Siemens XA30 ASL parameters and ImageTypeText 0021,1175

console/nii_dicom.cpp

@@ -712,6 +712,7 @@ struct TDICOMdata clear_dicom_data() {
 	strcpy(d.patientID, "");
 	strcpy(d.accessionNumber, "");
 	strcpy(d.imageType, "");
+	strcpy(d.imageTypeText, "");
 	strcpy(d.imageComments, "");
 	strcpy(d.imageBaseName, "");
 	strcpy(d.phaseEncodingDirectionDisplayedUIH, "");
@@ -4271,6 +4272,7 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 #define kImagingFrequency2 0x0018 + uint32_t(0x9098 << 16) //FD
 #define kParallelReductionFactorOutOfPlane 0x0018 + uint32_t(0x9155 << 16) //FD
 //#define kFrameAcquisitionDuration 0x0018+uint32_t(0x9220 << 16 ) //FD
+#define kArterialSpinLabelingContrast 0x0018 + uint32_t(0x9250 << 16) //CS
 #define kASLPulseTrainDuration 0x0018 + uint32_t(0x9258 << 16) //UL
 #define kDiffusionBValueXX 0x0018 + uint32_t(0x9602 << 16) //FD
 #define kDiffusionBValueXY 0x0018 + uint32_t(0x9603 << 16) //FD
@@ -4333,6 +4335,7 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 #define kBandwidthPerPixelPhaseEncode21 0x0021 + (0x1153 << 16) //FD
 #define kCoilElements 0x0021 + (0x114F << 16) //LO
 #define kAcquisitionMatrixText21 0x0021 + (0x1158 << 16) //SH
+#define kImageTypeText 0x0021 + (0x1175 << 16) //CS
 //Private Group 21 as used by GE:
 #define kLocationsInAcquisitionGE 0x0021 + (0x104F << 16) //SS 'LocationsInAcquisitionGE'
 #define kRTIA_timer 0x0021 + (0x105E << 16) //DS
@@ -6206,6 +6209,18 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 			d.xyzMM[3] = dcmStrFloat(lLength, &buffer[lPos]);
 			d.zThick = d.xyzMM[3];
 			break;
+		case kImageTypeText: {
+			if (d.manufacturer != kMANUFACTURER_SIEMENS)
+				break;
+			dcmStr(lLength, &buffer[lPos], d.imageTypeText);
+			int slen = (int)strlen(d.imageTypeText);
+			if (slen > 1) {
+				for (int i = 0; i < slen; i++)
+					if (d.imageTypeText[i] == '\\')
+						d.imageTypeText[i] = '_';
+			}
+			break;
+		}
 		case kAcquisitionMatrixText21:
 			//fall through to kAcquisitionMatrixText
 		case kAcquisitionMatrixText: {
@@ -6493,6 +6508,18 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 		//case kFrameAcquisitionDuration :
 		//	frameAcquisitionDuration = dcmFloatDouble(lLength, &buffer[lPos], d.isLittleEndian); //issue369
 		//	break;
+		case kArterialSpinLabelingContrast: { //CS
+			char st[kDICOMStr];
+			//aslFlags
+			dcmStr(lLength, &buffer[lPos], st);
+			if (strstr(st, "PSEUDOCONTINUOUS") != NULL)
+				d.aslFlags = (d.aslFlags | kASL_FLAG_GE_PSEUDOCONTINUOUS);
+			else if (strstr(st, "CONTINUOUS") != NULL)
+				d.aslFlags = (d.aslFlags | kASL_FLAG_GE_CONTINUOUS);
+			else if (strstr(st, "PULSED") != NULL)
+				d.aslFlags = (d.aslFlags | kASL_FLAG_GE_PULSED);
+			break;
+		}
 		case kASLPulseTrainDuration: {
 			d.postLabelDelay = dcmInt(4, &buffer[lPos], d.isLittleEndian);
 			break;

console/nii_dicom.h

@@ -50,7 +50,7 @@ extern "C" {
     #define kCPUsuf " " //unknown CPU
 #endif
 
-#define kDCMdate "v1.0.20220707"
+#define kDCMdate "v1.0.20220717"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
@@ -133,6 +133,7 @@ static const int kMaxDTI4D = kMaxSlice2D; //issue460: maximum number of DTI dire
 #define kASL_FLAG_GE_CONTINUOUS 8
 #define kASL_FLAG_PHILIPS_CONTROL 16
 #define kASL_FLAG_PHILIPS_LABEL 32
+#define kASL_FLAG_GE_PULSED 64
 
 
 //for spoiling 0018,9016
@@ -230,7 +231,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
         float pixelPaddingValue;  // used for both FloatPixelPaddingValue (0028, 0122) and PixelPaddingValue (0028, 0120); NaN if not present.
         double acquisitionDuration, triggerDelayTime, RWVScale, RWVIntercept, dateTime, acquisitionTime, acquisitionDate, bandwidthPerPixelPhaseEncode;
         char parallelAcquisitionTechnique[kDICOMStr], radiopharmaceutical[kDICOMStr], convolutionKernel[kDICOMStr], unitsPT[kDICOMStr], decayCorrection[kDICOMStr], attenuationCorrectionMethod[kDICOMStr],reconstructionMethod[kDICOMStr];
-        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr];
+        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageTypeText[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr];
         char scanOptions[kDICOMStrLarge], institutionAddress[kDICOMStrLarge], imageComments[kDICOMStrLarge];
         uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
         struct TCSAdata CSA;

console/nii_dicom_batch.cpp

@@ -652,12 +652,14 @@ typedef struct {
 	float alFree[kMaxWipFree];
 	float adFree[kMaxWipFree];
 	float alTI[kMaxWipFree];
-	float dAveragesDouble, dThickness, ulShape, sPositionDTra, sNormalDTra;
+	float sPostLabelingDelay, ulLabelingDuration, dAveragesDouble, dThickness, ulShape, sPositionDTra, sNormalDTra;
 } TCsaAscii;
 
 void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, int csaLength, float *shimSetting, char *coilID, char *consistencyInfo, char *coilElements, char *pulseSequenceDetails, char *fmriExternalInfo, char *protocolName, char *wipMemBlock) {
 	//reads ASCII portion of CSASeriesHeaderInfo and returns lEchoTrainDuration or lEchoSpacing value
 	// returns 0 if no value found
+	csaAscii->sPostLabelingDelay = 0.0;
+	csaAscii->ulLabelingDuration = 0.0;
 	csaAscii->TE0 = 0.0;
 	csaAscii->TE1 = 0.0;
 	csaAscii->delayTimeInTR = -0.001;
@@ -786,6 +788,10 @@ void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, i
 		csaAscii->TE0 = readKeyFloatNan(keyStrTE0, keyPos, csaLengthTrim);
 		char keyStrTE1[] = "alTE[1]";
 		csaAscii->TE1 = readKeyFloatNan(keyStrTE1, keyPos, csaLengthTrim);
+		char keyStrPLD[] = "sAsl.sPostLabelingDelay[0]";
+		csaAscii->sPostLabelingDelay = readKeyFloatNan(keyStrPLD, keyPos, csaLengthTrim);
+		char keyStrLD[] = "sAsl.ulLabelingDuration";
+		csaAscii->ulLabelingDuration = readKeyFloatNan(keyStrLD, keyPos, csaLengthTrim);
 		//read ALL alTI[*] values
 		for (int k = 0; k < kMaxWipFree; k++)
 			csaAscii->alTI[k] = NAN;
@@ -1306,6 +1312,20 @@ tse3d: T2*/
 			fprintf(fp, "\", \"FIELDMAPHZ");
 		fprintf(fp, "\"],\n");
 	}
+	if (strlen(d.imageTypeText) > 0) {
+		fprintf(fp, "\t\"ImageTypeText\": [\"");
+		bool isSep = false;
+		for (size_t i = 0; i < strlen(d.imageTypeText); i++) {
+			if (d.imageTypeText[i] != '_') {
+				if (isSep)
+					fprintf(fp, "\", \"");
+				isSep = false;
+				fprintf(fp, "%c", d.imageTypeText[i]);
+			} else
+				isSep = true;
+		}
+		fprintf(fp, "\"],\n");
+	}
 	if (d.isDerived) //DICOM is derived image or non-spatial file (sounds, etc)
 		fprintf(fp, "\t\"RawImage\": false,\n");
 	if (d.seriesNum > 0)
@@ -1518,6 +1538,11 @@ tse3d: T2*/
 		bool isPCASL = false;
 		bool isPASL = false;
 		//ASL specific tags - 2D pCASL Danny J.J. Wang http://www.loft-lab.org
+		//ASL specific tags - 2D PASL Siemens Product XA30, n.b pasl/casl/pcasl set using 0018,9250
+		if (strstr(pulseSequenceDetails, "ep2d_asl")) {
+			json_FloatNotNan(fp, "\t\"LabelingDuration\": %g,\n", csaAscii.ulLabelingDuration * (1.0 / 1000000.0)); //usec->sec
+			json_FloatNotNan(fp, "\t\"PostLabelingDelay\": %g,\n", csaAscii.sPostLabelingDelay * (1.0 / 1000000.0)); //usec -> sec
+		}
 		if ((strstr(pulseSequenceDetails, "ep2d_pcasl")) || (strstr(pulseSequenceDetails, "ep2d_pcasl_UI_PHC"))) {
 			isPCASL = true;
 			repetitionTimePreparation = d.TR;
@@ -1781,15 +1806,13 @@ tse3d: T2*/
 	//generic public ASL tags
 	if (d.postLabelDelay > 0)
 		json_Float(fp, "\t\"PostLabelDelay\": %g,\n", float(d.postLabelDelay) / 1000.0);
-	//GE ASL specific tags
-	if (d.aslFlags & kASL_FLAG_GE_CONTINUOUS)
-		fprintf(fp, "\t\"ASLContrastTechnique\": \"CONTINUOUS\",\n");
-	if (d.aslFlags & kASL_FLAG_GE_PSEUDOCONTINUOUS)
-		fprintf(fp, "\t\"ASLContrastTechnique\": \"PSEUDOCONTINUOUS\",\n");
-	if (d.aslFlags & kASL_FLAG_GE_3DPCASL)
-		fprintf(fp, "\t\"ASLLabelingTechnique\": \"3D pulsed continuous ASL technique\",\n");
-	if (d.aslFlags & kASL_FLAG_GE_3DCASL)
-		fprintf(fp, "\t\"ASLLabelingTechnique\": \"3D continuous ASL technique\",\n");
+	//ASL BIDS tags
+	if ((d.aslFlags & kASL_FLAG_GE_CONTINUOUS) || (d.aslFlags & kASL_FLAG_GE_3DCASL))
+		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"CASL\",\n");
+	if ((d.aslFlags & kASL_FLAG_GE_PSEUDOCONTINUOUS) || (d.aslFlags &  kASL_FLAG_GE_3DPCASL))
+		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PCASL\",\n");
+	if (d.aslFlags & kASL_FLAG_GE_PULSED)
+		fprintf(fp, "\t\"ArterialSpinLabelingType\": \"PASL\",\n");
 	if (d.durationLabelPulseGE > 0) {
 		json_Float(fp, "\t\"LabelingDuration\": %g,\n", d.durationLabelPulseGE / 1000.0);
 		json_Float(fp, "\t\"PostLabelDelay\": %g,\n", d.TI / 1000.0); //For GE ASL: InversionTime -> Post-label delay