From 9d136f4f572749fdf33ca1b60391093ba514a36a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 3 Oct 2024 15:53:44 -0400
Subject: [PATCH 1/3] fix: Only check for sorted times in arrays

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

diff --git a/src/schema/rules/checks/mri.yaml b/src/schema/rules/checks/mri.yaml
index 91a1520179..1aad6d7259 100644
--- a/src/schema/rules/checks/mri.yaml
+++ b/src/schema/rules/checks/mri.yaml
@@ -109,7 +109,7 @@ BolusCutOffDelayTimeNotMonotonicallyIncreasing:
     level: error
   selectors:
     - modality == "mri"
-    - sidecar.BolusCutOffDelayTime != null
+    - type(sidecar.BolusCutOffDelayTime) == 'array'
   checks:
     - allequal(sorted(sidecar.BolusCutOffDelayTime), sidecar.BolusCutOffDelayTime)
 

From e7a23e25345e33162e7fa074827ddef6a37bbd4f Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Oct 2024 10:26:24 -0400
Subject: [PATCH 2/3] fix(schema): Limit MRI metadata checks to NIfTIs

---
 src/schema/rules/sidecars/mri.yaml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 1edcdb157b..ba1d43fda2 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -195,8 +195,9 @@ PhaseEncodingDirectionRec:
 
 PhaseEncodingDirectionReq:
   selectors:
-    - modality == "mri"
+    - datatype == "fmap"
     - suffix == "epi"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     PhaseEncodingDirection:
       level: required
@@ -244,6 +245,7 @@ SliceTimingMRI:
   selectors:
     - modality == "mri"
     - sidecar.MRAcquisitionType == "2D"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     SliceTiming:
       level: recommended
@@ -257,6 +259,7 @@ SliceTimingASL:
     - datatype == "perf"
     - intersects([suffix], ["asl", "m0scan"])
     - sidecar.MRAcquisitionType == "2D"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     SliceTiming:
       level: required
@@ -288,6 +291,7 @@ MRIFlipAngleLookLockerFalse:
   selectors:
     - modality == "mri"
     - sidecar.LookLocker != true
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     FlipAngle:
       level: recommended
@@ -304,6 +308,7 @@ MRIFlipAngleLookLockerTrue:
   selectors:
     - modality == "mri"
     - sidecar.LookLocker == true
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     FlipAngle:
       level: required
@@ -377,6 +382,7 @@ MRIInstitutionInformation:
 DeidentificationMethod:
   selectors:
     - intersects([modality], ["mri", "pet"])
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     DeidentificationMethod:
       level: optional

From c1200b5aeb70bcad08e6586688650973f66b99dd Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Oct 2024 16:03:33 -0400
Subject: [PATCH 3/3] fix(schema): Disable TaskName check for channels and
 markers files

closes bids-standard/bids-validator#2154
---
 src/schema/rules/sidecars/entity_rules.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/entity_rules.yaml b/src/schema/rules/sidecars/entity_rules.yaml
index 54b3c256a0..cd54e72752 100644
--- a/src/schema/rules/sidecars/entity_rules.yaml
+++ b/src/schema/rules/sidecars/entity_rules.yaml
@@ -10,7 +10,7 @@
 EntitiesTaskMetadata:
   selectors:
     - '"task" in entities'
-    - suffix != 'events'
+    - '!intersects([suffix], ["events", "channels", "markers"])'
   fields:
     TaskName: recommended