fix(schema): Fix checks to reduce false positives (bids-standard#1878)

* fix(schema): Limit EVENTS_TSV_MISSING to data files

* fix(schema): Move VolumeTiming check into checks

* fix(schema): Associated file checks only apply to data files

* fix(schema): Improve targeting of B0Field* recommendations

* fix(schema): Improve targeting of MRIAnatomicalLandmarks

* fix(schema): Check sidecars of data files only

* fix(schema): NIRS SamplingFrequency check should look in sidecar

Author: effigies

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

@@ -160,7 +160,11 @@ The definitions of the fields specified in these tables may be found in
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_sidecar_table("mri.MRIEchoPlanarImagingAndB0Mapping") }}
+{{ MACROS___make_sidecar_table([
+     "mri.MRIB0FieldIdentifier",
+     "mri.MRIEchoPlanarImagingAndB0FieldSource",
+   ])
+}}
 
 #### Tissue description
 

src/schema/rules/checks/events.yaml

@@ -13,6 +13,7 @@ EventsMissing:
     - '"task" in entities'
     - '!match(entities.task, "rest")'
     - suffix != "events"
+    - extension != ".json"
   checks:
     - '"events" in associations'
 

src/schema/rules/checks/fmap.yaml

@@ -9,6 +9,7 @@ EchoTime12DifferenceUnreasonable:
     level: error
   selectors:
     - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - sidecar.EchoTime2 - sidecar.EchoTime1 >= 0.0001
     - sidecar.EchoTime2 - sidecar.EchoTime1 <= 0.01
@@ -22,6 +23,7 @@ FmapFieldmapWithoutMagnitude:
     level: error
   selectors:
     - suffix == "fieldmap"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - '"magnitude" in associations'
 
@@ -34,6 +36,7 @@ FmapPhasediffWithoutMagnitude:
     level: warning
   selectors:
     - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - '"magnitude1" in associations'
 

src/schema/rules/checks/func.yaml

@@ -127,3 +127,14 @@ SliceTimingAcquisitionDurationMutex:
   checks:
     - type(sidecar.AcquisitionDuration) == "null"
     - type(sidecar.DelayTime) == "null"
+
+VolumeTimingMissingAcquisitionDuration:
+  issue:
+    code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
+    message: |
+      The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
+    level: error
+  selectors:
+    - type(sidecar.VolumeTiming) != "null"
+  checks:
+    - '"SliceTiming" in sidecar || "AcquisitionDuration" in sidecar'

src/schema/rules/checks/nirs.yaml

@@ -2,14 +2,15 @@
 NASamplingFreq:
   selectors:
     - suffix == "nirs"
-    - samplingFrequency == "n/a"
+    - sidecar.SamplingFrequency == "n/a"
   checks:
     - associations.channels.sampling_frequency != null
 
 NIRSChannelCount:
   selectors:
     - datatype == "nirs"
     - suffix == "nirs"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - |
       sidecar.NIRSChannelCount

src/schema/rules/sidecars/func.yaml

@@ -57,10 +57,6 @@ MRIFuncTimingParameters:
         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"
-      issue:
-        code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
-        message: |
-          The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
     DelayAfterTrigger: recommended
 
 # fMRI task information

src/schema/rules/sidecars/mri.yaml

@@ -296,15 +296,23 @@ MRISliceAcceleration:
 
 MRIAnatomicalLandmarks:
   selectors:
-    - modality == "mri"
+    - datatype == "anat"
+    - intersects(dataset.datatypes, ["meg"])
   fields:
     AnatomicalLandmarkCoordinates__mri: recommended
 
-MRIEchoPlanarImagingAndB0Mapping:
+MRIB0FieldIdentifier:
   selectors:
-    - modality == "mri"
+    - datatype == 'fmap'
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     B0FieldIdentifier: recommended
+
+MRIEchoPlanarImagingAndB0FieldSource:
+  selectors:
+    - intersects(datatype, ['dwi', 'func', 'perf'])
+    - intersects(dataset.datatypes, ['fmap'])
+  fields:
     B0FieldSource: recommended
 
 MRIInstitutionInformation: