Merge pull request #467 from chrisfilo/enh/echospacing_check

Extra echo spacing check

Author: chrisgorgo

utils/issues/list.js

@@ -171,21 +171,11 @@ module.exports = {
         severity: 'error',
         reason: "DWI scans should have a corresponding .bval file."
     },
-    34: {
-        key: 'PHASE_ENCODING_DIRECTION',
-        severity: 'error',
-        reason: "'PhaseEncodingDirection' needs to be one of 'i', 'i-, 'j', 'j-', 'k', or k-'"
-    },
     36: {
         key: 'NIFTI_TOO_SMALL',
         severity: 'error',
         reason: "This file is too small to contain the minimal NIfTI header."
     },
-    35: {
-        key: 'SLICE_ENCODING_DIRECTION',
-        severity: 'error',
-        reason: "'SliceEncodingDirection' needs to be one of 'i', 'i-, 'j', 'j-', 'k', or k-'"
-    },
     37: {
         key: 'INTENDED_FOR',
         severity: 'error',
@@ -376,5 +366,10 @@ module.exports = {
         key: 'NIFTI_PIXDIM4',
         severity: 'error',
         reason: "Nifti file's header is missing time dimension information."
+    },
+    76: {
+        key: 'EFFECTIVEECHOSPACING_TOO_LARGE',
+        severity: 'error',
+        reason: "Abnormally high value of 'EffectiveEchoSpacing'."
     }
 };

validators/json.js

@@ -88,17 +88,5 @@ function checkUnits (file, sidecar) {
             code: 5
         }));
     }
-    if (sidecar.hasOwnProperty('PhaseEncodingDirection') && ["i", "i-", "j", "j-", "k", "k-"].indexOf(sidecar["PhaseEncodingDirection"]) == -1) {
-        issues.push(new Issue({
-            file: file,
-            code: 34
-        }));
-    }
-    if (sidecar.hasOwnProperty('SliceEncodingDirection') && ["i", "i-", "j", "j-", "k", "k-"].indexOf(sidecar["SliceEncodingDirection"]) == -1) {
-        issues.push(new Issue({
-            file: file,
-            code: 35
-        }));
-    }
     return issues;
 }

validators/nii.js

@@ -157,6 +157,15 @@ module.exports = function NIFTI (header, file, jsonContentsDict, bContentsDict,
                     code: 10,
                     reason: "You have to define 'RepetitionTime' for this file. " + sidecarMessage
                 }));
+            } else if (header && mergedDictionary.EffectiveEchoSpacing && mergedDictionary.PhaseEncodingDirection) {
+                var axes = { i:0, j:1, k:2 };
+                if (mergedDictionary.EffectiveEchoSpacing * header.dim[axes[mergedDictionary.PhaseEncodingDirection[0]]] > mergedDictionary.RepetitionTime){
+                    issues.push(new Issue({
+                        file: file,
+                        code: 76,
+                        reason: "Abnormally high value of 'EffectiveEchoSpacing' (" + mergedDictionary.EffectiveEchoSpacing + " seconds)."
+                    }));
+                }
             }
 
             if (typeof repetitionTime === 'undefined' && header) {

validators/schemas/bold.json

@@ -9,19 +9,24 @@
             "type": "string"
         },
         "EchoTime": {
-            "type": "number"
+            "type": "number",
+            "exclusiveMinimum": 0
         },
         "EffectiveEchoSpacing": {
-            "type": "number"
+            "type": "number",
+            "exclusiveMinimum": 0
         },
         "PhaseEncodingDirection": {
-            "type": "string"
+            "type": "string",
+            "enum": ["i", "j", "k", "i-", "j-", "k-"]
         },
         "RepetitionTime": {
-            "type": "number"
+            "type": "number",
+            "exclusiveMinimum": 0
         },
         "SliceEncodingDirection": {
-            "type": "string"
+            "type": "string",
+            "enum": ["i", "j", "k", "i-", "j-", "k-"]
         },
         "SliceTiming": {
             "type": "array",