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XA10A tag substitutes (#240)
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@neurolabusc
neurolabusc committed Nov 2, 2018
1 parent 908812d commit 5b696cc
Showing 1 changed file with 19 additions and 10 deletions.
29 changes: 19 additions & 10 deletions console/nii_dicom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3912,6 +3912,7 @@ const uint32_t kEffectiveTE = 0x0018+ (0x9082 << 16);
#define kDiffusionOrientation 0x0018+uint32_t(0x9089<< 16 ) // FD, seen in enhanced
// DICOM from Philips 5.*
// and Siemens XA10.
#define kImagingFrequency2 0x0018+uint32_t(0x9098 << 16 ) //FD
#define kMREchoSequence 0x0018+uint32_t(0x9114<< 16 ) //SQ
#define kMRAcquisitionPhaseEncodingStepsInPlane 0x0018+uint32_t(0x9231<< 16 ) //US
#define kNumberOfImagesInMosaic 0x0019+(0x100A<< 16 ) //US NumberOfImagesInMosaic
Expand Down Expand Up @@ -3941,13 +3942,14 @@ const uint32_t kEffectiveTE = 0x0018+ (0x9082 << 16);
#define kDimensionIndexValues 0x0020+uint32_t(0x9157<< 16 ) // UL n-dimensional index of frame.
#define kInStackPositionNumber 0x0020+uint32_t(0x9057<< 16 ) // UL can help determine slices in volume
//Private Group 21 as Used by Siemens:
#define kSequenceVariant21 0x0021+(0x105B<< 16 )//CS
#define kPATModeText 0x0021+(0x1009<< 16 )//LO, see kImaPATModeText
#define kTimeAfterStart 0x0021+(0x1104<< 16 )//DS
#define kPhaseEncodingDirectionPositive 0x0021+(0x111C<< 16 )//IS
//#define kRealDwellTime 0x0021+(0x1142<< 16 )//IS
#define kBandwidthPerPixelPhaseEncode21 0x0021+(0x1153<< 16 )//FD
#define kCoilElements 0x0021+(0x114F<< 16 )//LO
//g21
#define kAcquisitionMatrixText21 0x0021+(0x1158 << 16 ) //SH
//Private Group 21 as used by GE:
#define kLocationsInAcquisitionGE 0x0021+(0x104F<< 16 )//SS 'LocationsInAcquisitionGE'
#define kRTIA_timer 0x0021+(0x105E<< 16 )//DS
Expand Down Expand Up @@ -4065,7 +4067,7 @@ double TE = 0.0; //most recent echo time recorded
int encapsulatedDataFragmentStart = 0; //position of first FFFE,E000 for compressed images
int encapsulatedDataImageStart = 0; //position of 7FE0,0010 for compressed images (where actual image start should be start of first fragment)
bool isOrient = false;
bool isDcm4Che = false;
//bool isDcm4Che = false;
bool isMoCo = false;
bool isIconImageSequence = false;
bool isSwitchToImplicitVR = false;
Expand Down Expand Up @@ -4156,7 +4158,7 @@ double TE = 0.0; //most recent echo time recorded
is2005140FSQ = false;
if (sqDepth < 0) sqDepth = 0; //should not happen, but protect for faulty anonymization
//if we leave the folder MREchoSequence 0018,9114
if (( nDimIndxVal > 0) && ((isDcm4Che) || (d.manufacturer == kMANUFACTURER_PHILIPS)) && (sqDepth00189114 >= sqDepth)) {
if (( nDimIndxVal > 0) && ((d.manufacturer == kMANUFACTURER_BRUKER) || (d.manufacturer == kMANUFACTURER_PHILIPS)) && (sqDepth00189114 >= sqDepth)) {
sqDepth00189114 = -1; //triggered
//printf("%d--->\n", inStackPositionNumber);
if (inStackPositionNumber > 0) {
Expand Down Expand Up @@ -4456,8 +4458,8 @@ double TE = 0.0; //most recent echo time recorded
char impTxt[kDICOMStr];
dcmStr (lLength, &buffer[lPos], impTxt);
int slen = (int) strlen(impTxt);
if ((slen > 5) && (strstr(impTxt, "dcm4che") != NULL) )
isDcm4Che = true;
//if ((slen > 5) && (strstr(impTxt, "dcm4che") != NULL) )
// isDcm4Che = true;
if((slen < 5) || (strstr(impTxt, "XA10A") == NULL) ) break;
d.isXA10A = true;
break; }
Expand Down Expand Up @@ -4688,7 +4690,7 @@ double TE = 0.0; //most recent echo time recorded
isPhilipsDerived = true;
break; }
case kMREchoSequence :
if (isDcm4Che) break;
if (d.manufacturer != kMANUFACTURER_BRUKER) break;
if (sqDepth == 0) sqDepth = 1; //should not happen, in case faulty anonymization
sqDepth00189114 = sqDepth - 1;
break;
Expand Down Expand Up @@ -4791,13 +4793,13 @@ double TE = 0.0; //most recent echo time recorded
if (d.imageNum < 1) d.imageNum = dcmStrInt(lLength, &buffer[lPos]); //Philips renames each image again in 2001,9000, which can lead to duplicates
break;
case kInStackPositionNumber:
if ((d.manufacturer != kMANUFACTURER_PHILIPS) && (!isDcm4Che)) break;
if ((d.manufacturer != kMANUFACTURER_PHILIPS) && (d.manufacturer != kMANUFACTURER_BRUKER)) break;
inStackPositionNumber = dcmInt(4,&buffer[lPos],d.isLittleEndian);
//printf("<%d>\n",inStackPositionNumber);
if (inStackPositionNumber > maxInStackPositionNumber) maxInStackPositionNumber = inStackPositionNumber;
break;
case kFrameContentSequence :
if (!isDcm4Che) 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 @@ -5070,7 +5072,9 @@ double TE = 0.0; //most recent echo time recorded
d.xyzMM[3] = dcmStrFloat(lLength, &buffer[lPos]);
d.zThick = d.xyzMM[3];
break;
case kAcquisitionMatrixText : {
case kAcquisitionMatrixText21:
//fall through to kAcquisitionMatrixText
case kAcquisitionMatrixText : {
if (d.manufacturer == kMANUFACTURER_SIEMENS) {
char matStr[kDICOMStr];
dcmStr (lLength, &buffer[lPos], matStr);
Expand Down Expand Up @@ -5143,6 +5147,8 @@ double TE = 0.0; //most recent echo time recorded
dcmStr (lLength, &buffer[lPos], d.scanningSequence);
break;
}
case kSequenceVariant21 :
//fall through...
case kSequenceVariant : {
dcmStr (lLength, &buffer[lPos], d.sequenceVariant);
break;
Expand Down Expand Up @@ -5280,6 +5286,9 @@ double TE = 0.0; //most recent echo time recorded
//case kSliceNumberMrPhilips :
// sliceNumberMrPhilips3D = dcmStrInt(lLength, &buffer[lPos]);
// break;
case kImagingFrequency2 :
d.imagingFrequency = dcmFloatDouble(lLength, &buffer[lPos], d.isLittleEndian);
break;
case kSliceNumberMrPhilips : {
if (d.manufacturer != kMANUFACTURER_PHILIPS)
break;
Expand Down Expand Up @@ -5916,7 +5925,7 @@ if (d.isHasPhase)
#endif
//printf("%g\t\t%g\t%g\t%g\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3]);
//printMessage("buffer usage %d %d %d\n",d.imageStart, lPos+lFileOffset, MaxBufferSz);
return d;
return d;
} // readDICOM()

struct TDICOMdata readDICOM(char * fname) {
Expand Down

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