Siemens series instance UID issues (#394)

console/nii_dicom.cpp

@@ -4838,6 +4838,7 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 	//	philDTI[i].V[0] = -1;
 	// array for storing DimensionIndexValues
 	int numDimensionIndexValues = 0;
+	bool isSiemensXA = false;
 	//don't use stack! TDCMdim dcmDim[kMaxSlice2D];
 	TDCMdim *dcmDim = (TDCMdim *)malloc(kMaxSlice2D * sizeof(TDCMdim));
 	for (int i = 0; i < kMaxSlice2D; i++) {
@@ -5818,6 +5819,8 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 		case kSoftwareVersions: {
 			dcmStr(lLength, &buffer[lPos], d.softwareVersions);
 			int slen = (int)strlen(d.softwareVersions);
+			if ((slen > 4) && (strstr(d.softwareVersions, "XA10") != NULL))
+				d.isXA10A = true;
 			if ((slen > 4) && (strstr(d.softwareVersions, "XA11") != NULL))
 				d.isXA10A = true;
 			if ((slen > 4) && (strstr(d.softwareVersions, "XA20") != NULL))
@@ -5826,9 +5829,15 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 				d.isXA10A = true;
 			if ((slen > 4) && (strstr(d.softwareVersions, "XA31") != NULL))
 				d.isXA10A = true;
-			if ((slen < 5) || (strstr(d.softwareVersions, "XA10") == NULL))
-				break;
-			d.isXA10A = true;
+			//isXA10A is designed to catch early Siemens bugs, while isSiemensXA also detect modern XA
+			if (d.isXA10A)
+				isSiemensXA = true;
+			if ((slen > 4) && (strstr(d.softwareVersions, "XA5") != NULL))
+				isSiemensXA = true; //XA50/XA51
+			if ((slen > 4) && (strstr(d.softwareVersions, "XA6") != NULL))
+				isSiemensXA = true; //XA60
+			if ((slen > 4) && (strstr(d.softwareVersions, "XA7") != NULL))
+				isSiemensXA = true; //XA70
 			break;
 		}
 		case kProtocolName: {
@@ -8265,7 +8274,7 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 	if (d.phaseNumber > 0) // Philips TurboQUASAR set this uniquely for each slice
 		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)) {
+	if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (strlen(seriesTimeTxt) > 1) && (isSiemensXA) && (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;
 		d.imageNum += (d.seriesNum * 1000);

console/nii_dicom.h

@@ -50,7 +50,7 @@ extern "C" {
 #define kCPUsuf " " // unknown CPU
 #endif
 
-#define kDCMdate "v1.0.20241025"
+#define kDCMdate "v1.0.20241106"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf
 
 static const int kMaxEPI3D = 1024; // maximum number of EPI images in Siemens Mosaic

console/nii_dicom_batch.cpp

@@ -2611,6 +2611,10 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 	if (isnan(dcmList[indx0].patientPosition[1]))
 		return NULL; // issue606 do not save bvec for non-spatial data (e.g. physio)
 	int numDti = dcmList[indx0].CSA.numDti;
+	if ((numDti > nConvert) && (numDti > kMaxSlice2D)) {
+		printError("nii_saveDTI unable to save vectors.\n");
+		return NULL;
+	}
 #ifdef USING_R
 	ImageList *images = (ImageList *)opts.imageList;
 #endif
@@ -2674,15 +2678,16 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 	TDTI *vx = NULL;
 	if (numDti > 1) {
 		vx = (TDTI *)malloc(numDti * sizeof(TDTI));
-		for (int i = 0; i < numDti; i++) // for each direction
-			for (int v = 0; v < 4; v++)	 // for each vector+B-value
+		for (int i = 0; i < numDti; i++) {// for each direction
+			for (int v = 0; v < 4; v++) 	 // for each vector+B-value
 				vx[i].V[v] = dti4D->S[i].V[v];
+			}
 	} else { // if (numDti == 1) {//extract DTI from different slices
 		vx = (TDTI *)malloc(nConvert * sizeof(TDTI));
 		numDti = 0;
 		for (int i = 0; i < nConvert; i++) { // for each image
 			if ((dcmList[indx0].CSA.mosaicSlices > 1) || (isSamePosition(dcmList[indx0], dcmList[dcmSort[i].indx]))) {
-				// if (numDti < kMaxDTIv)
+				int idx = dcmSort[i].indx;
 				for (int v = 0; v < 4; v++)									// for each vector+B-value
 					vx[numDti].V[v] = dcmList[dcmSort[i].indx].CSA.dtiV[v]; // dcmList[indx0].CSA.dtiV[numDti][v] = dcmList[dcmSort[i].indx].CSA.dtiV[0][v];
 				numDti++;
@@ -6696,6 +6701,10 @@ void sliceTimingXA(struct TDCMsort *dcmSort, struct TDICOMdata *dcmList, struct
 	uint64_t indx0 = dcmSort[0].indx; // first volume
 	if ((!dcmList[indx0].isXA10A) || (hdr->dim[3] < 1) || (hdr->dim[4] < 1))
 		return;
+	if (hdr->dim[3] > kMaxEPI3D) {
+		printWarning("Unable to set Siemens XA sliceTiming due to excessive slices per volume (%d).\n", hdr->dim[3]);
+		return;
+	}
 	if ((nConvert == (hdr->dim[3] * hdr->dim[4])) && (hdr->dim[3] < (kMaxEPI3D - 1)) && (hdr->dim[3] > 1)) {
 		// issue875 use 2nd volume
 		int offset = 0;
@@ -8081,7 +8090,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata d
 #ifdef USING_DCM2NIIXFSWRAPPER
 	printMessage("load Image %s\n", nameList->str[indx]);
 #endif
-
 	// printMessage(" %d %d %d %d %lu\n", hdr0.dim[1], hdr0.dim[2], hdr0.dim[3], hdr0.dim[4], (unsigned long)[imgM length]);
 	bool isHasOverlay = dcmList[indx0].isHasOverlay;
 	bool isDerived = dcmList[indx0].isDerived;
@@ -8465,7 +8473,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata d
 			checkDateTimeOrder(&dcmList[dcmSort[0].indx], &dcmList[dcmSort[nConvert - 1].indx]);
 	}
 	bool ok = setBids(&dcmList[indx0], nameList->str[dcmSort[0].indx], nConvert, opts.isVerbose);
-
 	if (opts.isIgnoreDerivedAnd2D && !ok) {
 		printMessage("Ignoring derived image(s) of series %ld %s\n", dcmList[indx].seriesNum, nameList->str[indx]);
 		return EXIT_SUCCESS;