GEIIS icons and Bruker diffusion (#760; #761)

console/nii_dicom.cpp

@@ -4340,6 +4340,7 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 #define kReferencedImageEvidenceSQ (uint32_t)0x0008 + (0x9092 << 16)
 #define kComplexImageComponent (uint32_t)0x0008 + (0x9208 << 16) //'0008' '9208' 'CS' 'ComplexImageComponent'
 #define kAcquisitionContrast (uint32_t)0x0008 + (0x9209 << 16) //'0008' '9209' 'CS' 'AcquisitionContrast'
+#define kIconSQ 0x0009 + (0x1110 << 16)
 #define kPatientName 0x0010 + (0x0010 << 16)
 #define kPatientID 0x0010 + (0x0020 << 16)
 #define kAccessionNumber 0x0008 + (0x0050 << 16)
@@ -5557,6 +5558,13 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 			if (strlen(d.studyTime) < 2)
 				dcmStr(lLength, &buffer[lPos], d.studyTime);
 			break;
+		case kIconSQ: {//issue760 GEIIS icon strikes again
+			if ((vr[0] != 'S') || (vr[1] != 'Q') || (lLength != 8)) break; //only risk kludge for explicit VR with length
+			isIconImageSequence = true;
+			if (sqDepthIcon < 0)
+				sqDepthIcon = sqDepth;
+			break;
+		}
 		case kPatientName:
 			dcmStr(lLength, &buffer[lPos], d.patientName);
 			break;
@@ -7711,7 +7719,7 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		qsort(objects, numberOfFrames, sizeof(struct fidx), fcmp);
 		numDimensionIndexValues = numberOfFrames;
 		for (int i = 0; i < numberOfFrames; i++) {
-			//	printf("%d > %g\n", objects[i].index, objects[i].value);
+			//printf("%d > %g\n", objects[i].index, objects[i].value);
 			dcmDim[objects[i].index].dimIdx[0] = i;
 		}
 		for (int i = 0; i < 4; i++) {
@@ -7830,7 +7838,10 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 			if (dti4D->intenScalePhilips[i] != dti4D->intenScalePhilips[0])
 				d.isScaleVariesEnh = true;
 		}
-		if (!(d.manufacturer == kMANUFACTURER_BRUKER && d.isDiffusion) && (d.xyzDim[4] > 1) && (d.xyzDim[4] < kMaxDTI4D)) { //record variations in TE
+		//Revert Bruker change as new Bruker data uses DimensionIndexValues 0020,9157 for diffusion vectors
+		// https://github.com/rordenlab/dcm2niix/commit/8207877de984dab59e0374906c7ad212756f85a6#diff-120bb215d28dcbddeca8ea56dbb97e237501901ac2dfa1fbe4182282a8dd2b75
+		//if (!(d.manufacturer == kMANUFACTURER_BRUKER && d.isDiffusion) && (d.xyzDim[4] > 1) && (d.xyzDim[4] < kMaxDTI4D)) { //record variations in TE
+		if ((d.xyzDim[4] > 1) && (d.xyzDim[4] < kMaxDTI4D)) { //record variations in TE
 			d.isScaleOrTEVaries = false;
 			bool isTEvaries = false;
 			bool isScaleVaries = false;
@@ -8121,6 +8132,13 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		d.rawDataRunNumber = philMRImageDiffVolumeNumber;
 		d.phaseNumber  = 0; 
 	}
+	// Phase encoding polarity
+	//next conditionals updated: make GE match Siemens
+	// it also rescues Siemens XA20 images without CSA header but with 0021,111C
+	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
+		d.CSA.phaseEncodingDirectionPositive = 1;
+	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_FLIPPED)
+		d.CSA.phaseEncodingDirectionPositive = 0;
 	//issue 668: several SAR levels for different regions (IEC_HEAD, IEC_LOCAL, etc)
 	d.SAR = fmax(maxSAR, d.SAR);
 	// d.rawDataRunNumber =  (d.rawDataRunNumber > d.phaseNumber) ? d.rawDataRunNumber : d.phaseNumber; //will not work: conflict for MultiPhase ASL with multiple averages

console/nii_dicom.h

@@ -50,7 +50,7 @@ extern "C" {
     #define kCPUsuf " " //unknown CPU
 #endif
 
-#define kDCMdate "v1.0.20230904"
+#define kDCMdate "v1.0.20231005"
 #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

@@ -2094,16 +2094,20 @@ tse3d: T2*/
 	if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.dwellTime > 0))
 		fprintf(fp, "\t\"DwellTime\": %g,\n", d.dwellTime * 1E-9);
 	// Phase encoding polarity
+/*
+following logic now occurs earlier to aid bids guess
 	int phPos = d.CSA.phaseEncodingDirectionPositive;
 	//next two conditionals updated: make GE match Siemens
 	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_UNFLIPPED)
 		phPos = 1;
 	if (d.phaseEncodingGE == kGE_PHASE_ENCODING_POLARITY_FLIPPED)
 		phPos = 0;
+*/
 	//if ((phPos >= 0) && (d.phaseEncodingRC == 'R') && (d.manufacturer == kMANUFACTURER_UIH)) phPos = 1 - phPos; //issue410
 	bool isSkipPhaseEncodingAxis = d.is3DAcq;
 	if (d.echoTrainLength > 1)
 		isSkipPhaseEncodingAxis = false; //issue 371: ignore phaseEncoding for 3D MP-RAGE/SPACE, but report for 3D EPI
+	int phPos = d.CSA.phaseEncodingDirectionPositive;
 	if (((d.phaseEncodingRC == 'R') || (d.phaseEncodingRC == 'C')) && (!isSkipPhaseEncodingAxis) && (phPos < 0)) {
 		//when phase encoding axis is known but we do not know phase encoding polarity
 		// https://github.com/rordenlab/dcm2niix/issues/163
@@ -6661,15 +6665,16 @@ void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const cha
 	}
 	//add dir
 	//nb for func dir comes before echo
+	int phPos = d->CSA.phaseEncodingDirectionPositive;
 	if (isDirLabel) {
 		char dirLabel[kDICOMStrLarge]  = "_dir-";
 		if (d->phaseEncodingRC == 'C') {
-			if (d->CSA.phaseEncodingDirectionPositive)
+			if (phPos)
 				strcat(dirLabel, "AP");
 			else
 				strcat(dirLabel, "PA");
 		} else {
-			if (d->CSA.phaseEncodingDirectionPositive)
+			if (phPos)
 				strcat(dirLabel, "RL");
 			else
 				strcat(dirLabel, "LR");
@@ -6783,11 +6788,17 @@ void setBidsPhilips(struct TDICOMdata *d, int nConvert, int isVerbose) {
 		else
 			strcpy(modalityBIDS, "magnitude");
 	} else if ((strstr(seqName, "SP") != NULL) && (strstr(d->scanningSequence, "GR") != NULL)) {
+		//issue 753 need to distinguish different types of phase map see Levitas example B0_DTI_MED_RES
+		// https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-3-direct-field-mapping
+		printWarning("Unable to distinguish Philips fieldmaps: phase difference, two phase/magnitude, direct fieldmapping.");
 		isReportEcho = false;
 		strcpy(dataTypeBIDS, "fmap");
-		strcpy(modalityBIDS, "phasediff");
+		if (d->isHasPhase)
+			strcpy(modalityBIDS, "phasediff");
+		else if (d->echoTrainLength < 2) 
+			snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "magnitude%d", d->echoNum);
+
 		if (d->echoTrainLength > 1) {
-			isReportEcho = false;
 			if (d->isHasPhase)
 				snprintf(modalityBIDS, kDICOMStrLarge - strlen(modalityBIDS), "phase%d", d->echoNum);
 			else if (d->isHasImaginary)
@@ -6853,7 +6864,7 @@ void setBidsPhilips(struct TDICOMdata *d, int nConvert, int isVerbose) {
 		strcat(suffixBIDS,modalityBIDS);
 	}
 	//if ((isVerbose > 0) || (strlen(dataTypeBIDS) < 1))
-	if (isVerbose > 0)
+	//if (isVerbose > 0)
 		printf("::autoBids:Philips pulseSeq:'%s' scanSeq:'%s' seqVariant:'%s'\n", 
 			d->pulseSequenceName, d->scanningSequence, d->sequenceVariant);
 	if (isDerived)