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New stable release (v1.0.20201102)
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@neurolabusc
neurolabusc committed Nov 3, 2020
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -25,7 +25,7 @@ DICOM provides many ways to store/compress image data, known as [transfer syntax

## Versions

[See the VERSIONS.md file for details on releases](./VERSIONS.md).
[See releases](https://github.com/rordenlab/dcm2niix/releases) for recent release notes. [See the VERSIONS.md file for details on earlier releases](./VERSIONS.md).

## Running

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8 changes: 4 additions & 4 deletions console/main_console.cpp
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Expand Up @@ -374,13 +374,13 @@ int main(int argc, const char * argv[])
opts.isIgnoreDerivedAnd2D = false;
else
opts.isIgnoreDerivedAnd2D = true;
/*} else if ((argv[i][1] == 'j') && ((i+1) < argc)) {
} else if ((argv[i][1] == 'j') && ((i+1) < argc)) {
i++;
if (invalidParam(i, argv)) return 0;
if ((argv[i][0] == 'y') || (argv[i][0] == 'Y') || (argv[i][0] == '1')) {
opts.isIgnorex0021x105E = true;
printf("undocumented '-j y' ignores slice timing from 0021,105E\n");
}*/
opts.isTestx0021x105E = true;
printf("undocumented '-j y' compares GE slice timing from 0021,105E\n");
}
} else if ((argv[i][1] == 'l') && ((i+1) < argc)) {
i++;
if (invalidParam(i, argv)) return 0;
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2 changes: 1 addition & 1 deletion console/nii_dicom.cpp
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Expand Up @@ -7014,7 +7014,7 @@ if (d.isHasPhase)
dti4D->S[i].V[2] = dcmDim[j+(i * d.xyzDim[3])].V[2];
dti4D->S[i].V[3] = dcmDim[j+(i * d.xyzDim[3])].V[3];
//printf("te=\t%g\tscl=\t%g\tintercept=\t%g\n",dti4D->TE[i], dti4D->intenScale[i],dti4D->intenIntercept[i]);
if (dti4D->TE[i] != d.TE) isTEvaries = true;
if ((!isSameFloatGE(dti4D->TE[i],0.0)) && (dti4D->TE[i] != d.TE)) isTEvaries = true;
if (dti4D->isPhase[i] != isPhase) d.isScaleOrTEVaries = true;
if (dti4D->triggerDelayTime[i] != d.triggerDelayTime) d.isScaleOrTEVaries = true;
if (dti4D->isReal[i] != isReal) d.isScaleOrTEVaries = true;
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2 changes: 1 addition & 1 deletion console/nii_dicom.h
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Expand Up @@ -50,7 +50,7 @@ extern "C" {
#define kCPUsuf " " //unknown CPU
#endif

#define kDCMdate "v1.0.20201030"
#define kDCMdate "v1.0.20201102"
#define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf

static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
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163 changes: 99 additions & 64 deletions console/nii_dicom_batch.cpp
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Expand Up @@ -2741,7 +2741,17 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt
strcat (newdir,ch);
}
}
//printMessage("path='%s' name='%s'\n", pathoutname, outname);
//remove redundant underscores
int len = strlen(outname);
int outpos = 0;
for (int inpos = 0; inpos < len; inpos ++) {
if ((outpos > 0) && (outname[inpos] == '_') && (outname[outpos-1] == '_'))
continue;
outname[outpos] = outname[inpos];
outpos++;
}
outname[outpos] = 0;
//printMessage("path='%s' name='%s'\n", pathoutname, outname);
//make sure outname is unique
strcat (baseoutname,outname);
char pathoutname[2048] = {""};
Expand Down Expand Up @@ -4663,26 +4673,50 @@ void readSoftwareVersionsGE(char softwareVersionsGE[], int verbose,char geVersio
}
} // readSoftwareVersionsGE()

void sliceTimingGE_Testx0021x105E(struct TDICOMdata * d, struct TDCMopts opts, struct nifti_1_header * hdr, struct TDCMsort *dcmSort,struct TDICOMdata *dcmList) {
if ((!opts.isTestx0021x105E) || (hdr->dim[3] < 2) || (hdr->dim[4] < 1)) return;
if (d->rtia_timerGE <= 0.0) {
printMessage("DICOM images do not report RTIA timer(0021,105E)\n");
return;
}
int j = hdr->dim[3];
float sliceTiming[kMaxEPI3D];
float mn = INFINITY;
for (int v = 0; v < hdr->dim[3]; v++) {
sliceTiming[v] = dcmList[dcmSort[v+j].indx].rtia_timerGE;
mn = min(mn, sliceTiming[v]);
}
if (mn < 0.0) return;
float mxErr = 0.0;
for (int v = 0; v < hdr->dim[3]; v++) {
sliceTiming[v] = (sliceTiming[v] - mn) * 1000.0; //subtract offset, convert sec -> ms
mxErr = max(mxErr, fabs(sliceTiming[v] - d->CSA.sliceTiming[v]));
}
printMessage("Slice Timing Error between calculated and RTIA timer(0021,105E): %gms\n", mxErr);
if ((mxErr < 1.0) && (opts.isVerbose < 1)) return;
for (int v = 0; v < hdr->dim[3]; v++)
printMessage("\t%g\t%g\n", d->CSA.sliceTiming[v], sliceTiming[v]);
}

void sliceTimingGE(struct TDICOMdata * d, int verbose, int nSL, const char * filename, struct TDCMopts opts) {
void sliceTimingGE(struct TDICOMdata * d, const char * filename, struct TDCMopts opts, struct nifti_1_header * hdr, struct TDCMsort *dcmSort,struct TDICOMdata *dcmList) {
//we can often read GE slice timing from TriggerTime (0018,1060) or RTIA Timer (0021,105E)
// if both of these methods fail, we can often guess based on slice order stored in the Private Protocol Data Block (0025,101B)
// this is referred to as "rescue" as we only know the TR, not the TA. So assumes continuous scans with no gap
if ((d->is3DAcq) || (d->isLocalizer)) return; //no need for slice times
if (nSL < 2) return;
if ((d->is3DAcq) || (d->isLocalizer) || (hdr->dim[4] < 2)) return; //no need for slice times
if (hdr->dim[3] < 2) return;
if (d->manufacturer != kMANUFACTURER_GE) return;
//start version check:
float geMajorVersion = 0;
int geMajorVersionInt = 0, geMinorVersionInt = 0, geReleaseVersionInt = 0;
char geVersionPrefix[2] = " ";
bool is27r3 = false;
readSoftwareVersionsGE(d->softwareVersions, verbose, geVersionPrefix, &geMajorVersion, &geMajorVersionInt, &geMinorVersionInt, &geReleaseVersionInt, &is27r3);
//readSoftwareVersionsGE(&geMajorVersion);
int geMajorVersionInt = 0, geMinorVersionInt = 0, geReleaseVersionInt = 0;
char geVersionPrefix[2] = " ";
bool is27r3 = false;
readSoftwareVersionsGE(d->softwareVersions, opts.isVerbose, geVersionPrefix, &geMajorVersion, &geMajorVersionInt, &geMinorVersionInt, &geReleaseVersionInt, &is27r3);
//readSoftwareVersionsGE(&geMajorVersion);
/*
//used for oldSliceTimingGE
if (!opts.isIgnorex0021x105E) {
if ((geMajorVersionInt >= 28) && (d->CSA.sliceTiming[0] >= 0.0)) {
//if (verbose > 1)
//if (opts.isVerbose > 1)
printMessage("GEversion %.1f, slice timing from DICOM (0021,105E).\n", geMajorVersion);
return; //trust slice timings for versions > 27, see issue 336
}
Expand All @@ -4703,74 +4737,74 @@ void sliceTimingGE(struct TDICOMdata * d, int verbose, int nSL, const char * fil
float groupDelay = 0.0;
char ioptGE[3000] = "";
//printWarning("Using GE Protocol Data Block for BIDS data (beware: new feature)\n");
int ok = geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, verbose, &sliceOrderGE, &viewOrderGE, &mbAccel, &nSlices, &groupDelay, ioptGE);
int ok = geProtocolBlock(filename, d->protocolBlockStartGE, d->protocolBlockLengthGE, opts.isVerbose, &sliceOrderGE, &viewOrderGE, &mbAccel, &nSlices, &groupDelay, ioptGE);
if (ok != EXIT_SUCCESS) {
printWarning("Unable to estimate slice times: issue decoding GE protocol block.\n");
return;
}
mbAccel = max(mbAccel, 1);
if (nSlices != nSL) //redundant with locationsInAcquisition check?
printWarning("Missing DICOMs, number of slices estimated (%d) differs from Protocol Block (0025,101B) report (%d).\n", nSL, nSlices);
if (nSlices != hdr->dim[3]) //redundant with locationsInAcquisition check?
printWarning("Missing DICOMs, number of slices estimated (%d) differs from Protocol Block (0025,101B) report (%d).\n", hdr->dim[3], nSlices);
d->CSA.multiBandFactor = max(d->CSA.multiBandFactor, mbAccel);
bool isInterleaved = (sliceOrderGE != 0);
groupDelay *= 1000.0; //sec -> ms
//
// Estimate GE Slice Time only for EPI Multi-Phase (epi) or EPI fMRI/BrainWave (epiRT)
//
//
// Estimate GE Slice Time only for EPI Multi-Phase (epi) or EPI fMRI/BrainWave (epiRT)
//
// BrainWave (epiRT)
if ((d->epiVersionGE == 1) || (strstr(ioptGE,"FMRI") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
d->epiVersionGE = 1;
d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
if (!isSameFloatGE(groupDelay, d->groupDelay)) {
printWarning("With epiRT (i.e. FMRI option), Group delay reported in private tag (0043,107C = %g) and Protocol Block (0025,101B = %g) differ.\n", d->groupDelay, groupDelay);
}
}
// EPI Multi-Phase (epi)
else if ((d->epiVersionGE == 0) || (strstr(ioptGE,"MPh") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
d->epiVersionGE = 0;
d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
if (groupDelay > 0) {
d->TR += groupDelay;
d->groupDelay = groupDelay;
}
// EPI Multi-Phase (epi) with Variable Delays (Unsupported)
if (groupDelay < -0.5) {
printWarning("SliceTiming Unspported: GE Multi-Phase EPI with Variable Delays\n");
d->CSA.sliceTiming[0] = -1;
return;
}
}
// Diffusion (Unsupported)
else if ( (d->epiVersionGE == 2) || (d->internalepiVersionGE == 2) || (strstr(ioptGE,"DIFF") != NULL) ) {
printWarning("Unable to compute slice times for GE Diffusion\n");
d->CSA.sliceTiming[0] = -1.0;
return;
}
// Others (Unsupported)
else {
printWarning("Unable to compute slice times for this GE dataset\n");
d->CSA.sliceTiming[0] = -1.0;
if ((d->epiVersionGE == 1) || (strstr(ioptGE,"FMRI") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
d->epiVersionGE = 1;
d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
if (!isSameFloatGE(groupDelay, d->groupDelay))
printWarning("With epiRT (i.e. FMRI option), Group delay reported in private tag (0043,107C = %g) and Protocol Block (0025,101B = %g) differ.\n", d->groupDelay, groupDelay);
}
// EPI Multi-Phase (epi)
else if ((d->epiVersionGE == 0) || (strstr(ioptGE,"MPh") != NULL)) { //-1 = not epi, 0 = epi, 1 = epiRT
d->epiVersionGE = 0;
d->internalepiVersionGE = 1; // 'EPI'(gradient echo)/'EPI2'(spin echo)
if (groupDelay > 0) {
d->TR += groupDelay;
d->groupDelay = groupDelay;
}
// EPI Multi-Phase (epi) with Variable Delays (Unsupported)
if (groupDelay < -0.5) {
printWarning("SliceTiming Unspported: GE Multi-Phase EPI with Variable Delays\n");
d->CSA.sliceTiming[0] = -1;
return;
}
}
// Diffusion (Unsupported)
else if ( (d->epiVersionGE == 2) || (d->internalepiVersionGE == 2) || (strstr(ioptGE,"DIFF") != NULL) ) {
printWarning("Unable to compute slice times for GE Diffusion\n");
d->CSA.sliceTiming[0] = -1.0;
return;
}
if (verbose > 1) {
printMessage("GEiopt: %s, groupDelay (%g), internalepiVersionGE (%d), epiVersionGE(%d)\n", ioptGE, groupDelay, d->internalepiVersionGE, d->epiVersionGE);
printMessage("GEversion %s%.1f_R0%d, TRms %g, interleaved %d, multiband %d, groupdelayms %g\n", geVersionPrefix, geMajorVersion, geReleaseVersionInt, d->TR, isInterleaved, d->CSA.multiBandFactor, d->groupDelay);
}
sliceTimeGE(d, d->CSA.multiBandFactor, nSL, d->TR, isInterleaved, is27r3, d->groupDelay);
}
// Others (Unsupported)
else {
printWarning("Unable to compute slice times for this GE dataset\n");
d->CSA.sliceTiming[0] = -1.0;
return;
}
if (opts.isVerbose > 1) {
printMessage("GEiopt: %s, groupDelay (%g), internalepiVersionGE (%d), epiVersionGE(%d)\n", ioptGE, groupDelay, d->internalepiVersionGE, d->epiVersionGE);
printMessage("GEversion %s%.1f_R0%d, TRms %g, interleaved %d, multiband %d, groupdelayms %g\n", geVersionPrefix, geMajorVersion, geReleaseVersionInt, d->TR, isInterleaved, d->CSA.multiBandFactor, d->groupDelay);
}
sliceTimeGE(d, d->CSA.multiBandFactor, hdr->dim[3], d->TR, isInterleaved, is27r3, d->groupDelay);
sliceTimingGE_Testx0021x105E(d, opts, hdr, dcmSort, dcmList);
#endif
} //sliceTimingGE()

void reverseSliceTiming(struct TDICOMdata * d, int verbose, int nSL) {
void reverseSliceTiming(struct TDICOMdata * d, int verbose, int nSL) {
if ((d->CSA.protocolSliceNumber1 == 0) || ((d->CSA.protocolSliceNumber1 == 1))) return; //slices not flipped
if (d->is3DAcq) return; //no need for slice times
if (d->CSA.sliceTiming[0] < 0.0) return; //no slice times
if (nSL > kMaxEPI3D) return;
if (nSL < 2) return;
if (verbose)
printMessage("Slices were spatially flipped, so slice times are flipped\n");
d->CSA.protocolSliceNumber1 = 0;
float sliceTiming[kMaxEPI3D];
for (int i = 0; i < nSL; i++)
printMessage("Slices were spatially flipped, so slice times are flipped\n");
d->CSA.protocolSliceNumber1 = 0;
float sliceTiming[kMaxEPI3D];
for (int i = 0; i < nSL; i++)
sliceTiming[i] = d->CSA.sliceTiming[i];
for (int i = 0; i < nSL; i++)
d->CSA.sliceTiming[i] = sliceTiming[(nSL-1)-i];
Expand Down Expand Up @@ -4976,7 +5010,7 @@ int sliceTimingCore(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct
if ((dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_UIH) || (dcmList[dcmSort[0].indx].manufacturer == kMANUFACTURER_GE))
dcmList[dcmSort[0].indx].CSA.protocolSliceNumber1 = -1;
}
sliceTimingGE(d0, verbose, hdr->dim[3], filename, opts); //desperate attempts if conventional methods fail
sliceTimingGE(d0, filename, opts, hdr, dcmSort, dcmList);
reverseSliceTiming(d0, verbose, hdr->dim[3]);
return sliceDir;
} //sliceTiming()
Expand Down Expand Up @@ -5173,7 +5207,7 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc
}
}
//next options removed: features now thoroughly detected in nii_loadDir()
for (int i = 0; i < nConvert; i++) { //make sure 1st volume describes shared features
for (int i = 0; i < nConvert; i++) { //make sure 1st volume describes shared features
if (dcmList[dcmSort[i].indx].isHasOverlay) isHasOverlay = true;
if (dcmList[dcmSort[i].indx].isCoilVaries) dcmList[indx0].isCoilVaries = true;
if (dcmList[dcmSort[i].indx].isMultiEcho) dcmList[indx0].isMultiEcho = true;
Expand Down Expand Up @@ -6031,9 +6065,9 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt
#endif
if ((opts->isForceStackSameSeries == 1) || ((opts->isForceStackSameSeries == 2) && (d1.isXRay) )) {
// "isForceStackSameSeries == 2" will automatically stack CT scans but not MR
//if ((d1.TE != d2.TE) || (d1.echoNum != d2.echoNum))
if ((!(isSameFloat(d1.TE, d2.TE))) || (d1.echoNum != d2.echoNum))
*isMultiEcho = true;
//if (((!(isSameFloat(d1.TE, d2.TE))) || (d1.echoNum != d2.echoNum)) && (!d1.isXRay)) {
// *isMultiEcho = true;
//}
return true; //we will stack these images, even if they differ in the following attributes
}
if ((d1.isHasImaginary != d2.isHasImaginary) || (d1.isHasPhase != d2.isHasPhase) || ((d1.isHasReal != d2.isHasReal))) {
Expand Down Expand Up @@ -7137,6 +7171,7 @@ void setDefaultOpts (struct TDCMopts *opts, const char * argv[]) { //either "set
opts->isGz = false;
opts->isSaveNativeEndian = true;
opts->isAddNamePostFixes = true; //e.g. "_e2" added for second echo
opts->isTestx0021x105E = false; //GE test slice times stored in 0021,105E
opts->isSaveNRRD = false;
opts->isPipedGz = false; //e.g. pipe data directly to pigz instead of saving uncompressed to disk
opts->isSave3D = false;
Expand Down
2 changes: 1 addition & 1 deletion console/nii_dicom_batch.h
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Expand Up @@ -35,7 +35,7 @@ extern "C" {
#define MAX_NUM_SERIES 16

struct TDCMopts {
bool isAddNamePostFixes, isSaveNativeEndian, isSaveNRRD, isOneDirAtATime, isRenameNotConvert, isSave3D, isGz, isPipedGz, isFlipY, isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isForceOnsetTimes,isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackDCE, isRotate3DAcq, isCrop;
bool isTestx0021x105E, isAddNamePostFixes, isSaveNativeEndian, isSaveNRRD, isOneDirAtATime, isRenameNotConvert, isSave3D, isGz, isPipedGz, isFlipY, isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isForceOnsetTimes,isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackDCE, isRotate3DAcq, isCrop;
int isMaximize16BitRange, isForceStackSameSeries, nameConflictBehavior, isVerbose, isProgress, compressFlag, dirSearchDepth, gzLevel; //support for compressed data 0=none,
char filename[512], outdir[512], indir[512], pigzname[512], optsname[512], indirParent[512], imageComments[24];
double seriesNumber[MAX_NUM_SERIES]; //requires double must store -1 (report but do not convert) as well as seriesUidCrc (uint32)
Expand Down

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