Merge pull request #778 from mr-jaemin/development

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rordenlab · Jan 22, 2024 · 980b4ed · 980b4ed
2 parents 1485cc5 + 2a515f5
commit 980b4ed
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Showing 3 changed files with 15 additions and 10 deletions.
diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
@@ -4734,6 +4734,7 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 	char imageType1st[kDICOMStr] = "";
 	bool isEncapsulatedData = false;
 	int diffusionDirectionTypeGE = 0; //issue690
+	int seriesdiffusionDirectionTypeGE = 0; //issue690, 777
 	int multiBandFactor = 0;
 	int frequencyRows = 0;
 	int numberOfImagesInMosaic = 0;
@@ -6660,8 +6661,8 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		case kScanningSequenceSiemens:
 			if (d.manufacturer == kMANUFACTURER_SIEMENS) 
 				dcmStr(lLength, &buffer[lPos], scanningSequenceSiemens);
-			if (d.manufacturer == kMANUFACTURER_GE) //issue690
-				diffusionDirectionTypeGE = dcmInt(lLength, &buffer[lPos], d.isLittleEndian);
+			if (d.manufacturer == kMANUFACTURER_GE) //issue690, series-level 16=DFAXDTI
+				seriesdiffusionDirectionTypeGE = dcmInt(lLength, &buffer[lPos], d.isLittleEndian);
 			break;
 		case kSequenceVariant21:
 			if (d.manufacturer != kMANUFACTURER_SIEMENS)
@@ -7068,7 +7069,7 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 				break;
 			d.shimGradientZ = dcmIntSS(lLength, &buffer[lPos], d.isLittleEndian);
 			break;
-		case kVasCollapseFlagGE: //SS issue 690 16=DiffusionDtiDicomValue
+		case kVasCollapseFlagGE: //SS issue 690 image-level 16=DiffusionDtiDicomValue or 14=DiffusionT2DicomValue (initial b0)
 			if (d.manufacturer != kMANUFACTURER_GE)
 				break;
 			diffusionDirectionTypeGE = dcmIntSS(lLength, &buffer[lPos], d.isLittleEndian);
@@ -8126,8 +8127,11 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 		//in practice 0020,0110 not used
 		//https://github.com/bids-standard/bep001/blob/repetitiontime/Proposal_RepetitionTime.md
 	}
-	//issue690
-	if ((d.manufacturer == kMANUFACTURER_GE) && (diffusionDirectionTypeGE > 0) && (diffusionDirectionTypeGE != 16))
+	//issue690, 777 
+	// detect non-DTI for GE 
+	if ((d.manufacturer == kMANUFACTURER_GE) && (diffusionDirectionTypeGE > 0) && (diffusionDirectionTypeGE != 16) && (diffusionDirectionTypeGE != 14))
+		d.numberOfDiffusionDirectionGE = 0;
+	if ((d.manufacturer == kMANUFACTURER_GE) && (seriesdiffusionDirectionTypeGE > 0) && (seriesdiffusionDirectionTypeGE != 16))
 		d.numberOfDiffusionDirectionGE = 0;
 	//issue 542
 	if ((d.manufacturer == kMANUFACTURER_GE) && (isNeologica) && (!isSameFloat(d.CSA.dtiV[0], 0.0f)) && ((isSameFloat(d.CSA.dtiV[1], 0.0f)) && (isSameFloat(d.CSA.dtiV[2], 0.0f)) && (isSameFloat(d.CSA.dtiV[3], 0.0f)) ) )

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 "v1.0.20240109"
+#define kDCMdate "v1.0.20240117"
 #define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf
 
 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
@@ -2534,7 +2534,7 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 	*numADC = 0;
 	bvals = (float *)malloc(numDti * sizeof(float));
 	int numGEwarn = 0;
-	bool isGEADC = (dcmList[indx0].numberOfDiffusionDirectionGE == 0);
+	bool isGEADC = (dcmList[indx0].numberOfDiffusionDirectionGE == 0); // GE non-DTI
 	for (int i = 0; i < numDti; i++) {
 		bvals[i] = vx[i].V[0];
 		//printMessage("---bxyz %g %g %g %g\n",vx[i].V[0],vx[i].V[1],vx[i].V[2],vx[i].V[3]);
@@ -2556,8 +2556,9 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 		}
 		bvals[i] = bvals[i] + (0.5 * i / numDti); //add a small bias so ties are kept in sequential order
 	}
-	if (numGEwarn > 0)
-		printWarning("Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)\n");
+	// See issue 777: removed the warning because GE DTI b=0 with bval>0 but bvec=0 (prior to version 29.1) will be handled by geCorrectBvecs()
+	// if (numGEwarn > 0)
+	//	printWarning("Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)\n");
 	/*if ((*numADC == numDti) || (numGEwarn == numDti)) { //issue 405: we now save bvals file for isotropic series
 		//all isotropic/ADC images - no valid bvecs
 		*numADC = 0;
@@ -7225,7 +7226,7 @@ void sliceTimingGE(struct TDICOMdata *d, const char *filename, struct TDCMopts o
 		}
 	}*/
 	//end: version check
-	if (d->maxEchoNumGE > 0)
+	if ((d->maxEchoNumGE > 0) && (d->internalepiVersionGE != 2)) // GE non-Diffusion only
 		printWarning("GE sequence with %d echoes. See issue 359\n", d->maxEchoNumGE);
 	if ((d->protocolBlockStartGE < 1) || (d->protocolBlockLengthGE < 19))
 		return;