From 1ef102b9fa579d0237183c9cdf1d78ab02cbd511 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 25 Jul 2024 19:23:10 -0400
Subject: [PATCH] FIX: Add MRS events files, restrict sidecar metadata checks
 to data files (#1875)

* FIX: Add MRS events files, restrict sidecar metadata checks to data files

* FIX: Do not limit suffixes for filename template
---
 .../magnetic-resonance-spectroscopy.md              |  2 +-
 src/schema/rules/files/raw/task.yaml                | 10 ++++++++++
 src/schema/rules/sidecars/mrs.yaml                  | 13 +++++++++++++
 3 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/modality-specific-files/magnetic-resonance-spectroscopy.md b/src/modality-specific-files/magnetic-resonance-spectroscopy.md
index d5a0d992ac..22ec6540e0 100644
--- a/src/modality-specific-files/magnetic-resonance-spectroscopy.md
+++ b/src/modality-specific-files/magnetic-resonance-spectroscopy.md
@@ -21,7 +21,7 @@ The inputs for this macro can be found in the directory
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template("raw", datatypes=["mrs"], suffixes=["svs", "mrsi", "unloc", "mrsref"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["mrs"]) }}
 
 MRS is a spectroscopic technique based on the phenomenon of nuclear magnetic resonance
 that allows for the noninvasive detection and quantification of molecules in biochemical samples, such as brain tissue.
diff --git a/src/schema/rules/files/raw/task.yaml b/src/schema/rules/files/raw/task.yaml
index b7171e568f..812765a063 100644
--- a/src/schema/rules/files/raw/task.yaml
+++ b/src/schema/rules/files/raw/task.yaml
@@ -91,6 +91,16 @@ events__pet:
     reconstruction: optional
     run: optional
 
+events__mrs:
+  $ref: rules.files.raw.task.events
+  datatypes:
+    - mrs
+  entities:
+    $ref: rules.files.raw.task.events.entities
+    reconstruction: optional
+    nucleus: optional
+    volume: optional
+
 timeseries__func:
   $ref: rules.files.raw.task.timeseries
   datatypes:
diff --git a/src/schema/rules/sidecars/mrs.yaml b/src/schema/rules/sidecars/mrs.yaml
index 75fe94bd2b..28796eb5e4 100644
--- a/src/schema/rules/sidecars/mrs.yaml
+++ b/src/schema/rules/sidecars/mrs.yaml
@@ -9,6 +9,7 @@
 MRSScannerHardware:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     InstitutionName: recommended
     InstitutionAddress: recommended
@@ -27,6 +28,7 @@ MRSScannerHardware:
 MRSSample:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     BodyPart:
       level: optional
@@ -40,6 +42,7 @@ MRSSample:
 MRSSampleVOI:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - '"volume" in entities'
   fields:
     BodyPart: required
@@ -48,6 +51,7 @@ MRSSampleVOI:
 MRSSequenceSpecifics:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     PulseSequenceType:
       level: recommended
@@ -65,6 +69,7 @@ MRSSequenceSpecifics:
 MRSRequiredFields:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     ResonantNucleus: required
     SpectrometerFrequency: required
@@ -74,6 +79,7 @@ MRSRequiredFields:
 MRSRecommendedFields:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     NumberOfSpectralPoints: recommended
     MixingTime: recommended
@@ -84,6 +90,7 @@ MRSRecommendedFields:
 MRSRepetitionTime:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - '!("VolumeTiming" in sidecar)'
   fields:
     RepetitionTime:
@@ -93,6 +100,7 @@ MRSRepetitionTime:
 MRSVolumeTiming:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - '!("RepetitionTime" in sidecar)'
   fields:
     VolumeTiming:
@@ -102,6 +110,7 @@ MRSVolumeTiming:
 MRSConditionalInversionTime:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - entities.inversion
   fields:
     InversionTime:
@@ -111,6 +120,7 @@ MRSConditionalInversionTime:
 MRSConditionalAnatomicalImage:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - intersects(dataset.datatypes, ["anat"])
   fields:
     AnatomicalImage:
@@ -120,6 +130,7 @@ MRSConditionalAnatomicalImage:
 MRSConditionalNumTransients:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - intersects([suffix], ["svs", "unloc"])
   fields:
     NumberOfTransients:
@@ -129,6 +140,7 @@ MRSConditionalNumTransients:
 MRSIRecommendedFields:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
     - suffix == "mrsi"
   fields:
     MRAcquisitionType:
@@ -147,6 +159,7 @@ MRSIRecommendedFields:
 MRSOptionalFields:
   selectors:
     - modality == "mrs"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     ChemicalShiftOffset: optional
     ChemicalShiftReference: optional