[ENH][SCHEMA] Allow .bval and .bvec files for pepolar fmaps (bids-sta…

…ndard#1754) * add epi.bval, epi.bvec * update contributors.md * add lines for sentence Co-authored-by: Taylor Salo <[email protected]> * update preprocessed_data.yaml * override for m0scan * Update src/schema/rules/files/deriv/preprocessed_data.yaml Co-authored-by: Taylor Salo <[email protected]> * Whitespace and table pipes * remove ref * Add EPI-with-b[val|vec] suffix checks. * Add EPI+bval check. * Remove Latin phrase. * Update src/schema/rules/checks/fmap.yaml Co-authored-by: Chris Markiewicz <[email protected]> * Change max to min. * Address review. * Bump schema version. --------- Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]>
markmikkelsen · Apr 24, 2024 · b5fd938 · b5fd938
1 parent 5ed9030
commit b5fd938
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Showing 8 changed files with 52 additions and 6 deletions.
diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -1254,6 +1254,7 @@ EPI scans with different phase encoding directions to estimate the distortion
 map corresponding to the nonuniformities of the *B<sub>0</sub>* field.
 These `*_epi.nii[.gz]` - or `*_m0scan.nii[.gz]` for arterial spin labeling perfusion data - files can be 3D or 4D --
 in the latter case, all timepoints share the same scanning parameters.
+Some 4D scans intended for correcting DWIs may have accompanying `*_epi.bval` and `*_epi.bvec` files.
 Examples of software tools using these kinds of images are FSL TOPUP and
 AFNI `3dqwarp`.
 

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.8.1-dev
+0.8.2-dev
diff --git a/src/schema/meta/associations.yaml b/src/schema/meta/associations.yaml
@@ -59,15 +59,15 @@ magnitude1:
 
 bval:
   selectors:
-    - suffix == 'dwi'
+    - intersects([suffix], ['dwi', 'epi'])
     - match(extension, '\.nii(\.gz)?$')
   target:
     extension: .bval
   inherit: true
 
 bvec:
   selectors:
-    - suffix == 'dwi'
+    - intersects([suffix], ['dwi', 'epi'])
     - match(extension, '\.nii(\.gz)?$')
   target:
     extension: .bvec

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
@@ -183,6 +183,11 @@ context:
             n_rows:
               description: 'Number of rows in bval file'
               type: integer
+            values:
+              description: 'B-values contained in bval file'
+              type: array
+              items:
+                type: number
         bvec:
           description: 'B vector file'
           type: object

diff --git a/src/schema/rules/checks/dwi.yaml b/src/schema/rules/checks/dwi.yaml
@@ -9,7 +9,7 @@ DWIVolumeCount:
       associated '.bvec' and '.bval' files.
     level: error
   selectors:
-    - suffix == "dwi"
+    - intersects([suffix], ["dwi", "epi"])
     - '"bval" in associations'
     - '"bvec" in associations'
     - type(nifti_header) != "null"
@@ -25,7 +25,7 @@ DWIBvalRows:
       '.bval' files should contain exactly one row of values.
     level: error
   selectors:
-    - suffix == "dwi"
+    - intersects([suffix], ["dwi", "epi"])
     - '"bval" in associations'
   checks:
     - associations.bval.n_rows == 1
@@ -38,7 +38,7 @@ DWIBvecRows:
       '.bvec' files should contain exactly three rows of values.
     level: error
   selectors:
-    - suffix == "dwi"
+    - intersects([suffix], ["dwi", "epi"])
     - '"bvec" in associations'
   checks:
     - associations.bvec.n_rows == 3

diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
@@ -49,3 +49,16 @@ MagnitudeFileWithTooManyDimensions:
     - nifti_header != null
   checks:
     - nifti_header.dim[0] == 3
+
+EPISmallBVals:
+  issue:
+    code: EPI_WITH_BVALS_NEEDS_SMALL_BVALS
+    message: |
+      EPI field maps with b-values should include small (b<100) values.
+    level: error
+  selectors:
+    - datatype == "fmap"
+    - suffix == "epi"
+    - '"bval" in associations'
+  checks:
+    - min(associations.bval.values) < 100
diff --git a/src/schema/rules/files/deriv/preprocessed_data.yaml b/src/schema/rules/files/deriv/preprocessed_data.yaml
@@ -104,6 +104,13 @@ fmap_pepolar_common:
     space: optional
     description: optional
 
+fmap_pepolar_m0scan:
+  $ref: rules.files.raw.fmap.pepolar_m0scan
+  entities:
+    $ref: rules.files.raw.fmap.pepolar.entities
+    space: optional
+    description: optional
+
 fmap_TB1DAM_common:
   $ref: rules.files.raw.fmap.TB1DAM
   entities:

diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml
@@ -24,6 +24,26 @@ fieldmaps:
 pepolar:
   suffixes:
     - epi
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+    - .bval
+    - .bvec
+  datatypes:
+    - fmap
+  entities:
+    subject: required
+    session: optional
+    acquisition: optional
+    ceagent: optional
+    direction: required
+    run: optional
+    part: optional
+    chunk: optional
+
+pepolar_m0scan:
+  suffixes:
     - m0scan
   extensions:
     - .nii.gz