Add NIRS support to BIDS

bids-standard · May 8, 2020 · b1716a1 · b1716a1
1 parent 1888b87
commit b1716a1
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Showing 5 changed files with 60 additions and 1 deletion.
diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -221,5 +221,23 @@
 
   "stimuli": {
     "regexp": "^\\/(?:stimuli)\\/(?:.*)$"
+  },
+
+  "nirs": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?nirs\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_nirs\\.(@@@_nirs_type_@@@)|(@@@_nirs_ext_@@@))$",
+    "tokens": {
+      "@@@_nirs_type_@@@": ["snirf"],
+      "@@@_nirs_ext_@@@": [
+        "_events\\.json",
+        "_events\\.tsv",
+        "_optodes\\.json",
+        "_optodes\\.tsv",
+        "_channels\\.json",
+        "_channels\\.tsv",
+        "_nirs\\.json",
+        "_coordsystem\\.json",
+        "_photo\\.jpg"
+      ]
+    }
   }
 }
diff --git a/bids-validator/bids_validator/rules/session_level_rules.json b/bids-validator/bids_validator/rules/session_level_rules.json
@@ -88,5 +88,19 @@
         "_photo.jpg"
       ]
     }
+  },
+
+  "nirs_ses": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_nirs_ses_type_@@@)$",
+    "tokens": {
+      "@@@_nirs_ses_type_@@@": [
+        "_events.tsv",
+        "_channels.tsv",
+        "_optodes.tsv",
+        "_nirs.json",
+        "_coordsystem.json",
+        "_photo.jpg"
+      ]
+    }
   }
 }
diff --git a/bids-validator/bids_validator/rules/top_level_rules.json b/bids-validator/bids_validator/rules/top_level_rules.json
@@ -79,6 +79,18 @@
       ]
     }
   },
+  "nirs_top": {
+    "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_nirs_top_ext_@@@)$",
+    "tokens": {
+      "@@@_nirs_top_ext_@@@": [
+        "_nirs\\.json",
+        "_channels\\.tsv",
+        "_optodes\\.tsv",
+        "_photo\\.jpg",
+        "_coordsystem\\.json"
+      ]
+    }
+  },
   "multi_dir_fieldmap": {
     "regexp": "^\\/(?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$"
   },

diff --git a/bids-validator/utils/modalities.js b/bids-validator/utils/modalities.js
@@ -60,7 +60,11 @@ export default {
           isCorrectModality = true
           break
         case 'ieeg':
-          // iEEG
+          // EEG
+          isCorrectModality = true
+          break
+        case 'nirs':
+          // NIRS
           isCorrectModality = true
           break
         default:

diff --git a/bids-validator/utils/type.js b/bids-validator/utils/type.js
@@ -34,6 +34,7 @@ const funcBoldData = buildRegExp(file_level_rules.func_bold)
 const ieegData = buildRegExp(file_level_rules.ieeg)
 const megData = buildRegExp(file_level_rules.meg)
 const stimuliData = buildRegExp(file_level_rules.stimuli)
+const nirsData = buildRegExp(file_level_rules.nirs)
 // Phenotypic data
 const phenotypicData = buildRegExp(phenotypic_rules.phenotypic_data)
 // Session level
@@ -44,6 +45,7 @@ const funcSes = buildRegExp(session_level_rules.func_ses)
 const ieegSes = buildRegExp(session_level_rules.ieeg_ses)
 const megSes = buildRegExp(session_level_rules.meg_ses)
 const scansSes = buildRegExp(session_level_rules.scans)
+const nirsSes = buildRegExp(session_level_rules.nirs_ses)
 // Subject level
 const subjectLevel = buildRegExp(subject_level_rules.subject_level)
 // Top level
@@ -56,6 +58,7 @@ const ieegTop = buildRegExp(top_level_rules.ieeg_top)
 const multiDirFieldmap = buildRegExp(top_level_rules.multi_dir_fieldmap)
 const otherTopFiles = buildRegExp(top_level_rules.other_top_files)
 const megTop = buildRegExp(top_level_rules.meg_top)
+const nirsTop = buildRegExp(top_level_rules.nirs_top)
 
 export default {
   /**
@@ -74,6 +77,7 @@ export default {
       this.file.isDWI(path) ||
       this.file.isFunc(path) ||
       this.file.isMeg(path) ||
+      this.file.isNIRS(path) ||
       this.file.isIEEG(path) ||
       this.file.isEEG(path) ||
       this.file.isBehavioral(path) ||
@@ -99,6 +103,7 @@ export default {
         multiDirFieldmap.test(path) ||
         otherTopFiles.test(path) ||
         megTop.test(path) ||
+        nirsTop.test(path) ||
         eegTop.test(path) ||
         ieegTop.test(path)
       )
@@ -147,6 +152,7 @@ export default {
         conditionalMatch(anatSes, path) ||
         conditionalMatch(dwiSes, path) ||
         conditionalMatch(megSes, path) ||
+        conditionalMatch(nirsSes, path) ||
         conditionalMatch(eegSes, path) ||
         conditionalMatch(ieegSes, path)
       )
@@ -198,6 +204,10 @@ export default {
       return conditionalMatch(megData, path)
     },
 
+    isNIRS: function(path) {
+      return conditionalMatch(nirsData, path)
+    },
+
     isEEG: function(path) {
       return conditionalMatch(eegData, path)
     },
@@ -226,6 +236,7 @@ export default {
         this.isFieldMapMainNii(path) ||
         this.isFunc(path) ||
         this.isMeg(path) ||
+        this.isNIRS(path) ||
         this.isEEG(path) ||
         this.isIEEG(path) ||
         this.isBehavioral(path) ||