Merge pull request #619 from mr-jaemin/development

Thank @mr-jaemin this will close GE Direct field mapping (TE1/TE2) (#617)
rordenlab · Jul 20, 2022 · f2ceab6 · f2ceab6
2 parents 160aaa2 + cfa4b98
commit f2ceab6
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 4 deletions.
diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
@@ -861,6 +861,7 @@ struct TDICOMdata clear_dicom_data() {
 	d.isLittleEndian = true; //DICOM initially always little endian
 	d.converted2NII = 0;
 	d.numberOfDiffusionDirectionGE = -1;
+	d.velocityEncodeScaleGE = 1.0;
 	d.phaseEncodingGE = kGE_PHASE_ENCODING_POLARITY_UNKNOWN;
 	d.rtia_timerGE = -1.0;
 	d.rawDataRunNumber = -1;
@@ -4301,6 +4302,7 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 #define kDiffusionDirectionGEY 0x0019 + (0x10BC << 16) //DS frequency diffusion direction
 #define kDiffusionDirectionGEZ 0x0019 + (0x10BD << 16) //DS slice diffusion direction
 #define kNumberOfDiffusionDirectionGE 0x0019 + (0x10E0 << 16) ///DS NumberOfDiffusionDirection:UserData24
+#define kVelocityEncodeScaleGE 0x0019 + (0x10E2 << 16) ///DS Velocity Encode Scale
 #define kStudyID 0x0020 + (0x0010 << 16)
 #define kSeriesNum 0x0020 + (0x0011 << 16)
 #define kAcquNum 0x0020 + (0x0012 << 16)
@@ -5633,6 +5635,12 @@ const uint32_t kEffectiveTE = 0x0018 + (0x9082 << 16);
 			d.numberOfDiffusionDirectionGE = round(f);
 			break;
 		}
+		case kVelocityEncodeScaleGE: {
+			if (d.manufacturer != kMANUFACTURER_GE)
+				break;
+			d.velocityEncodeScaleGE = dcmStrFloat(lLength, &buffer[lPos]);
+			break;
+		}
 		case kLastScanLoc:
 			d.lastScanLoc = dcmStrFloat(lLength, &buffer[lPos]);
 			break;

diff --git a/console/nii_dicom.h b/console/nii_dicom.h
@@ -50,7 +50,7 @@ extern "C" {
     #define kCPUsuf " " //unknown CPU
 #endif
 
-#define kDCMdate "v1.0.20220717"
+#define kDCMdate "v1.0.20220720"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf
 
 static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
@@ -224,7 +224,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
         uint32_t coilCrc, seriesUidCrc, instanceUidCrc;
         int overlayStart[kMaxOverlay];
         int postLabelDelay, shimGradientX, shimGradientY, shimGradientZ, phaseNumber, spoiling, mtState, partialFourierDirection, interp3D, aslFlags, durationLabelPulseGE, epiVersionGE, internalepiVersionGE, maxEchoNumGE, rawDataRunNumber, numberOfImagesInGridUIH, numberOfDiffusionDirectionGE, phaseEncodingGE, protocolBlockStartGE, protocolBlockLengthGE, modality, dwellTime, effectiveEchoSpacingGE, phaseEncodingLines, phaseEncodingSteps, echoTrainLength, echoNum, sliceOrient, manufacturer, converted2NII, acquNum, imageNum, imageStart, imageBytes, bitsStored, bitsAllocated, samplesPerPixel,locationsInAcquisition, locationsInAcquisitionConflict, compressionScheme;
-        float  xRayTubeCurrent, exposureTimeMs, numberOfExcitations, numberOfArms, numberOfPointsPerArm, groupDelay, decayFactor, percentSampling,waterFatShift, numberOfAverages, imagingFrequency, patientWeight, zSpacing, zThick, pixelBandwidth, SAR, phaseFieldofView, accelFactPE, accelFactOOP, flipAngle, fieldStrength, TE, TI, TR, intenScale, intenIntercept, intenScalePhilips, gantryTilt, lastScanLoc, angulation[4];
+        float  xRayTubeCurrent, exposureTimeMs, numberOfExcitations, numberOfArms, numberOfPointsPerArm, groupDelay, decayFactor, percentSampling,waterFatShift, numberOfAverages, imagingFrequency, patientWeight, zSpacing, zThick, pixelBandwidth, SAR, phaseFieldofView, accelFactPE, accelFactOOP, flipAngle, fieldStrength, TE, TI, TR, intenScale, intenIntercept, intenScalePhilips, gantryTilt, lastScanLoc, angulation[4], velocityEncodeScaleGE;
         float orient[7], patientPosition[4], patientPositionLast[4], xyzMM[4], stackOffcentre[4];
         float rtia_timerGE, radionuclidePositronFraction, radionuclideTotalDose, radionuclideHalfLife, doseCalibrationFactor; //PET ISOTOPE MODULE ATTRIBUTES (C.8-57)
         float frameReferenceTime, frameDuration, ecat_isotope_halflife, ecat_dosage;

diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
@@ -1466,8 +1466,15 @@ tse3d: T2*/
 		json_Float(fp, "\t\"NumberOfAverages\": %g,\n", d.numberOfAverages);
 	if ((d.echoNum > 1) || ((d.isMultiEcho) && (d.echoNum > 0)))
 		fprintf(fp, "\t\"EchoNumber\": %d,\n", d.echoNum);
-	if ((d.TE > 0.0) && (!d.isXRay))
-		fprintf(fp, "\t\"EchoTime\": %g,\n", d.TE / 1000.0);
+	if ((d.TE > 0.0) && (!d.isXRay)) {
+		if ((d.manufacturer == kMANUFACTURER_GE) && (d.isRealIsPhaseMapHz) && (d.velocityEncodeScaleGE < 0))  { //issue617, only set for GE fieldmaphz
+			json_Float(fp, "\t\"EchoTime1\": %g,\n", d.TE / 1000.0 );
+			json_Float(fp, "\t\"EchoTime2\": %g,\n", d.TE / 1000.0 - 1.0/(2.0 * M_PI * d.velocityEncodeScaleGE));
+			// delta TE = -1/(2 * pi * velocityEncodeScaleGE)
+		}
+		else
+			fprintf(fp, "\t\"EchoTime\": %g,\n", d.TE / 1000.0);
+	}	
 	//if ((d.TE2 > 0.0) && (!d.isXRay)) fprintf(fp, "\t\"EchoTime2\": %g,\n", d.TE2 / 1000.0 );
 	if (dti4D->frameDuration[0] < 0.0) //e.g. PET scans can have variable TR
 		json_Float(fp, "\t\"RepetitionTime\": %g,\n", d.TR / 1000.0);