Bruker enhanced 4D data (#241)

rordenlab · Nov 5, 2018 · da64ebc · da64ebc
1 parent 5b696cc
commit da64ebc
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Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
@@ -4160,11 +4160,11 @@ double TE = 0.0; //most recent echo time recorded
     	//if we leave the folder MREchoSequence 0018,9114
     	if (( nDimIndxVal > 0) && ((d.manufacturer == kMANUFACTURER_BRUKER) || (d.manufacturer == kMANUFACTURER_PHILIPS)) && (sqDepth00189114 >= sqDepth)) {
     		sqDepth00189114 = -1; //triggered
-    		//printf("%d--->\n", inStackPositionNumber);
+    		//printf("slice %d---> 0020,9157 = %d %d %d\n", inStackPositionNumber, d.dimensionIndexValues[0], d.dimensionIndexValues[1], d.dimensionIndexValues[2]);
 			if (inStackPositionNumber > 0) {
 				//for images without SliceNumberMrPhilips (2001,100A)
 				int sliceNumber = inStackPositionNumber;
-				//printf("%d>>>>>>\n", sliceNumber);
+				//printf("slice %d \n", sliceNumber);
 				if ((sliceNumber == 1) && (!isnan(patientPosition[1])) ) {
 					for (int k = 0; k < 4; k++)
 						patientPositionStartPhilips[k] = patientPosition[k];
@@ -4617,7 +4617,7 @@ double TE = 0.0; //most recent echo time recorded
                 dcmStr (lLength, &buffer[lPos], aotTxt);
                 int slen = (int) strlen(aotTxt);
 				if((slen < 9) || (strstr(aotTxt, "QUADRUPED") == NULL) ) break;
-                printError("Anatomical Orientation Type (0010,2210) is QUADRUPED: rotate coordinates accordingly");
+                printError("Anatomical Orientation Type (0010,2210) is QUADRUPED: rotate coordinates accordingly\n");
             	break; }
             case kPatientID :
                 dcmStr (lLength, &buffer[lPos], d.patientID);
@@ -5148,6 +5148,7 @@ double TE = 0.0; //most recent echo time recorded
                 break;
             }
             case kSequenceVariant21 :
+            	if (d.manufacturer != kMANUFACTURER_SIEMENS) break; //see GE dataset in dcm_qa_nih
             	//fall through...
             case kSequenceVariant : {
                 dcmStr (lLength, &buffer[lPos], d.sequenceVariant);
@@ -5806,12 +5807,14 @@ if (d.isHasPhase)
 				if (mn[i] != mx[i])
 					printMessage(" Dimension %d Range: %d..%d\n", i, mn[i], mx[i]);
     	} //verbose > 1
+    	if (d.manufacturer != kMANUFACTURER_BRUKER) { //only single sample Bruker - perhaps use 0020,9057 to identify if space or time is 3rd dimension
     	//sort dimensions
 #ifdef USING_R
         std::sort(dcmDim.begin(), dcmDim.begin() + numberOfFrames, compareTDCMdim);
 #else
         qsort(dcmDim, numberOfFrames, sizeof(struct TDCMdim), compareTDCMdim);
 #endif
+		}
 		//for (int i = 0; i < numberOfFrames; i++)
 		//	printf("%d -> %d  %d %d %d\n", i,  dcmDim[i].diskPos, dcmDim[i].dimIdx[1], dcmDim[i].dimIdx[2], dcmDim[i].dimIdx[3]);
 		for (int i = 0; i < numberOfFrames; i++)

diff --git a/console/nii_dicom.h b/console/nii_dicom.h
@@ -43,7 +43,7 @@ extern "C" {
 	#define kCCsuf " CompilerNA" //unknown compiler!
 #endif
 
-#define kDCMvers "v1.0.20181030 " kJP2suf kLSsuf kCCsuf
+#define kDCMvers "v1.0.20181105 " kJP2suf kLSsuf kCCsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
 static const int kMaxDTI4D = 18000; //maximum number of DTI directions for 4D (Philips) images, also maximum number of 3D slices for Philips 3D and 4D images

diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
@@ -2888,12 +2888,16 @@ void checkSliceTiming(struct TDICOMdata * d, struct TDICOMdata * d1) {
 	float minT1 = d1->CSA.sliceTiming[0];
 	float maxT1 = minT1;
 	for (int i = 0; i < kMaxEPI3D; i++) {
-		if (d1->CSA.sliceTiming[i] < 0.0) break;
+		//if (d1->CSA.sliceTiming[i] < 0.0) break;
 		if (d1->CSA.sliceTiming[i] < minT1) minT1 = d1->CSA.sliceTiming[i];
 		if (d1->CSA.sliceTiming[i] > maxT1) maxT1 = d1->CSA.sliceTiming[i];
 	}
+	if (minT1 < 0.0) { //https://github.com/neurolabusc/MRIcroGL/issues/31
+		printWarning("Siemens MoCo? Bogus slice timing (range %g..%g, TR=%gms)\n", minT1, maxT1, d->TR);
+		return;
+	}
 	if ((minT1 == maxT1) || (maxT1 >= d->TR)) { //both first and second image corrupted
-		printWarning("CSA slice timing appears corrupted (range %g..%g, TR=%gms)\n", minT, maxT, d->TR);
+		printWarning("CSA slice timing appears corrupted (range %g..%g, TR=%gms)\n", minT1, maxT1, d->TR);
 		return;
 	}
 	//1st image corrupted, but 2nd looks ok - substitute values from 2nd image