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Development #745

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Development #745

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3587907
Changing maximal length of string read from
markus-nilsson Aug 28, 2023
16a9006
Allowing WIPMemBlock to be longer, and adding
markus-nilsson Aug 28, 2023
f2dd146
Pulling out free gradient directions too
markus-nilsson Oct 9, 2023
f15347a
Fix for older sequence names
markus-nilsson Oct 9, 2023
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2 changes: 2 additions & 0 deletions console/nii_dicom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,8 @@ static const int kMaxDTI4D = kMaxSlice2D; //issue460: maximum number of DTI dire

#define kDICOMStr 66 //64 characters plus NULL https://github.com/rordenlab/dcm2niix/issues/268
#define kDICOMStrLarge 256
#define kDICOMStrExtraLarge 65536 // for Siemens WipMemBlock only


#define kMANUFACTURER_UNKNOWN 0
#define kMANUFACTURER_SIEMENS 1
Expand Down
83 changes: 74 additions & 9 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -617,7 +617,7 @@ float readKeyFloat(const char *key, char *buffer, int remLength) { //look for te
return atof(str);
} //readKeyFloat()

void readKeyStr(const char *key, char *buffer, int remLength, char *outStr) {
void readKeyStr(const char *key, char *buffer, int remLength, char *outStr, int outStrLen) {
//if key is CoilElementID.tCoilID the string 'CoilElementID.tCoilID = ""Head_32""' returns 'Head32'
strcpy(outStr, "");
char *keyPos = (char *)memmem(buffer, remLength, key, strlen(key));
Expand All @@ -629,7 +629,7 @@ 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 < kDICOMStrLarge)) {
if ((isQuote) && (keyPos[i] != '"') && (outLen < outStrLen)) {
tmpstr[0] = keyPos[i];
strcat(outStr, tmpstr);
outLen++;
Expand All @@ -643,6 +643,10 @@ void readKeyStr(const char *key, char *buffer, int remLength, char *outStr) {
}
} //readKeyStr()

void readKeyStr(const char *key, char *buffer, int remLength, char *outStr) {
readKeyStr(key, buffer, remLength, outStr, kDICOMStrLarge);
} //readKeyStr()

int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
//returns offset to ASCII Phoenix data
if (lLength < 36)
Expand Down Expand Up @@ -680,6 +684,7 @@ int phoenixOffsetCSASeriesHeader(unsigned char *buff, int lLength) {
} //phoenixOffsetCSASeriesHeader()

#define kMaxWipFree 64
#define freeDiffusionMaxN 256
typedef struct {
float TE0, TE1, delayTimeInTR, phaseOversampling, phaseResolution, txRefAmp, accelFactTotal;
int lInvContrasts, lContrasts ,phaseEncodingLines, existUcImageNumb, ucMode, baseResolution, interp, partialFourier, echoSpacing,
Expand All @@ -688,6 +693,8 @@ typedef struct {
float adFree[kMaxWipFree];
float alTI[kMaxWipFree];
float sPostLabelingDelay, ulLabelingDuration, dAveragesDouble, dThickness, ulShape, sPositionDTra, sNormalDTra;
int freeDiffusionN;
vec3 freeDiffusionVec[freeDiffusionMaxN];
} TCsaAscii;

void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, int csaLength, float *shimSetting, char *coilID, char *consistencyInfo, char *coilElements, char *pulseSequenceDetails, char *fmriExternalInfo, char *protocolName, char *wipMemBlock) {
Expand Down Expand Up @@ -717,7 +724,8 @@ void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, i
csaAscii->refLinesPE = 0;
csaAscii->combineMode = 0;
csaAscii->patMode = 0;
csaAscii->ucMTC = 0;
csaAscii->ucMTC = 0;
csaAscii->freeDiffusionN = 0;
for (int i = 0; i < 8; i++)
shimSetting[i] = 0.0;
strcpy(coilID, "");
Expand Down Expand Up @@ -832,7 +840,7 @@ void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, i
char keyStrSeq[] = "tSequenceFileName";
readKeyStr(keyStrSeq, keyPos, csaLengthTrim, pulseSequenceDetails);
char keyStrWipMemBlock[] = "sWipMemBlock.tFree";
readKeyStr(keyStrWipMemBlock, keyPos, csaLengthTrim, wipMemBlock);
readKeyStr(keyStrWipMemBlock, keyPos, csaLengthTrim, wipMemBlock, kDICOMStrExtraLarge);
char keyStrPn[] = "tProtocolName";
readKeyStr(keyStrPn, keyPos, csaLengthTrim, protocolName);
char keyStrTE0[] = "alTE[0]";
Expand Down Expand Up @@ -939,6 +947,30 @@ void siemensCsaAscii(const char *filename, TCsaAscii *csaAscii, int csaOffset, i
shimSetting[6] = readKeyFloat(keyStrSh6, keyPos, csaLengthTrim);
char keyStrSh7[] = "sGRADSPEC.alShimCurrent[4]";
shimSetting[7] = readKeyFloat(keyStrSh7, keyPos, csaLengthTrim);

// pull out the directions in the DVI
char keyStrDVIn[] = "sDiffusion.sFreeDiffusionData.lDiffDirections";
int nDiffDir = readKey(keyStrDVIn, keyPos, csaLengthTrim);
csaAscii->freeDiffusionN = min(nDiffDir, freeDiffusionMaxN);

printMessage("Free diffusion: %i\n", csaAscii->freeDiffusionN);

for (int k = 0; k < csaAscii->freeDiffusionN; k++) {
char txt[128];

snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dSag", k);
float x = readKeyFloat(txt, keyPos, csaLengthTrim);

snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dCor", k);
float y = readKeyFloat(txt, keyPos, csaLengthTrim);

snprintf(txt, 128, "sDiffusion.sFreeDiffusionData.asDiffDirVector[%i].dTra", k);
float z = readKeyFloat(txt, keyPos, csaLengthTrim);

csaAscii->freeDiffusionVec[k].v[0] = x;
csaAscii->freeDiffusionVec[k].v[1] = y;
csaAscii->freeDiffusionVec[k].v[2] = z;
}
}
free(buffer);
return;
Expand Down Expand Up @@ -1168,7 +1200,7 @@ void rescueProtocolName(struct TDICOMdata *d, const char *filename) {
return;
#ifdef myReadAsciiCsa
float shimSetting[8];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrLarge];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
TCsaAscii csaAscii;
siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
if (strlen(protocolName) >= kDICOMStr)
Expand Down Expand Up @@ -1607,7 +1639,7 @@ tse3d: T2*/
if ((d.manufacturer == kMANUFACTURER_SIEMENS) && (d.CSA.SeriesHeader_offset > 0) && (d.CSA.SeriesHeader_length > 0)) {
float pf = 1.0f; //partial fourier
float shimSetting[8];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrLarge];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
TCsaAscii csaAscii;
siemensCsaAscii(filename, &csaAscii, d.CSA.SeriesHeader_offset, d.CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
if ((d.phaseEncodingLines < 1) && (csaAscii.phaseEncodingLines > 0))
Expand Down Expand Up @@ -1786,7 +1818,39 @@ tse3d: T2*/
// https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#common-metadata-fields-applicable-to-both-pcasl-and-pasl
if (((isPASL) || (isPCASL)) && (csaAscii.interp <= 0))
fprintf(fp, "\t\"AcquisitionVoxelSize\": [\n\t\t%g,\n\t\t%g,\n\t\t%g\t],\n", d.xyzMM[1], d.xyzMM[2], d.zThick);
//general properties

// lund free waveform sequence, see https://github.com/filip-szczepankiewicz/fwf_sequence_tools
if ( (strstr(pulseSequenceDetails, "ep2d_diff_fwf") != 0) || (strstr(pulseSequenceDetails, "ep2d_diff_sms_fwf_simple") != 0))
{
for (int i = 0; i < kMaxWipFree; i++) {
if (!isnan(csaAscii.adFree[i]))
fprintf(fp, "\t\"FWF_adFree[%i]\": %g,\n", i, csaAscii.adFree[i]);
}

for (int i = 0; i < kMaxWipFree; i++) {
if (!isnan(csaAscii.alFree[i]))
fprintf(fp, "\t\"FWF_alFree[%i]\": %g,\n", i, csaAscii.alFree[i]);
}

for (int d = 0; d < 3; d++)
{
char str [4096];
strcpy(str, "");
for (int i = 0; i < csaAscii.freeDiffusionN;i++) {
char tmp[10];
snprintf(tmp, 10, "%1.4f", csaAscii.freeDiffusionVec[i].v[d]);
strcat(str, tmp);
if ( (i+1) < csaAscii.freeDiffusionN)
strcat(str, ", ");
}
char dchar = 'x' + d;
fprintf(fp, "\t\"FWF_DVS%c\": [ %s ],\n", dchar, str);
}


}

//general properties
if ((csaAscii.partialFourier > 0) && ((d.modality == kMODALITY_MR))) { //check MR, e.g. do not report for Siemens PET
//https://github.com/ismrmrd/siemens_to_ismrmrd/blob/master/parameter_maps/IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl
if (csaAscii.partialFourier == 1)
Expand Down Expand Up @@ -2571,6 +2635,7 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
fprintf(fp, "\n");
fclose(fp);
#endif

dcmList[indx0].CSA.numDti = numDti; //warning structure not changed outside scope!
geCorrectBvecs(&dcmList[indx0], sliceDir, vx, opts.isVerbose);
siemensPhilipsCorrectBvecs(&dcmList[indx0], sliceDir, vx, opts.isVerbose);
Expand Down Expand Up @@ -6445,7 +6510,7 @@ void setBidsSiemens(struct TDICOMdata *d, int nConvert, int isVerbose, const cha
if ((d->CSA.SeriesHeader_offset > 0) && (d->CSA.SeriesHeader_length > 0)) {
float pf = 1.0f; //partial fourier
float shimSetting[8];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], wipMemBlock[kDICOMStrLarge];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
TCsaAscii csaAscii;
siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, seqDetails, fmriExternalInfo, protocolName, wipMemBlock);
inv1 = csaAscii.alTI[0] / 1000.0;
Expand Down Expand Up @@ -7223,7 +7288,7 @@ void rescueSliceTimingSiemens(struct TDICOMdata *d, int verbose, int nSL, const
return;
#ifdef myReadAsciiCsa
float shimSetting[8];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrLarge];
char protocolName[kDICOMStrLarge], fmriExternalInfo[kDICOMStrLarge], coilID[kDICOMStrLarge], consistencyInfo[kDICOMStrLarge], coilElements[kDICOMStrLarge], pulseSequenceDetails[kDICOMStrLarge], wipMemBlock[kDICOMStrExtraLarge];
TCsaAscii csaAscii;
siemensCsaAscii(filename, &csaAscii, d->CSA.SeriesHeader_offset, d->CSA.SeriesHeader_length, shimSetting, coilID, consistencyInfo, coilElements, pulseSequenceDetails, fmriExternalInfo, protocolName, wipMemBlock);
int ucMode = csaAscii.ucMode;
Expand Down