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Improved GE support
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@neurolabusc
neurolabusc committed Mar 26, 2018
1 parent 66ae53c commit dd527d9
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Showing 3 changed files with 178 additions and 60 deletions.
9 changes: 6 additions & 3 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -719,6 +719,8 @@ struct TDICOMdata clear_dicom_data() {
d.echoTrainLength = 0;
d.phaseFieldofView = 0.0;
d.dwellTime = 0;
d.protocolBlockStartGE = 0;
d.protocolBlockLengthGE = 0;
d.phaseEncodingSteps = 0;
d.coilNum = 0;
d.accelFactPE = 0.0;
Expand Down Expand Up @@ -3444,7 +3446,7 @@ double TE = 0.0; //most recent echo time recorded
uint32_t groupElement;
long lPos = 0;
bool isPhilipsDerived = false;
bool isPhilipsDiffusion = false;
//bool isPhilipsDiffusion = false;
if (isPart10prefix) { //for part 10 files, skip preamble and prefix
lPos = 128+4; //4-byte signature starts at 128
groupElement = buffer[lPos] | (buffer[lPos+1] << 8) | (buffer[lPos+2] << 16) | (buffer[lPos+3] << 24);
Expand Down Expand Up @@ -4072,8 +4074,9 @@ double TE = 0.0; //most recent echo time recorded
break;
case kProtocolDataBlockGE :
if (d.manufacturer != kMANUFACTURER_GE) break;
//printError("ProtocolDataBlockGE to do %d %d %2x%2x\n", lPos, lLength, (uint8_t)buffer[lPos], (uint8_t)buffer[lPos+1]);
//readProtocolDataBlockGE(&buffer[lPos], lLength, &d.CSA, isVerbose); //, dti4D);
d.protocolBlockLengthGE = dcmInt(lLength,&buffer[lPos],d.isLittleEndian);
d.protocolBlockStartGE = lPos+lFileOffset+4;
//printError("ProtocolDataBlockGE %d @ %d\n", d.protocolBlockLengthGE, d.protocolBlockStartGE);
break;
case kDoseCalibrationFactor :
d.doseCalibrationFactor = dcmStrFloat(lLength, &buffer[lPos]);
Expand Down
4 changes: 2 additions & 2 deletions console/nii_dicom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ extern "C" {
#define kCCsuf " CompilerNA" //unknown compiler!
#endif

#define kDCMvers "v1.0.20180307" kDCMsuf kCCsuf
#define kDCMvers "v1.0.20180325" kDCMsuf kCCsuf

static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
static const int kMaxDTI4D = 4096; //maximum number of DTI directions for 4D (Philips) images, also maximum number of 3D slices for Philips 3D and 4D images
Expand Down Expand Up @@ -127,7 +127,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
//numberOfDynamicScans, patientPositionNumPhilips
//patientPositionSequentialRepeats,patientPositionRepeats,
//maxGradDynVol, gradDynVol,
int modality, dwellTime, effectiveEchoSpacingGE, phaseEncodingLines, phaseEncodingSteps, echoTrainLength, coilNum, echoNum, sliceOrient, manufacturer, converted2NII, acquNum, imageNum, imageStart, imageBytes, bitsStored, bitsAllocated, samplesPerPixel,locationsInAcquisition, compressionScheme;
int protocolBlockStartGE, protocolBlockLengthGE, modality, dwellTime, effectiveEchoSpacingGE, phaseEncodingLines, phaseEncodingSteps, echoTrainLength, coilNum, echoNum, sliceOrient, manufacturer, converted2NII, acquNum, imageNum, imageStart, imageBytes, bitsStored, bitsAllocated, samplesPerPixel,locationsInAcquisition, compressionScheme;
float patientWeight, zSpacing, zThick, pixelBandwidth, SAR, phaseFieldofView, accelFactPE, flipAngle, fieldStrength, TE, TI, TR, intenScale, intenIntercept, intenScalePhilips, gantryTilt, lastScanLoc, angulation[4];
float orient[7], patientPosition[4], patientPositionLast[4], xyzMM[4], stackOffcentre[4];
float radionuclidePositronFraction, radionuclideTotalDose, radionuclideHalfLife, doseCalibrationFactor; //PET ISOTOPE MODULE ATTRIBUTES (C.8-57)
Expand Down
225 changes: 170 additions & 55 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -407,6 +407,28 @@ const void * memmem(const char *l, size_t l_len, const char *s, size_t s_len) {
//n.b. memchr returns "const void *" not "void *" for Windows C++ https://msdn.microsoft.com/en-us/library/d7zdhf37.aspx
#endif //for systems without memmem

/*int readKeyX(const char * key, char * buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
int ret = 0;
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
printWarning("<><><>\n");
if (!keyPos) return 0;
printWarning("<><> %d\n", strlen(keyPos));
int i = (int)strlen(key);
int numDigits = 0;
while( ( i< remLength) && (numDigits >= 0) ) {
printMessage("%c", keyPos[i]);
if( keyPos[i] >= '0' && keyPos[i] <= '9' ) {
ret = (10 * ret) + keyPos[i] - '0';
numDigits ++;
} else if (numDigits > 0)
numDigits = -1;
i++;
}
printWarning("---> %d\n", ret);
return ret;
} //readKey()
*/

int readKey(const char * key, char * buffer, int remLength) { //look for text key in binary data stream, return subsequent integer value
int ret = 0;
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
Expand Down Expand Up @@ -609,6 +631,81 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
} // siemensCsaAscii()
#endif //myReadAsciiCsa()

#ifndef myDisableMiniZ
#define myReadGeProtocolBlock
#endif
#ifdef myReadGeProtocolBlock
int geProtocolBlock(const char * filename, int geOffset, int geLength, int isVerbose, int* sliceOrder, int* viewOrder) {
*sliceOrder = 0;
*viewOrder = 0;
int ret = EXIT_FAILURE;
if ((geOffset < 0) || (geLength < 20)) return ret;
FILE * pFile = fopen ( filename, "rb" );
if(pFile==NULL) return ret;
fseek (pFile , 0 , SEEK_END);
long lSize = ftell (pFile);
if (lSize < (geOffset+geLength)) {
fclose (pFile);
return ret;
}
fseek(pFile, geOffset, SEEK_SET);
mz_uint8 * pCmp = (mz_uint8*) malloc (geLength);
if(pCmp == NULL) return ret;
size_t result = fread (pCmp,1,geLength,pFile);
if ((int)result != geLength) return ret;
int cmpSz = geLength;
//http://www.forensicswiki.org/wiki/Gzip
// always little endia! http://www.onicos.com/staff/iz/formats/gzip.html
if (cmpSz < 20) return ret;
if ((pCmp[0] != 31) || (pCmp[1] != 139) || (pCmp[2] != 8)) return ret; //check signature and deflate algorithm
uint8_t flags = pCmp[3];
bool isFNAME = ((flags & 0x08) == 0x08);
bool isFCOMMENT = ((flags & 0x10) == 0x10);
size_t hdrSz = 10;
if (isFNAME) {//skip null-terminated string FNAME
for (hdrSz = hdrSz; hdrSz < cmpSz; hdrSz++)
if (pCmp[hdrSz] == 0) break;
hdrSz++;
}
if (isFCOMMENT) {//skip null-terminated string COMMENT
for (hdrSz = hdrSz; hdrSz < cmpSz; hdrSz++)
if (pCmp[hdrSz] == 0) break;
hdrSz++;
}
size_t unCmpSz = ((size_t)pCmp[cmpSz-4])+((size_t)pCmp[cmpSz-3] << 8)+((size_t)pCmp[cmpSz-2] << 16)+((size_t)pCmp[cmpSz-1] << 24);
//printf(">> %d %d %zu %zu %zu\n", isFNAME, isFCOMMENT, cmpSz, unCmpSz, hdrSz);

z_stream s;
memset (&s, 0, sizeof (z_stream));
inflateInit2(&s, -MZ_DEFAULT_WINDOW_BITS);
mz_uint8 *pUnCmp = (mz_uint8 *)malloc((size_t)unCmpSz);
s.avail_out = unCmpSz;
s.next_in = pCmp+ hdrSz;
s.avail_in = cmpSz-hdrSz-8;
s.next_out = (uint8_t *) pUnCmp;
ret = mz_inflate(&s, MZ_SYNC_FLUSH);
if (ret != MZ_STREAM_END) {
free(pUnCmp);
return EXIT_FAILURE;
}
//https://groups.google.com/forum/#!msg/comp.protocols.dicom/mxnCkv8A-i4/W_uc6SxLwHQJ
// DISCOVERY MR750 / 24\MX\MR Software release:DV24.0_R01_1344.a) are now storing an XML file
// <?xml version="1.0" encoding="UTF-8"?>
if ((pUnCmp[0] == '<') && (pUnCmp[1] == '?'))
printWarning("New XML-based GE Protocol Block is not yet supported: please report issue on dcm2niix Github page\n");
char keyStrSO[] = "SLICEORDER";
*sliceOrder = readKey(keyStrSO, (char *) pUnCmp, unCmpSz);
char keyStrVO[] = "VIEWORDER"; //"MATRIXX";
*viewOrder = readKey(keyStrVO, (char *) pUnCmp, unCmpSz);
if (isVerbose > 1) {
printMessage("GE Protocol Block %s bytes %d compressed, %d uncompressed @ %d\n", filename, geLength, unCmpSz, geOffset);
printMessage(" ViewOrder %d SliceOrder %d\n", *viewOrder, *sliceOrder);
printMessage("%s\n", pUnCmp);
}
free(pUnCmp);
return EXIT_SUCCESS;
}
#endif //myReadGeProtocolBlock()
void json_Str(FILE *fp, const char *sLabel, char *sVal) {
if (strlen(sVal) < 1) return;
//fprintf(fp, sLabel, sVal );
Expand Down Expand Up @@ -792,6 +889,17 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
float pf = 1.0f; //partial fourier
bool interp = false; //2D interpolation
float phaseOversampling = 0.0;
int viewOrderGE = -1;
#ifdef myReadGeProtocolBlock
int sliceOrderGE = -1;
if ((d.manufacturer == kMANUFACTURER_GE) && (d.protocolBlockStartGE> 0) && (d.protocolBlockLengthGE > 19)) {
printWarning("Using GE Protocol Data Block for BIDS data (beware: new feature)\n");
int ok = geProtocolBlock(filename, d.protocolBlockStartGE, d.protocolBlockLengthGE, opts.isVerbose, &sliceOrderGE, &viewOrderGE);
if (ok != EXIT_SUCCESS)
printWarning("Unable to decode GE protocol block\n");
printMessage(" ViewOrder %d SliceOrder %d\n", viewOrderGE, sliceOrderGE);
} //read protocolBlockGE
#endif
#ifdef myReadAsciiCsa
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.SeriesHeader_offset > 0) && (d.CSA.SeriesHeader_length > 0)) {
int baseResolution, interpInt, partialFourier, echoSpacing, parallelReductionFactorInPlane;
Expand Down Expand Up @@ -913,7 +1021,10 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.dwellTime > 0))
fprintf(fp, "\t\"DwellTime\": %g,\n", d.dwellTime * 1E-9);
// Phase encoding polarity
if (((d.phaseEncodingRC == 'R') || (d.phaseEncodingRC == 'C')) && (!d.is3DAcq) && ((d.CSA.phaseEncodingDirectionPositive == 1) || (d.CSA.phaseEncodingDirectionPositive == 0))) {
int phPos = d.CSA.phaseEncodingDirectionPositive;
if (viewOrderGE > -1)
phPos = viewOrderGE;
if (((d.phaseEncodingRC == 'R') || (d.phaseEncodingRC == 'C')) && (!d.is3DAcq) && (phPos >= 0)) {
if (d.phaseEncodingRC == 'C') //Values should be "R"ow, "C"olumn or "?"Unknown
fprintf(fp, "\t\"PhaseEncodingDirection\": \"j");
else if (d.phaseEncodingRC == 'R')
Expand All @@ -924,17 +1035,40 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
//However, DICOM and NIfTI are reversed in the j (ROW) direction
//Equivalent to dicm2nii's "if flp(iPhase), phPos = ~phPos; end"
//for samples see https://github.com/rordenlab/dcm2niix/issues/125
if (d.CSA.phaseEncodingDirectionPositive == -1)
if (phPos < 0)
fprintf(fp, "?"); //unknown
else if ((d.CSA.phaseEncodingDirectionPositive == 0) && (d.phaseEncodingRC != 'C'))
else if ((phPos == 0) && (d.phaseEncodingRC != 'C'))
fprintf(fp, "-");
else if ((d.phaseEncodingRC == 'C') && (d.CSA.phaseEncodingDirectionPositive == 1) && (opts.isFlipY))
else if ((d.phaseEncodingRC == 'C') && (phPos == 1) && (opts.isFlipY))
fprintf(fp, "-");
else if ((d.phaseEncodingRC == 'C') && (d.CSA.phaseEncodingDirectionPositive == 0) && (!opts.isFlipY))
else if ((d.phaseEncodingRC == 'C') && (phPos == 0) && (!opts.isFlipY))
fprintf(fp, "-");
fprintf(fp, "\",\n");
} //only save PhaseEncodingDirection if BOTH direction and POLARITY are known
// Slice Timing
// Slice Timing GE
if ((viewOrderGE > -1) && (h->dim[3] > 1) && (h->dim[4] > 1) && (d.TR > 0)) { //
//Warning: not correct for multiband sequences... not sure how these are stored
//Warning: will not create correct times for sparse acquisitions where DelayTimeInTR > 0
float t = d.TR/ (float)h->dim[3] ;
fprintf(fp, "\t\"SliceTiming\": [\n");
if (viewOrderGE == 1) {//interleaved ascending
for (int i = 0; i < h->dim[3]; i++) {
if (i != 0)
fprintf(fp, ",\n");
int s = (i / 2);
if ((i % 2) != 0) s += (h->dim[3]+1)/2;
fprintf(fp, "\t\t%g", (float) s * t / 1000.0 );
}
} else { //sequential ascending
for (int i = 0; i < h->dim[3]; i++) {
if (i != 0)
fprintf(fp, ",\n");
fprintf(fp, "\t\t%g", (float) i * t / 1000.0 );
}
}
fprintf(fp, "\t],\n");
}
//Slice Timing Siemens
if (d.CSA.sliceTiming[0] >= 0.0) {
fprintf(fp, "\t\"SliceTiming\": [\n");
if (d.CSA.protocolSliceNumber1 > 1) {
Expand Down Expand Up @@ -2337,7 +2471,7 @@ void checkSliceTiming(struct TDICOMdata * d, struct TDICOMdata * d1) {
printMessage("CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range %g..%g, TR=%gms)\n", minT, maxT, d->TR);
}//checkSliceTiming

int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D, int vol) {
int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D, int segVol) {
bool iVaries = intensityScaleVaries(nConvert,dcmSort,dcmList);
float *sliceMMarray = NULL; //only used if slices are not equidistant
uint64_t indx = dcmSort[0].indx;
Expand Down Expand Up @@ -2448,7 +2582,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
hdr0.dim[5] = nConvert;
hdr0.dim[0] = 5;
}

/*if (nConvert > 1) { //next determine if TR is true time between volumes
double startTime = dcmList[indx0].acquisitionTime;
double endTime = startTime;
Expand Down Expand Up @@ -2479,27 +2612,33 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
free(img);
}
}
if ((vol >= 0) && (hdr0.dim[4] > 1) && (vol < hdr0.dim[4])) {
if ((segVol >= 0) && (hdr0.dim[4] > 1)) {
int inVol = hdr0.dim[4];
int nVol = 0;
for (int v = 0; v < inVol; v++)
if (dti4D->gradDynVol[v] == segVol)
nVol ++;
if (nVol < 1) {
printError("Series %d does not exist\n", segVol);
return EXIT_FAILURE;
}
size_t imgsz4D = imgsz;
if (vol < 2)
if (nVol < 2)
hdr0.dim[0] = 3; //3D
int inVol = hdr0.dim[4];
hdr0.dim[4] = 1;
size_t imgsz3D = nii_ImgBytes(hdr0);
unsigned char *img4D = (unsigned char *)malloc(imgsz4D);
memcpy(&img4D[0], &imgM[0], imgsz4D);
free(imgM);
imgM = (unsigned char *)malloc(imgsz3D * vol);
imgM = (unsigned char *)malloc(imgsz3D * nVol);
int outVol = 0;
for (int v = 0; v < inVol; v++) {
//dti4D cxc
if ((dti4D->gradDynVol[v] != 0) && (outVol < vol)) {
//printError("cxc -> %d %d %d\n", v, v * imgsz3D, imgsz4D);
if ((dti4D->gradDynVol[v] == segVol) && (outVol < nVol)) {
memcpy(&imgM[outVol * imgsz3D], &img4D[v * imgsz3D], imgsz3D);
outVol ++;
}
}
hdr0.dim[4] = vol;
hdr0.dim[4] = nVol;
imgsz = nii_ImgBytes(hdr0);
free(img4D);
saveAs3D = false;
Expand All @@ -2517,8 +2656,8 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
for(int i = 0; i < nConvert; ++i)
dcmList[dcmSort[i].indx].converted2NII = 1;
if (opts.numSeries < 0) { //report series number but do not convert
if (vol >= 0)
printMessage("\t%ld.%d\t%s\n", dcmList[dcmSort[0].indx].seriesNum, vol, pathoutname);
if (segVol >= 0)
printMessage("\t%ld.%d\t%s\n", dcmList[dcmSort[0].indx].seriesNum, segVol-1, pathoutname);
else
printMessage("\t%ld\t%s\n", dcmList[dcmSort[0].indx].seriesNum, pathoutname);
printMessage(" %s\n",nameList->str[dcmSort[0].indx]);
Expand All @@ -2542,8 +2681,8 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
if (opts.numSeries > 0) {
int i = 0;
float seriesNum = (float) dcmList[dcmSort[0].indx].seriesNum;
if (vol > 0)
seriesNum = seriesNum + (float) vol / 10.0; //n.b. we will have problems if vol > 9. However, 9 distinct TEs/scalings/PhaseMag seems unlikely
if (segVol > 0)
seriesNum = seriesNum + ((float) segVol - 1.0) / 10.0; //n.b. we will have problems if segVol > 9. However, 9 distinct TEs/scalings/PhaseMag seems unlikely
for (; i < opts.numSeries; i++) {
if (isSameFloatGE(opts.seriesNumber[i], seriesNum)) {
//if (opts.seriesNumber[i] == dcmList[dcmSort[0].indx].seriesNum) {
Expand Down Expand Up @@ -2642,9 +2781,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
return returnCode;//EXIT_SUCCESS;
}// saveDcm2NiiCore()

//int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D) {
// return saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4D, -1);
//}
int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmList[], struct TSearchList *nameList, struct TDCMopts opts, struct TDTI4D *dti4D) {
//this wrapper does nothing if all the images share the same echo time and scale
// however, it segments images when these properties vary
Expand Down Expand Up @@ -2673,57 +2809,36 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis
}
if (echo > 1) dcmList[indx].isMultiEcho = true;
//check for repeated volumes
int seriesNum[kMaxDTI4D];
int series = 1;
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
seriesNum[i] = 0;
seriesNum[0] = 1;
dti4D->gradDynVol[i] = 0;
dti4D->gradDynVol[0] = 1;
for (int i = 1; i < dcmList[indx].xyzDim[4]; i++) {
for (int j = 0; j < i; j++)
if ((dti4D->intenIntercept[i] == dti4D->intenIntercept[j]) && (dti4D->intenScale[i] == dti4D->intenScale[j]) && (dti4D->isPhase[i] == dti4D->isPhase[j]) && (dti4D->TE[i] == dti4D->TE[j])) seriesNum[i] = seriesNum[j];
if (seriesNum[i] == 0) {
if ((dti4D->intenIntercept[i] == dti4D->intenIntercept[j]) && (dti4D->intenScale[i] == dti4D->intenScale[j]) && (dti4D->isPhase[i] == dti4D->isPhase[j]) && (dti4D->TE[i] == dti4D->TE[j]))
dti4D->gradDynVol[i] = dti4D->gradDynVol[j];
if (dti4D->gradDynVol[i] == 0) {
series++;
seriesNum[i] = series;
dti4D->gradDynVol[i] = series;
}
}
for (int s = 1; s <= series; s++) {
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
dti4D->gradDynVol[i] = 0;
int nVol = 0;
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
if (seriesNum[i] == s) {
dti4D->gradDynVol[i] = 1;
nVol ++;
if (dti4D->gradDynVol[i] == s) {
//dti4D->gradDynVol[i] = s;
//nVol ++;
dcmList[indx].TE = dti4D->TE[i];
dcmList[indx].intenScale = dti4D->intenScale[i];
dcmList[indx].intenIntercept = dti4D->intenIntercept[i];
dcmList[indx].isHasPhase = dti4D->isPhase[i];
dcmList[indx].intenScalePhilips = dti4D->intenScalePhilips[i];
dcmList[indx].isHasMagnitude = false;
dcmList[indx].echoNum = echoNum[i];
//dcmList[indx].gradDynVol = dti4D->gradDynVol[i];
break;
}
//printError("cxc files %d %d %g\n", nVol,echo, dcmList[indx].TE);
int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4D, nVol);
int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4D, s);
if (ret2 != EXIT_SUCCESS) ret = ret2; //return EXIT_SUCCESS only if ALL are successful
}
//
//printError("cxc files %d %d %g\n", series,echo, dcmList[indx].TE);
//return ret;

/*for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) {
printMessage("volume %d TE=%g Slope=%g Inter=%g Phase=%d\n", i, dti4D->TE[i], dti4D->intenScale[i], dti4D->intenIntercept[i], dti4D->isPhase[i] );
dcmList[indx].TE = dti4D->TE[i];
dcmList[indx].intenScale = dti4D->intenScale[i];
dcmList[indx].intenIntercept = dti4D->intenIntercept[i];
dcmList[indx].isHasPhase = dti4D->isPhase[i];
dcmList[indx].intenScalePhilips = dti4D->intenScalePhilips[i];
dcmList[indx].isHasMagnitude = false;
dcmList[indx].echoNum = echoNum[i];
dcmList[indx].gradDynVol = dti4D->gradDynVol[i];
int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4D, i);
if (ret2 != EXIT_SUCCESS) ret = ret2; //return EXIT_SUCCESS only if ALL are successful
}*/
return ret;
}// saveDcm2Nii()

Expand Down

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