[FIX] Add qMRI fmap filename rules and reorganize fmap patterns (#1183)

* Model field map patterns on schema. * Add nii versions. * Update bids-validator/utils/type.js Co-authored-by: Chris Markiewicz <effigies@gmail.com> * Apply suggestions from code review Co-authored-by: Chris Markiewicz <effigies@gmail.com> * Update bids-validator/bids_validator/rules/file_level_rules.json * Update bids-validator/utils/type.js Co-authored-by: Chris Markiewicz <effigies@gmail.com>
bids-standard · Feb 10, 2021 · c1ad282 · c1ad282
1 parent 49810ac
commit c1ad282
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diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -198,8 +198,8 @@
     }
   },
 
-  "field_map": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
+  "fmap_gre": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
     "tokens": {
       "@@@_field_map_type_@@@": [
         "phasediff",
@@ -208,25 +208,40 @@
         "magnitude1",
         "magnitude2",
         "magnitude",
-        "fieldmap",
-        "epi",
-        "m0scan"
+        "fieldmap"
       ],
       "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"]
     }
   },
 
-  "field_map_main_nii": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
+  "fmap_pepolar_asl": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?_dir-[a-zA-Z0-9]+(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
     "tokens": {
       "@@@_field_map_type_@@@": [
-        "phasediff",
-        "phase1",
-        "phase2",
-        "fieldmap",
+        "m0scan",
         "epi"
       ],
-      "@@@_field_map_ext_@@@": ["nii\\.gz", "nii"]
+      "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"]
+    }
+  },
+
+  "fmap_TB1DAM": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)(?:_run-[0-9]+)?_flip-[0-9]+?(?:_part-(imag|mag|phase|real))?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
+    "tokens": {
+      "@@@_field_map_type_@@@": [
+        "TB1DAM"
+      ],
+      "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"]
+    }
+  },
+
+  "fmap_TB1EPI": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?fmap[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)(?:_run-[0-9]+)?_echo-[0-9]+?_flip-[0-9]+?(?:_part-(imag|mag|phase|real))?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
+    "tokens": {
+      "@@@_field_map_type_@@@": [
+        "TB1EPI"
+      ],
+      "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"]
     }
   },
 

diff --git a/bids-validator/utils/type.js b/bids-validator/utils/type.js
@@ -32,8 +32,10 @@ const anatMTR = buildRegExp(file_level_rules.anat_mtr)
 const behavioralData = buildRegExp(file_level_rules.behavioral)
 const dwiData = buildRegExp(file_level_rules.dwi)
 const eegData = buildRegExp(file_level_rules.eeg)
-const fieldmapData = buildRegExp(file_level_rules.field_map)
-const fieldmapMainNiiData = buildRegExp(file_level_rules.field_map_main_nii)
+const fmapGre = buildRegExp(file_level_rules.fmap_gre)
+const fmapPepolarAsl = buildRegExp(file_level_rules.fmap_pepolar_asl)
+const fmapTB1DAM = buildRegExp(file_level_rules.fmap_TB1DAM)
+const fmapTB1EPI = buildRegExp(file_level_rules.fmap_TB1EPI)
 const func = buildRegExp(file_level_rules.func)
 const funcPhaseDeprecated = buildRegExp(file_level_rules.func_phase_deprecated)
 const funcEvents = buildRegExp(file_level_rules.func_events)
@@ -206,11 +208,23 @@ export default {
      * Check if the file has a name appropriate for a fieldmap scan
      */
     isFieldMap: function(path) {
-      return conditionalMatch(fieldmapData, path)
+      return (
+        conditionalMatch(fmapGre, path) ||
+        conditionalMatch(fmapPepolarAsl, path) ||
+        conditionalMatch(fmapTB1DAM, path) ||
+        conditionalMatch(fmapTB1EPI, path)
+      )
     },
 
     isFieldMapMainNii: function(path) {
-      return conditionalMatch(fieldmapMainNiiData, path)
+      return (
+        !path.endsWith('.json') &&
+        /* isFieldMap */
+        (conditionalMatch(fmapGre, path) ||
+          conditionalMatch(fmapPepolarAsl, path) ||
+          conditionalMatch(fmapTB1DAM, path) ||
+          conditionalMatch(fmapTB1EPI, path))
+      )
     },
 
     /**