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Kludge for Siemens MoCo slice timing interfered with CMRR fix (CMRR-C…
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…2P/MB#29)
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@neurolabusc
neurolabusc committed Nov 5, 2018
1 parent da64ebc commit 3c31d18
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Showing 3 changed files with 10 additions and 10 deletions.
16 changes: 8 additions & 8 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -613,7 +613,7 @@ int headerDcm2NiiSForm(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_
if ((d.isDerived) || ((d.bitsAllocated == 8) && (d.samplesPerPixel == 3) && (d.manufacturer == kMANUFACTURER_SIEMENS))) {
printMessage("Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)\n");
} else {
printMessage("Unable to determine spatial orientation: 0020,0037 missing (Type 1 attribute: not a valid DICOM) Series %d\n", d.seriesNum);
printMessage("Unable to determine spatial orientation: 0020,0037 missing (Type 1 attribute: not a valid DICOM) Series %ld\n", d.seriesNum);
}
}
mat44 Q44 = set_nii_header_x(d, d2, h, &sliceDir, isVerbose);
Expand Down Expand Up @@ -1211,10 +1211,10 @@ int readCSAImageHeader(unsigned char *buff, int lLength, struct TCSAdata *CSA, i
int maxTimeIndex = minTimeIndex;
minTimeValue = sliceTimes[1];
maxTimeValue = minTimeValue;
if ((isVerbose) && (!is3D))
if (isVerbose)
printMessage(" sliceTimes %g\t", sliceTimes[1]);
for (int z = 2; z <= itemsOK; z++) { //find index and value of fastest time
if ((isVerbose) && (!is3D))
if (isVerbose)
printMessage("%g\t", sliceTimes[z]);
if (sliceTimes[z] == 0)
nTimeZero++;
Expand All @@ -1228,7 +1228,7 @@ int readCSAImageHeader(unsigned char *buff, int lLength, struct TCSAdata *CSA, i
}
if (sliceTimes[z] == timeValue1) CSA->multiBandFactor++;
}
if ((isVerbose) && (!is3D))
if (isVerbose)
printMessage("\n");
CSA->slice_start = minTimeIndex -1;
CSA->slice_end = maxTimeIndex -1;
Expand All @@ -1250,13 +1250,13 @@ int readCSAImageHeader(unsigned char *buff, int lLength, struct TCSAdata *CSA, i
[sliceTimesNS addObject:[NSNumber numberWithFloat:sliceTimes[z]]];
NSLog(@" Warning: unable to determine slice order for %lu slice mosaic: %@",(unsigned long)[sliceTimesNS count],sliceTimesNS );
*/
if (!is3D)
printWarning("Unable to determine slice order from CSA tag MosaicRefAcqTimes\n");
printWarning("Unable to determine slice order from CSA tag MosaicRefAcqTimes\n");
}
if ((CSA->sliceOrder != NIFTI_SLICE_UNKNOWN) && (nTimeZero > 1)) {
if (isVerbose)
printMessage(" Multiband x%d sequence: setting slice order as UNKNOWN (instead of %d)\n", nTimeZero, CSA->sliceOrder);
CSA->sliceOrder = NIFTI_SLICE_UNKNOWN;

}
//#ifdef _MSC_VER
free(sliceTimes);
Expand Down Expand Up @@ -4799,7 +4799,7 @@ double TE = 0.0; //most recent echo time recorded
if (inStackPositionNumber > maxInStackPositionNumber) maxInStackPositionNumber = inStackPositionNumber;
break;
case kFrameContentSequence :
if (!d.manufacturer == kMANUFACTURER_BRUKER) break; //see https://github.com/rordenlab/dcm2niix/issues/241
if (!(d.manufacturer == kMANUFACTURER_BRUKER)) break; //see https://github.com/rordenlab/dcm2niix/issues/241
if (sqDepth == 0) sqDepth = 1; //should not happen, in case faulty anonymization
sqDepth00189114 = sqDepth - 1;
break;
Expand Down Expand Up @@ -5785,7 +5785,7 @@ if (d.isHasPhase)
if (!isnan(patientPositionEndPhilips[1]))
printMessage(" patient position end (0020,0032)\t%g\t%g\t%g\n", patientPositionEndPhilips[1],patientPositionEndPhilips[2],patientPositionEndPhilips[3]);
printMessage(" orient (0020,0037)\t%g\t%g\t%g\t%g\t%g\t%g\n", d.orient[1],d.orient[2],d.orient[3], d.orient[4],d.orient[5],d.orient[6]);
printMessage(" acq %d img %d ser %ld dim %dx%dx%dx%d mm %gx%gx%g offset %d loc %d valid %d ph %d mag %d nDTI %d 3d %d bits %d littleEndian %d echo %d coil %d TE %g TR %g\n",d.acquNum,d.imageNum,d.seriesNum,d.xyzDim[1],d.xyzDim[2],d.xyzDim[3], d.xyzDim[4],d.xyzMM[1],d.xyzMM[2],d.xyzMM[3],d.imageStart, d.locationsInAcquisition, d.isValid, d.isHasPhase, d.isHasMagnitude, d.CSA.numDti, d.is3DAcq, d.bitsAllocated, d.isLittleEndian, d.echoNum, d.coilCrc, d.TE, d.TR);
printMessage(" acq %d img %d ser %ld dim %dx%dx%dx%d mm %gx%gx%g offset %d loc %d valid %d ph %d mag %d nDTI %d 3d %d bits %d littleEndian %d echo %d coilCRC %d TE %g TR %g\n",d.acquNum,d.imageNum,d.seriesNum,d.xyzDim[1],d.xyzDim[2],d.xyzDim[3], d.xyzDim[4],d.xyzMM[1],d.xyzMM[2],d.xyzMM[3],d.imageStart, d.locationsInAcquisition, d.isValid, d.isHasPhase, d.isHasMagnitude, d.CSA.numDti, d.is3DAcq, d.bitsAllocated, d.isLittleEndian, d.echoNum, d.coilCrc, d.TE, d.TR);
//if (d.CSA.dtiV[0] > 0)
// printMessage(" DWI bxyz %g %g %g %g\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3]);
}
Expand Down
2 changes: 1 addition & 1 deletion console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2887,7 +2887,7 @@ void checkSliceTiming(struct TDICOMdata * d, struct TDICOMdata * d1) {
//check if 2nd image has valud slice timing
float minT1 = d1->CSA.sliceTiming[0];
float maxT1 = minT1;
for (int i = 0; i < kMaxEPI3D; i++) {
for (int i = 0; i < nSlices; i++) {
//if (d1->CSA.sliceTiming[i] < 0.0) break;
if (d1->CSA.sliceTiming[i] < minT1) minT1 = d1->CSA.sliceTiming[i];
if (d1->CSA.sliceTiming[i] > maxT1) maxT1 = d1->CSA.sliceTiming[i];
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2 changes: 1 addition & 1 deletion console/ujpeg.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -663,7 +663,7 @@ static int njGetVLC(nj_vlc_code_t* vlc, unsigned char* code) {
if (!bits) return 0;
value = njGetBits(bits);
if (value < (1 << (bits - 1)))
value += shiftLeft(-1, bits) + 1;
value += (shiftLeft(-1, bits)) + 1;
return value;
}

Expand Down

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