36,6 @@ EEGTaskInformation:
 
 EEGInstitutionInformation:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
   fields:
@@ -48,7 +45,6 @@ EEGInstitutionInformation:
 
 EEGRequired:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
   fields:
@@ -63,7 +59,6 @@ EEGRequired:
 
 EEGRecommended:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "eeg"
   fields:
@@ -87,7 +82,6 @@ EEGRecommended:
 # General fields
 EEGCoordsystemGeneral:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
   fields:
@@ -100,7 +94,6 @@ EEGCoordsystemGeneral:
 # Fields relating to the EEG electrode positions
 EEGCoordsystemPositions:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
   fields:
@@ -112,7 +105,6 @@ EEGCoordsystemPositions:
 
 EEGCoordsystemOther:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
     - '"EEGCoordinateSystem" in sidecar'
@@ -123,7 +115,6 @@ EEGCoordsystemOther:
 # Fields relating to the position of fiducials measured during an EEG session/run
 EEGCoordsystemFiducials:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
   fields:
@@ -137,7 +128,6 @@ EEGCoordsystemFiducials:
 
 EEGCoordsystemOtherFiducialCoordinateSystem:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
     - sidecar.FiducialsCoordinateSystem == "Other"
@@ -147,7 +137,6 @@ EEGCoordsystemOtherFiducialCoordinateSystem:
 # Fields relating to the position of anatomical landmark measured during an EEG session/run
 EEGCoordsystemLandmark:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
   fields:
@@ -159,7 +148,6 @@ EEGCoordsystemLandmark:
 
 EEGCoordsystemLandmarkDescriptionRec:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
     - sidecar.AnatomicalLandmarkCoordinateSystem != "Other"
@@ -170,7 +158,6 @@ EEGCoordsystemLandmarkDescriptionRec:
 
 EEGCoordsystemLandmarkDescriptionReq:
   selectors:
-    - modality == "eeg"
     - datatype == "eeg"
     - suffix == "coordsystem"
     - sidecar.AnatomicalLandmarkCoordinateSystem == "Other"
diff --git a/src/schema/rules/sidecars/fmap.yaml b/src/schema/rules/sidecars/fmap.yaml
index adcc2ac692..c642394764 100644
--- a/src/schema/rules/sidecars/fmap.yaml
+++ b/src/schema/rules/sidecars/fmap.yaml
@@ -6,17 +6,10 @@
 
 ---
 # Fieldmap data
-MRIFieldmapB0FieldIdentifier:
-  selectors:
-    - modality == "mri"
-    - datatype == "fmap"
-  fields:
-    B0FieldIdentifier: recommended
-
 MRIFieldmapIntendedFor:
   selectors:
-    - modality == "mri"
     - datatype == "fmap"
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     IntendedFor:
       level: optional
@@ -24,12 +17,20 @@ MRIFieldmapIntendedFor:
         This field is optional, and in case the fieldmaps do not correspond
         to any particular scans, it does not have to be filled.
 
+MRIFieldmapB0FieldIdentifier:
+  selectors:
+    - datatype == "fmap"
+    - match(extension, '\.nii(\.gz)?$')
+    - '!("IntendedFor" in sidecar)'
+  fields:
+    B0FieldIdentifier: recommended
+
 # Case 1: Phase-difference map and at least one magnitude image
 MRIFieldmapPhaseDifferencePhasediff:
   selectors:
-    - modality == "mri"
     - datatype == "fmap"
     - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     EchoTime1: required
     EchoTime2: required
@@ -40,18 +41,18 @@ MRIFieldmapPhaseDifferencePhasediff:
 # but EchoTime1 if phasediff exists.
 MRIFieldmapTwoPhase:
   selectors:
-    - modality == "mri"
     - datatype == "fmap"
     - intersects([suffix], ["phase1", "phase2"])
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     EchoTime__fmap: required
 
 # Case 3: Direct field mapping
 MRIFieldmapDirectFieldMapping:
   selectors:
-    - modality == "mri"
     - datatype == "fmap"
     - suffix == "fieldmap"
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     Units:
       level: required
@@ -62,9 +63,9 @@ MRIFieldmapDirectFieldMapping:
 # Case 4: Multiple phase encoded directions ("pepolar")
 MRIFieldmapPepolar:
   selectors:
-    - modality == "mri"
     - datatype == "fmap"
     - suffix == "epi"
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     PhaseEncodingDirection: required
     TotalReadoutTime: required
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index 25dd418709..f3b7e70b69 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -77,3 +77,12 @@ MRIFuncTaskInformation:
     TaskDescription: recommended
     CogAtlasID: recommended
     CogPOID: recommended
+
+# Should now be `part-phase_bold.nii`, but still require units
+PhaseSuffixUnits:
+  selectors:
+    - datatype == "func"
+    - suffix == "phase"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    Units: required
diff --git a/src/schema/rules/sidecars/ieeg.yaml b/src/schema/rules/sidecars/ieeg.yaml
index 799931e4f3..066e17a8bf 100644
--- a/src/schema/rules/sidecars/ieeg.yaml
+++ b/src/schema/rules/sidecars/ieeg.yaml
@@ -7,7 +7,6 @@
 ---
 iEEGHardware:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -20,7 +19,6 @@ iEEGHardware:
 
 iEEGTaskInformation:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -40,7 +38,6 @@ iEEGTaskInformation:
 
 iEEGInstitutionInformation:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -51,7 +48,6 @@ iEEGInstitutionInformation:
 # Specific iEEG fields MUST be present
 iEEGRequired:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -67,7 +63,6 @@ iEEGRequired:
 # Specific iEEG fields SHOULD be present
 iEEGRecommended:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -94,7 +89,6 @@ iEEGRecommended:
 # Specific iEEG fields MAY be present
 iEEGOptional:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "ieeg"
   fields:
@@ -104,7 +98,6 @@ iEEGOptional:
 # General fields
 iEEGCoordsystemGeneral:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "coordsystem"
   fields:
@@ -126,7 +119,6 @@ iEEGCoordsystemGeneral:
 # Fields relating to the iEEG electrode positions
 iEEGCoordsystemPositions:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "coordsystem"
   fields:
@@ -140,7 +132,6 @@ iEEGCoordsystemPositions:
 
 iEEGCoordsystemOther:
   selectors:
-    - modality == "ieeg"
     - datatype == "ieeg"
     - suffix == "coordsystem"
     - '"iEEGCoordinateSystem" in sidecar'
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index ed9346b9f5..0b624e1559 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -6,12 +6,14 @@
 
 ---
 # Magnetoencephalography
+#
+# Note: "task" in entities identifies MEG data files and excludes calibration/crosstalk scans
 
 # Sidecar JSON (*_meg.json)
 MEGHardware:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
+    - '"task" in entities'
     - suffix == "meg"
   fields:
     Manufacturer:
@@ -32,8 +34,8 @@ MEGHardware:
 
 MEGTaskInformation:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
+    - '"task" in entities'
     - suffix == "meg"
   fields:
     TaskName:
@@ -52,8 +54,8 @@ MEGTaskInformation:
 
 MEGInstitutionInformation:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
+    - '"task" in entities'
     - suffix == "meg"
   fields:
     InstitutionName: recommended
@@ -63,8 +65,8 @@ MEGInstitutionInformation:
 # Specific MEG fields MUST be present
 MEGRequired:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
+    - '"task" in entities'
     - suffix == "meg"
   fields:
     SamplingFrequency:
@@ -81,8 +83,8 @@ MEGRequired:
 # Specific MEG fields SHOULD be present
 MEGRecommended:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
+    - '"task" in entities'
     - suffix == "meg"
   fields:
     MEGChannelCount: recommended
@@ -109,7 +111,6 @@ MEGRecommended:
 # NOTE: I'm not sure if "EEG is present" is enough to indicate simultaneous EEG/MEG.
 MEGwithEEG:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "meg"
     - intersects(dataset.modalities, ["eeg"])
@@ -122,7 +123,6 @@ MEGwithEEG:
 # MEG and EEG sensors
 MEGCoordsystemWithEEG:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
@@ -148,7 +148,6 @@ MEGCoordsystemWithEEG:
 # NOTE: The JSON isn't really a sidecar, so "sidecar.MEGCoordinateSystem" is misleading.
 MEGCoordsystemWithEEGMEGCoordinateSystem:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - '"MEGCoordinateSystem" in sidecar'
@@ -159,7 +158,6 @@ MEGCoordsystemWithEEGMEGCoordinateSystem:
 # NOTE: Not sure if this requires simult. EEG
 MEGCoordsystemWithEEGEEGCoordinateSystem:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - '"EEGCoordinateSystem" in sidecar'
@@ -170,7 +168,6 @@ MEGCoordsystemWithEEGEEGCoordinateSystem:
 # Head localization coils
 MEGCoordsystemHeadLocalizationCoils:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
@@ -183,7 +180,6 @@ MEGCoordsystemHeadLocalizationCoils:
 
 MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - '"HeadCoilCoordinateSystem" in sidecar'
@@ -194,7 +190,6 @@ MEGCoordsystemHeadLocalizationCoilsHeadCoilCoordinateSystem:
 # Digitized head points
 MEGCoordsystemDigitizedHeadPoints:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
@@ -207,7 +202,6 @@ MEGCoordsystemDigitizedHeadPoints:
 
 MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - '"DigitizedHeadPointsCoordinateSystem" in sidecar'
@@ -218,7 +212,6 @@ MEGCoordsystemDigitizedHeadPointsDigitizedHeadPointsCoordinateSystem:
 # Anatomical MRI
 MEGCoordsystemAnatomicalMRI:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - intersects(dataset.datatypes, ["anat"])
@@ -233,7 +226,6 @@ MEGCoordsystemAnatomicalMRI:
 # Anatomical landmarks
 MEGCoordsystemAnatomicalLandmarks:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
@@ -249,7 +241,6 @@ MEGCoordsystemAnatomicalLandmarks:
 
 MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
     - '"AnatomicalLandmarkCoordinateSystem" in sidecar'
@@ -260,7 +251,6 @@ MEGCoordsystemAnatomicalLandmarksAnatomicalLandmarkCoordinateSystem:
 # Fiducials information
 MEGCoordsystemFiducialsInformation:
   selectors:
-    - modality == "meg"
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml
index 1834e669c2..0fa46bfcf8 100644
--- a/src/schema/rules/sidecars/micr.yaml
+++ b/src/schema/rules/sidecars/micr.yaml
@@ -8,7 +8,6 @@
 # Device Hardware
 MicroscopyHardware:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
     - suffix != "photo"
   fields:
@@ -20,8 +19,8 @@ MicroscopyHardware:
 
 MicroscopyInstitutionInformation:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
+    - suffix != "photo"
   fields:
     InstitutionName: recommended
     InstitutionAddress: recommended
@@ -30,7 +29,6 @@ MicroscopyInstitutionInformation:
 # Image Acquisition
 MicroscopyImageAcquisition:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
     - suffix != "photo"
   fields:
@@ -45,7 +43,6 @@ MicroscopyImageAcquisition:
 # Sample
 MicroscopySample:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
     - suffix != "photo"
   fields:
@@ -71,7 +68,6 @@ MicroscopySample:
 # Chunk Transformations
 MicroscopyChunkTransformations:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
     - suffix != "photo"
     - '"chunk" in entities'
@@ -82,7 +78,6 @@ MicroscopyChunkTransformations:
 
 MicroscopyChunkTransformationsMatrixAxis:
   selectors:
-    - modality == "micr"
     - datatype == "micr"
     - suffix != "photo"
     - '"chunk" in entities'
@@ -94,7 +89,7 @@ MicroscopyChunkTransformationsMatrixAxis:
 
 Photo:
   selectors:
-    - modality == "micr"
+    - datatype == "micr"
     - suffix == "photo"
   fields:
     PhotoDescription: optional
diff --git a/src/schema/rules/sidecars/motion.yaml b/src/schema/rules/sidecars/motion.yaml
index 981e0b3ad7..a38e6a468d 100644
--- a/src/schema/rules/sidecars/motion.yaml
+++ b/src/schema/rules/sidecars/motion.yaml
@@ -7,7 +7,6 @@
 ---
 motionHardware:
   selectors:
-    - modality == "motion"
     - datatype == "motion"
     - suffix == "motion"
   fields:
@@ -18,7 +17,6 @@ motionHardware:
 
 motionInstitutionInformation:
   selectors:
-    - modality == "motion"
     - datatype == "motion"
     - suffix == "motion"
   fields:
@@ -28,7 +26,6 @@ motionInstitutionInformation:
 
 motionTaskInformation:
   selectors:
-    - modality == "motion"
     - datatype == "motion"
     - suffix == "motion"
   fields:
@@ -42,7 +39,6 @@ motionTaskInformation:
 
 motionRequired:
   selectors:
-    - modality == "motion"
     - datatype == "motion"
     - suffix == "motion"
   fields:
@@ -56,7 +52,6 @@ motionRequired:
 
 motionRecommended:
   selectors:
-    - modality == "motion"
     - datatype == "motion"
     - suffix == "motion"
   fields:
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index d95714de6b..f93c856690 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -77,7 +77,6 @@ PETMRISequenceSpecifics:
 
 ASLMRISequenceSpecifics:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - suffix == "asl"
   fields:
@@ -198,7 +197,6 @@ MRITimingParameters:
 
 SliceTimingASL:
   selectors:
-    - modality == "mri"
     - datatype == "perf"
     - intersects([suffix], ["asl", "m0scan"])
     - sidecar.MRAcquisitionType == "2D"
diff --git a/src/schema/rules/sidecars/nirs.yaml b/src/schema/rules/sidecars/nirs.yaml
index 08b02f3dbe..4870887c23 100644
--- a/src/schema/rules/sidecars/nirs.yaml
+++ b/src/schema/rules/sidecars/nirs.yaml
@@ -29,7 +29,6 @@ AnatomicalLandmark:
 
 CoordsystemGeneral:
   selectors:
-    - modality == "nirs"
     - datatype == "nirs"
     - suffix == "coordsystem"
   fields:
@@ -160,7 +159,7 @@ NirsRequired:
 
 NirsRecommend:
   selectors:
-    - modality == "nirs"
+    - datatype == "nirs"
     - suffix == "nirs"
   fields:
     CapManufacturer:
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index 353389de71..a2cedd3f54 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -2,7 +2,7 @@
 # PET common metadata fields
 PETHardware:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     Manufacturer:
@@ -22,7 +22,7 @@ PETHardware:
 
 PETInstitutionInformation:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     InstitutionName:
@@ -37,7 +37,7 @@ PETInstitutionInformation:
 
 PETRadioChemistry:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     TracerName:
@@ -86,7 +86,7 @@ PETRadioChemistry:
 # PET Infusion conditionally required entities
 EntitiesBolusMetadata:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
     - sidecar.ModeOfAdministration == 'bolus-infusion'
   fields:
@@ -98,7 +98,7 @@ EntitiesBolusMetadata:
 
 PETPharmaceuticals:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     PharmaceuticalName:
@@ -118,7 +118,7 @@ PETPharmaceuticals:
 
 PETTime:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     TimeZero: required
@@ -139,7 +139,7 @@ PETTime:
 
 PETReconstruction:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
   fields:
     AcquisitionMode: required
@@ -188,7 +188,7 @@ PETReconstruction:
 # set required reconstruction fields to optional when "none" is provided as a parameter label
 EntitiesReconMethodMetadata:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
     - '!intersects(sidecar.ReconMethodParameterLabels, ["none"])'
   fields:
@@ -198,7 +198,7 @@ EntitiesReconMethodMetadata:
 # set required recon filter fields to optional when FilterType is "None"
 EntitiesReconFilterMetadata:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "pet"
     - '!intersects(sidecar.ReconFilterType, ["none"])'
   fields:
@@ -206,7 +206,7 @@ EntitiesReconFilterMetadata:
 
 BloodRecording:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
   fields:
     PlasmaAvail: required
@@ -222,7 +222,7 @@ BloodRecording:
 
 BloodPlasmaFreeFraction:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - sidecar.PlasmaAvail == true
   fields:
@@ -235,7 +235,7 @@ BloodPlasmaFreeFraction:
 
 BloodMetaboliteMethod:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - sidecar.MetaboliteAvail == true
   fields:
@@ -249,7 +249,7 @@ BloodMetaboliteMethod:
 # PET task information
 PETTask:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - '"task" in entities'
   fields:
     TaskName:
diff --git a/src/schema/rules/tabular_data/pet.yaml b/src/schema/rules/tabular_data/pet.yaml
index 7c72b028ea..8410ee8481 100644
--- a/src/schema/rules/tabular_data/pet.yaml
+++ b/src/schema/rules/tabular_data/pet.yaml
@@ -1,7 +1,7 @@
 ---
 Blood:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
   columns:
@@ -14,7 +14,7 @@ Blood:
       level_addendum: required if `MetaboliteAvail` is `true`
     metabolite_polar_fraction:
       level: optional
-      level_addendum: required if `MetaboliteAvail` is `true`
+      level_addendum: recommended if `MetaboliteAvail` is `true`
     hplc_recovery_fractions:
       level: optional
       level_addendum: required if `MetaboliteRecoveryCorrectionApplied` is `true`
@@ -24,20 +24,18 @@ Blood:
 
 BloodPlasma:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - '"PlasmaAvail" in sidecar'
     - sidecar.PlasmaAvail == true
   columns:
     plasma_radioactivity: required
 
 BloodMetabolite:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - '"MetaboliteAvail" in sidecar'
     - sidecar.MetaboliteAvail == true
   columns:
     metabolite_parent_fraction: required
@@ -45,20 +43,18 @@ BloodMetabolite:
 
 BloodMetaboliteCorrection:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - '"MetaboliteRecoveryCorrectionApplied" in sidecar'
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
   columns:
     hplc_recovery_fractions: required
 
 BloodWholeBlood:
   selectors:
-    - modality == "pet"
+    - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
-    - '"WholeBloodAvail" in sidecar'
     - sidecar.WholeBloodAvail == true
   columns:
     whole_blood_radioactivity: required

From d5b3d23ebee33507287f7a9874a9fdbccf749338 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 29 Aug 2023 14:56:24 -0500
Subject: [PATCH 5/6] Update nirs.yaml ShortChannelCountReq check. (#1598)

---
 src/schema/rules/checks/nirs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/checks/nirs.yaml b/src/schema/rules/checks/nirs.yaml
index 29cd2f1b9b..c6b8f74548 100644
--- a/src/schema/rules/checks/nirs.yaml
+++ b/src/schema/rules/checks/nirs.yaml
@@ -42,7 +42,7 @@ ShortChannelCountReq:
   selectors:
     - suffix == "nirs"
   checks:
-    - sidecar.ShortChannelCount == count(associations.channels.short_channel, true)
+    - sidecar.ShortChannelCount == count(associations.channels.short_channel, "true")
 
 Component:
   selectors:

From fc98780caf366fbcef3b390ba61edc04da7ff2aa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 6 Sep 2023 17:37:42 +0200
Subject: [PATCH 6/6] [pre-commit.ci] pre-commit autoupdate (#1607)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/mirrors-prettier: v3.0.2 → v3.0.3](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.2...v3.0.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a825e940d9..fa428cfd96 100644
--- a/.pre-commit-config.yaml
+++ b/.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