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@xjqian & @mharms tags BaseResolution, PhaseResolution, VendorReporte…
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…dEchoSpacing, DerivedVendorReportedEchoSpacing #130
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@neurolabusc
neurolabusc committed Sep 21, 2017
1 parent f0220bf commit d48e359
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Showing 2 changed files with 15 additions and 16 deletions.
10 changes: 0 additions & 10 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -619,16 +619,6 @@ int headerDcm2Nii2(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_hea
sprintf(dtxt, ";phase=%d", d.CSA.phaseEncodingDirectionPositive);
strcat(txt,dtxt);
}
if ((d.CSA.bandwidthPerPixelPhaseEncode > 0) && ((d.phaseEncodingRC =='C') || (d.phaseEncodingRC =='R'))) {
float dwellTime = 0;
if (d.phaseEncodingRC =='C')
dwellTime = 1000/d.CSA.bandwidthPerPixelPhaseEncode/h->dim[2];
else
dwellTime = 1000/d.CSA.bandwidthPerPixelPhaseEncode/h->dim[1];
char dtxt[1024] = {""};
sprintf(dtxt, ";dwell=%.3f", dwellTime);
strcat(txt,dtxt);
}
//from dicm2nii 20151117 InPlanePhaseEncodingDirection
if (d.phaseEncodingRC =='R')
h->dim_info = (3 << 4) + (1 << 2) + 2;
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21 changes: 15 additions & 6 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -490,13 +490,15 @@ int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
return 0;
} // phoenixOffsetCSASeriesHeader()

void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float* phaseOversampling, int* interp, int* partialFourier, int* echoSpacing, int* parallelReductionFactorInPlane, char* coilID, char* consistencyInfo, char* coilElements, char* pulseSequenceDetails, char* fmriExternalInfo) {
void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float* phaseOversampling, float* phaseResolution, int* baseResolution, int* interp, int* partialFourier, int* echoSpacing, int* parallelReductionFactorInPlane, char* coilID, char* consistencyInfo, char* coilElements, char* pulseSequenceDetails, char* fmriExternalInfo) {
//reads ASCII portion of CSASeriesHeaderInfo and returns lEchoTrainDuration or lEchoSpacing value
// returns 0 if no value found
*phaseOversampling = 0.0;
*phaseResolution = 0.0;
*baseResolution = 0;
*interp = 0;
*partialFourier = 0;
*echoSpacing = 0;
*phaseOversampling = 0.0;
strcpy(coilID, "");
strcpy(consistencyInfo, "");
strcpy(coilElements, "");
Expand Down Expand Up @@ -533,6 +535,8 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
csaLengthTrim = (int)(keyPosEnd - keyPos);
char keyStrES[] = "sFastImaging.lEchoSpacing";
*echoSpacing = readKey(keyStrES, keyPos, csaLengthTrim);
char keyStrBase[] = "sKSpace.lBaseResolution";
*baseResolution = readKey(keyStrBase, keyPos, csaLengthTrim);
char keyStrInterp[] = "sKSpace.uc2DInterpolation";
*interp = readKey(keyStrInterp, keyPos, csaLengthTrim);
char keyStrPF[] = "sKSpace.ucPhasePartialFourier";
Expand All @@ -553,6 +557,8 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
readKeyStr(keyStrSeq, keyPos, csaLengthTrim, pulseSequenceDetails);
char keyStrExt[] = "FmriExternalInfo";
readKeyStr(keyStrExt, keyPos, csaLengthTrim, fmriExternalInfo);
char keyStrPhase[] = "sKSpace.dPhaseResolution";
*phaseResolution = readKeyFloat(keyStrPhase, keyPos, csaLengthTrim);
char keyStrOver[] = "sKSpace.dPhaseOversamplingForDialog";
*phaseOversampling = readKeyFloat(keyStrOver, keyPos, csaLengthTrim);
}
Expand Down Expand Up @@ -730,9 +736,10 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
float phaseOversampling = 0.0;
#ifdef myReadAsciiCsa
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.SeriesHeader_offset > 0) && (d.CSA.SeriesHeader_length > 0)) {
int interpInt, partialFourier, echoSpacing, parallelReductionFactorInPlane;
int baseResolution, interpInt, partialFourier, echoSpacing, parallelReductionFactorInPlane;
float phaseResolution;
char fmriExternalInfo[kDICOMStr], coilID[kDICOMStr], consistencyInfo[kDICOMStr], coilElements[kDICOMStr], pulseSequenceDetails[kDICOMStr];
siemensCsaAscii(filename, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, &phaseOversampling, &interpInt, &partialFourier, &echoSpacing, &parallelReductionFactorInPlane, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo);
siemensCsaAscii(filename, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, &phaseOversampling, &phaseResolution, &baseResolution, &interpInt, &partialFourier, &echoSpacing, &parallelReductionFactorInPlane, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo);
if (partialFourier > 0) {
//https://github.com/ismrmrd/siemens_to_ismrmrd/blob/master/parameter_maps/IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl
if (partialFourier == 1) pf = 0.5; // 4/8
Expand All @@ -745,8 +752,10 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
interp = true;
fprintf(fp, "\t\"Interpolation2D\": %d,\n", interp);
}
if (baseResolution > 0) fprintf(fp, "\t\"BaseResolution\": %d,\n", baseResolution );
json_Float(fp, "\t\"PhaseResolution\": %g,\n", phaseResolution);
json_Float(fp, "\t\"PhaseOversampling\": %g,\n", phaseOversampling); //usec -> sec
json_Float(fp, "\t\"EchoSpacing\": %g,\n", echoSpacing / 1000000.0); //usec -> sec
json_Float(fp, "\t\"VendorReportedEchoSpacing\": %g,\n", echoSpacing / 1000000.0); //usec -> sec
//ETD and epiFactor not useful/reliable https://github.com/rordenlab/dcm2niix/issues/127
//if (echoTrainDuration > 0) fprintf(fp, "\t\"EchoTrainDuration\": %g,\n", echoTrainDuration / 1000000.0); //usec -> sec
//if (epiFactor > 0) fprintf(fp, "\t\"EPIFactor\": %d,\n", epiFactor);
Expand Down Expand Up @@ -804,7 +813,7 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
float trueEchoSpacingCalc = 0.0;
trueEchoSpacingCalc = bandwidthPerPixelPhaseEncode * trueESfactor * d.phaseEncodingLines;
if (trueEchoSpacingCalc != 0) trueEchoSpacingCalc = 1/trueEchoSpacingCalc;
json_Float(fp, "\t\"TrueEchoSpacingCalc\": %g,\n", trueEchoSpacingCalc);
json_Float(fp, "\t\"DerivedVendorReportedEchoSpacing\": %g,\n", trueEchoSpacingCalc);

//TotalReadOutTime: Really should be called "EffectiveReadOutTime", by analogy with "EffectiveEchoSpacing".
// But BIDS spec calls it "TotalReadOutTime".
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