Discrepant uses for TriggerTime (#395)

rordenlab · Apr 27, 2020 · ad0e1c8 · ad0e1c8
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Showing 4 changed files with 18 additions and 7 deletions.
diff --git a/Philips/README.md b/Philips/README.md
@@ -90,7 +90,7 @@ MyCustomDirections
 
 ```
 
-## Missing Information.
+## Missing Information
 
 Philips DICOMs do not contain all the information desired by many neuroscientists. Due to this, the [BIDS](http://bids.neuroimaging.io/) files created by dcm2niix are impoverished relative to data from other vendors. This reflects a limitation in the Philips DICOMs, not dcm2niix.
 

diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
@@ -4354,6 +4354,8 @@ uint32_t kItemTag = 0xFFFE +(0xE000 << 16 );
 uint32_t kItemDelimitationTag = 0xFFFE +(0xE00D << 16 );
 uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );
 double TE = 0.0; //most recent echo time recorded
+float MRImageDynamicScanBeginTime = 0.0;
+
 	bool is2005140FSQ = false;
 	bool isDICOMANON = false; //issue383
 	bool isMATLAB = false; //issue383
@@ -4580,7 +4582,10 @@ double TE = 0.0; //most recent echo time recorded
 			dcmDim[numDimensionIndexValues].intenScalePhilips = d.intenScalePhilips;
 			dcmDim[numDimensionIndexValues].RWVScale = d.RWVScale;
 			dcmDim[numDimensionIndexValues].RWVIntercept = d.RWVIntercept;
-			dcmDim[numDimensionIndexValues].triggerDelayTime = d.triggerDelayTime;
+			if (isSameFloat(MRImageDynamicScanBeginTime * 1000.0, d.triggerDelayTime))
+				dcmDim[numDimensionIndexValues].triggerDelayTime = 0.0; //issue395
+			else
+				dcmDim[numDimensionIndexValues].triggerDelayTime = d.triggerDelayTime;
 			dcmDim[numDimensionIndexValues].V[0] = -1.0;
 			#ifdef MY_DEBUG
 			if (numDimensionIndexValues < 19) {
@@ -5657,9 +5662,9 @@ double TE = 0.0; //most recent echo time recorded
 
             case kMRImageDynamicScanBeginTime: { //FL
                 if (lLength != 4) break;
-                float dyn = dcmFloat(lLength, &buffer[lPos],d.isLittleEndian);
-                if (dyn < minDynamicScanBeginTime) minDynamicScanBeginTime = dyn;
-                if (dyn > maxDynamicScanBeginTime) maxDynamicScanBeginTime = dyn;
+                MRImageDynamicScanBeginTime = dcmFloat(lLength, &buffer[lPos],d.isLittleEndian);
+                if (MRImageDynamicScanBeginTime < minDynamicScanBeginTime) minDynamicScanBeginTime = MRImageDynamicScanBeginTime;
+                if (MRImageDynamicScanBeginTime > maxDynamicScanBeginTime) maxDynamicScanBeginTime = MRImageDynamicScanBeginTime;
                 break;
             }
             case kIntercept :
@@ -6739,6 +6744,9 @@ if (d.isHasPhase)
 		strcpy(d.seriesInstanceUID, d.studyInstanceUID);
 		d.seriesUidCrc = mz_crc32X((unsigned char*) &d.protocolName, strlen(d.protocolName));
 	}
+	if (isSameFloat(MRImageDynamicScanBeginTime * 1000.0, d.triggerDelayTime)) //issue395
+		d.triggerDelayTime = 0.0;
+	//printf("%d\t%g\t%g\t%g\n", d.imageNum, d.acquisitionTime, d.triggerDelayTime, MRImageDynamicScanBeginTime);
     if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (strlen(seriesTimeTxt) > 1) && (d.isXA10A) && (d.xyzDim[3] == 1) && (d.xyzDim[4] < 2)) {
     	//printWarning("Ignoring series number of XA data saved as classic DICOM (issue 394)\n");
     	d.isStackableSeries = true;

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 kDCMdate "v1.0.20200420"
+#define kDCMdate "v1.0.20200427"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic

diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
@@ -4851,7 +4851,10 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
 					#endif
 					int imageNumRange = 1 + abs( dcmList[dcmSort[nConvert-1].indx].imageNum -  dcmList[dcmSort[0].indx].imageNum);
 					if ((imageNumRange > 1) && (imageNumRange != nConvert)) {
-						printWarning("Missing images? Expected %d images, but instance number (0020,0013) ranges from %d to %d\n", nConvert, dcmList[dcmSort[0].indx].imageNum, dcmList[dcmSort[nConvert-1].indx].imageNum);
+						if ((dcmList[dcmSort[0].indx].locationsInAcquisition > 0) && ((nConvert % dcmList[dcmSort[0].indx].locationsInAcquisition) != 0) )
+							printError("Missing images. Found %d images, expected %d slices per volume and instance number (0020,0013) ranges from %d to %d\n", nConvert, dcmList[dcmSort[0].indx].locationsInAcquisition, dcmList[dcmSort[0].indx].imageNum, dcmList[dcmSort[nConvert-1].indx].imageNum);
+						else
+							printWarning("Missing images? Expected %d images, but instance number (0020,0013) ranges from %d to %d\n", nConvert, dcmList[dcmSort[0].indx].imageNum, dcmList[dcmSort[nConvert-1].indx].imageNum);
 						if (opts.isVerbose) {
 							printMessage("instance=[");
 							for (int i = 0; i < nConvert; i++) {