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Include Siemens "WipMemBlock" in BIDS (@mharms, #127)
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@neurolabusc
neurolabusc committed Aug 18, 2018
1 parent 8e973b9 commit 664676a
Showing 1 changed file with 15 additions and 7 deletions.
22 changes: 15 additions & 7 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -458,7 +458,7 @@ void readKeyStr(const char * key, char * buffer, int remLength, char* outStr) {
tmpstr[1] = 0;
bool isQuote = false;
while( ( i < remLength) && (keyPos[i] != 0x0A) ) {
if ((isQuote) && (keyPos[i] != '"') && (outLen < kDICOMStr)) {
if ((isQuote) && (keyPos[i] != '"') && (outLen < kDICOMStrLarge)) {
tmpstr[0] = keyPos[i];
strcat (outStr, tmpstr);
outLen ++;
Expand Down Expand Up @@ -501,7 +501,7 @@ int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
return 0;
} // phoenixOffsetCSASeriesHeader()

void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float* delayTimeInTR, float* phaseOversampling, float* phaseResolution, float* txRefAmp, float* shimSetting, int* baseResolution, int* interp, int* partialFourier, int* echoSpacing, int* parallelReductionFactorInPlane, char* coilID, char* consistencyInfo, char* coilElements, char* pulseSequenceDetails, char* fmriExternalInfo, char * protocolName) {
void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float* delayTimeInTR, float* phaseOversampling, float* phaseResolution, float* txRefAmp, float* shimSetting, int* baseResolution, int* interp, int* partialFourier, int* echoSpacing, int* parallelReductionFactorInPlane, char* coilID, char* consistencyInfo, char* coilElements, char* pulseSequenceDetails, char* fmriExternalInfo, char* protocolName, char* wipMemBlock) {
//reads ASCII portion of CSASeriesHeaderInfo and returns lEchoTrainDuration or lEchoSpacing value
// returns 0 if no value found
*delayTimeInTR = 0.0;
Expand All @@ -519,6 +519,7 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
strcpy(coilElements, "");
strcpy(pulseSequenceDetails, "");
strcpy(fmriExternalInfo, "");
strcpy(wipMemBlock, "");
strcpy(protocolName, "");
if ((csaOffset < 0) || (csaLength < 8)) return;
FILE * pFile = fopen ( filename, "rb" );
Expand Down Expand Up @@ -547,10 +548,16 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
if (keyPos) {
//We could detect multi-echo MPRAGE here, e.g. "lContrasts = 4"- but ideally we want an earlier detection
csaLengthTrim -= (keyPos-bufferTrim);
//FmriExternalInfo listed AFTER AscConvEnd and uses different delimiter ||
// char keyStrExt[] = "FmriExternalInfo";
// readKeyStr(keyStrExt, keyPos, csaLengthTrim, fmriExternalInfo);
#define myCropAtAscConvEnd
#ifdef myCropAtAscConvEnd
char keyStrEnd[] = "### ASCCONV END";
char *keyPosEnd = (char *)memmem(keyPos, csaLengthTrim, keyStrEnd, strlen(keyStrEnd));
if ((keyPosEnd) && ((keyPosEnd - keyPos) < csaLengthTrim)) //ignore binary data at end
csaLengthTrim = (int)(keyPosEnd - keyPos);
#endif
char keyStrES[] = "sFastImaging.lEchoSpacing";
*echoSpacing = readKey(keyStrES, keyPos, csaLengthTrim);
char keyStrBase[] = "sKSpace.lBaseResolution";
Expand All @@ -573,8 +580,8 @@ void siemensCsaAscii(const char * filename, int csaOffset, int csaLength, float
readKeyStr(keyStrCS, keyPos, csaLengthTrim, coilElements);
char keyStrSeq[] = "tSequenceFileName";
readKeyStr(keyStrSeq, keyPos, csaLengthTrim, pulseSequenceDetails);
char keyStrExt[] = "FmriExternalInfo";
readKeyStr(keyStrExt, keyPos, csaLengthTrim, fmriExternalInfo);
char keyStrWipMemBlock[] = "sWipMemBlock.tFree";
readKeyStr(keyStrWipMemBlock, keyPos, csaLengthTrim, wipMemBlock);
char keyStrPn[] = "tProtocolName";
readKeyStr(keyStrPn, keyPos, csaLengthTrim, protocolName);
char keyStrDelay[] = "lDelayTimeInTR";
Expand Down Expand Up @@ -914,8 +921,8 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.SeriesHeader_offset > 0) && (d.CSA.SeriesHeader_length > 0)) {
int baseResolution, interpInt, partialFourier, echoSpacing, parallelReductionFactorInPlane;
float delayTimeInTR, phaseResolution, txRefAmp, shimSetting[8];
char protocolName[kDICOMStr], fmriExternalInfo[kDICOMStr], coilID[kDICOMStr], consistencyInfo[kDICOMStr], coilElements[kDICOMStr], pulseSequenceDetails[kDICOMStr];
siemensCsaAscii(filename, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, &delayTimeInTR, &phaseOversampling, &phaseResolution, &txRefAmp, shimSetting, &baseResolution, &interpInt, &partialFourier, &echoSpacing, &parallelReductionFactorInPlane, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName);
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrLarge];
siemensCsaAscii(filename, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, &delayTimeInTR, &phaseOversampling, &phaseResolution, &txRefAmp, shimSetting, &baseResolution, &interpInt, &partialFourier, &echoSpacing, &parallelReductionFactorInPlane, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
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 Down Expand Up @@ -953,6 +960,7 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
json_Str(fp, "\t\"ReceiveCoilActiveElements\": \"%s\",\n", coilElements);
json_Str(fp, "\t\"PulseSequenceDetails\": \"%s\",\n", pulseSequenceDetails);
json_Str(fp, "\t\"FmriExternalInfo\": \"%s\",\n", fmriExternalInfo);
json_Str(fp, "\t\"WipMemBlock\": \"%s\",\n", wipMemBlock);
if (strlen(d.protocolName) < 1) //insert protocol name if it exists in CSA but not DICOM header: https://github.com/nipy/heudiconv/issues/80
json_Str(fp, "\t\"ProtocolName\": \"%s\",\n", protocolName);
json_Str(fp, "\t\"ConsistencyInfo\": \"%s\",\n", consistencyInfo);
Expand Down Expand Up @@ -3644,7 +3652,7 @@ int nii_loadDir(struct TDCMopts* opts) {
if ((dcmList[i].imageNum > 0) && (opts->isRenameNotConvert > 0)) { //use imageNum instead of isValid to convert non-images (kWaveformSq will have instance number but is not a valid image)
char outname[PATH_MAX] = {""};
nii_createFilename(dcmList[i], outname, *opts);
copyFile (nameList.str[i], outname); //xxxxx
copyFile (nameList.str[i], outname);
if (opts->isVerbose > 0)
printf("Renaming %s -> %s\n", nameList.str[i], outname);
dcmList[i].isValid = false;
Expand Down

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