Merge pull request #352 from suyashdb/checkSliceTimingArray

Validate slice timing array with RepetitionTime

Author: chrisgorgo

tests/json.spec.js

@@ -24,5 +24,4 @@ describe('JSON', function(){
 			assert(issues && issues.length === 1);
 		});
 	});
-
 });

tests/nii.spec.js

@@ -135,4 +135,37 @@ describe('NIFTI', function(){
       });
     });
 
-});
+    it('SliceTiming should not be greater than RepetitionTime', function(){
+        var jsonContentsDict_new = {
+            '/sub-15/func/sub-15_task-mixedeventrelatedprobe_run-01_bold.json': {
+                "RepetitionTime": 1.5,
+                "TaskName": "AntiSaccade (AS) Rewarded & Neutral with varying dot position",
+                "EchoTime": 0.025,
+                "NumberofPhaseEncodingSteps": 64,
+                "FlipAngle": 70,
+                "PhaseEncodingDirection": "j",
+                "SliceTiming": [
+                    0.0,
+                    1.3448,
+                    1.6207,
+                    1.3966,
+                    0.6724,
+                    1.4483,
+                    1.7241
+                ]
+            }
+        };
+        var file_new = {
+            name: 'sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz',
+            relativePath: '/sub-15/func/sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz'
+        };
+        var events = [
+            '/sub-15/func/sub-14_task-mixedeventrelatedprobe_run-01_events.tsv',
+            '/sub-15/run-01_events.tsv'
+        ];
+        validate.NIFTI(null, file_new, jsonContentsDict_new, {}, [], events, function (issues) {
+            assert(issues[2].code === 66 && issues.length === 3);
+        });
+    });
+
+});

utils/issues/list.js

@@ -326,5 +326,10 @@ module.exports = {
         key: 'SESSION_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY',
         severity: 'error',
         reason: 'Session label in the filename doesn\'t match with the path of the file. File seems to be saved in incorrect session directory.'
+    },
+    66: {
+        key: 'SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME',
+        severity: 'error',
+        reason: '"SliceTiming" value/s contains invalid value as it is greator than RepetitionTime.  SliceTiming values should be in seconds not milliseconds (common mistake).'
     }
 };

validators/nii.js

@@ -164,6 +164,18 @@ module.exports = function NIFTI (header, file, jsonContentsDict, bContentsDict,
                     reason: "You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. " + sidecarMessage
                 }));
             }
+
+            if (mergedDictionary.hasOwnProperty('SliceTiming') && mergedDictionary["SliceTiming"].constructor === Array) {
+                var SliceTimingArray = mergedDictionary["SliceTiming"];
+                var invalid_valuesArray = checkSliceTimingArray(SliceTimingArray, mergedDictionary['RepetitionTime']);
+                if (invalid_valuesArray.length > 0){
+                    issues.push(new Issue({
+                        file: file,
+                        code: 66,
+                        evidence: invalid_valuesArray
+                    }));
+                }
+            }
         }
         else if (path.includes("_phasediff.nii")){
             if (!mergedDictionary.hasOwnProperty('EchoTime1') || !mergedDictionary.hasOwnProperty('EchoTime2')) {
@@ -341,7 +353,20 @@ function generateMergedSidecarDict(potentialSidecars, jsonContents) {
     }
     return mergedDictionary;
 }
+/**
+ * Function to check each SoliceTime from SliceTiming Array
+ *
+ */
 
+function checkSliceTimingArray(array, repetitionTime){
+    for (var t = 0; t < array.length; t++){
+        var invalid_timesArray = [];
+        if (array[t] > repetitionTime){
+            invalid_timesArray.push(array[t]);
+        }
+    }
+    return invalid_timesArray;
+}
 /**
  * Get B-File Contents
  *