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Development #778

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Jan 22, 2024
Merged

Development #778

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1d99849
GE Diffusion issue #777
mr-jaemin Jan 18, 2024
279ce6e
GE Diffusion issue #777 minor
mr-jaemin Jan 18, 2024
2a515f5
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mr-jaemin Jan 18, 2024
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14 changes: 9 additions & 5 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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)) ) )
Expand Down
2 changes: 1 addition & 1 deletion console/nii_dicom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
9 changes: 5 additions & 4 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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]);
Expand All @@ -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;
Expand Down Expand Up @@ -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;
Expand Down