From dd527d986c50bcc7fdd5980e6601382137c4d641 Mon Sep 17 00:00:00 2001 From: Chris Rorden Date: Sun, 25 Mar 2018 23:24:46 -0400 Subject: [PATCH] Improved GE support --- console/nii_dicom.cpp | 9 +- console/nii_dicom.h | 4 +- console/nii_dicom_batch.cpp | 225 +++++++++++++++++++++++++++--------- 3 files changed, 178 insertions(+), 60 deletions(-) diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp index 7d619903..93c5a8c1 100644 --- a/console/nii_dicom.cpp +++ b/console/nii_dicom.cpp @@ -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; @@ -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); @@ -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]); diff --git a/console/nii_dicom.h b/console/nii_dicom.h index 064c9d01..6fea7b85 100644 --- a/console/nii_dicom.h +++ b/console/nii_dicom.h @@ -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 @@ -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) diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp index bd782b5d..15144a0e 100644 --- a/console/nii_dicom_batch.cpp +++ b/console/nii_dicom_batch.cpp @@ -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)); @@ -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 + // + 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 ); @@ -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; @@ -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') @@ -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) { @@ -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; @@ -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; @@ -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; @@ -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]); @@ -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) { @@ -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 @@ -2673,27 +2809,24 @@ 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]; @@ -2701,29 +2834,11 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis 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()