checks Source Application Entity Title for “oasis” to detect bogus Se…

…gami spatial transforms.

console/nii_dicom.cpp

@@ -345,16 +345,6 @@ int verify_slice_dir (struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_
         for (int i = 0; i < 4; i++)
             R->m[i][2] = -R->m[i][2];
     }
-    /*if (d.manufacturer == kMANUFACTURER_SEGAMI) { //set origin as center of volume
-    	for (int i = 0; i < 3; i++)
-            R->m[i][3] = 0; //remove old offset
-    	vec4 originVx = setVec4( (h->dim[1]+1.0f)/2.0f, (h->dim[2]+1.0f)/2.0f, (h->dim[3]+1.0f)/2.0f);
-    	printMessage("origin (vx) %g %g %g\n",originVx.v[0],originVx.v[1],originVx.v[2]);
-    	vec4 originMm = nifti_vect44mat44_mul(originVx, *R);
-    	printMessage("origin (mm) %g %g %g\n",originMm.v[0],originMm.v[1],originMm.v[2]);
-    	for (int i = 0; i < 3; i++)
-            R->m[i][3] = originMm.v[i]; //remove old offset
-    }*/
     if (flip)
         iSL = -iSL;
 	#ifdef MY_DEBUG
@@ -539,7 +529,7 @@ mat44 set_nii_header(struct TDICOMdata d) {
 mat44 set_nii_header_x(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, int* sliceDir, int isVerbose) {
     *sliceDir = 0;
     mat44 Q44 = nifti_dicom2mat(d.orient, d.patientPosition, d.xyzMM);
-	if (d.manufacturer == kMANUFACTURER_SEGAMI) {
+	if (d.isSegamiOasis == true) {
 		//Segami reconstructions appear to disregard DICOM spatial parameters: assume center of volume is isocenter and no table tilt
 		// Consider sample image with d.orient (0020,0037) = -1 0 0; 0 1 0: this suggests image RAI (L->R, P->A, S->I) but the vendors viewing software suggests LPS
 		//Perhaps we should ignore 0020,0037 and 0020,0032 as they are hidden in sequence 0054,0022, but in this case no positioning is provided
@@ -742,6 +732,7 @@ struct TDICOMdata clear_dicom_data() {
     d.is3DAcq = false; //e.g. MP-RAGE, SPACE, TFE
     d.isSlicesSpatiallySequentialPhilips = true; //Philips can save slices in random order, e.g. 4,5,6,1,2,3
     d.isDerived = false; //0008,0008 = DERIVED,CSAPARALLEL,POSDISP
+    d.isSegamiOasis = false; //these images do not store spatial coordinates
     d.bitsAllocated = 16;//bits
     d.bitsStored = 0;
     d.samplesPerPixel = 1;
@@ -938,8 +929,6 @@ int dcmStrManufacturer (int lByteLength, unsigned char lBuffer[]) {//read float
         ret = kMANUFACTURER_PHILIPS;
     if ((toupper(cString[0])== 'T') && (toupper(cString[1])== 'O'))
         ret = kMANUFACTURER_TOSHIBA;
-    if ((toupper(cString[0])== 'S') && (toupper(cString[1])== 'E'))
-        ret = kMANUFACTURER_SEGAMI;
 //#ifdef _MSC_VER
 	free(cString);
 //#endif
@@ -2689,6 +2678,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
 #define  kUnused 0x0001+(0x0001 << 16 )
 #define  kStart 0x0002+(0x0000 << 16 )
 #define  kTransferSyntax 0x0002+(0x0010 << 16)
+#define  kSourceApplicationEntityTitle 0x0002+(0x0016 << 16 )
 //#define  kSpecificCharacterSet 0x0008+(0x0005 << 16 ) //someday we should handle foreign characters...
 #define  kImageTypeTag 0x0008+(0x0008 << 16 )
 #define  kStudyDate 0x0008+(0x0020 << 16 )
@@ -2988,6 +2978,13 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
                     d.imageStart = 1;//abort as invalid (imageStart MUST be >128)
                 }
                 break;} //{} provide scope for variable 'transferSyntax
+            case kSourceApplicationEntityTitle: {
+            	char saeTxt[kDICOMStr];
+                dcmStr (lLength, &buffer[lPos], saeTxt);
+                int slen = (int) strlen(saeTxt);
+				if((slen < 5) || (strstr(saeTxt, "oasis") == NULL) ) break;
+                d.isSegamiOasis = true;
+            	break; }
             case kImageTypeTag:
             	dcmStr (lLength, &buffer[lPos], d.imageType);
                 int slen;

console/nii_dicom.h

@@ -48,7 +48,6 @@ static const int kMaxDTI4D = 4096; //maximum number of DTI directions for 4D (Ph
 #define kMANUFACTURER_GE  2
 #define kMANUFACTURER_PHILIPS  3
 #define kMANUFACTURER_TOSHIBA  4
-#define kMANUFACTURER_SEGAMI 5
 
 //note: note a complete modality list, e.g. XA,PX, etc
 #define kMODALITY_UNKNOWN  0
@@ -118,7 +117,7 @@ static const int kCompressRLE = 4; //run length encoding
         float radionuclidePositronFraction, radionuclideTotalDose, radionuclideHalfLife, doseCalibrationFactor; //PET ISOTOPE MODULE ATTRIBUTES (C.8-57)
 		float ecat_isotope_halflife, ecat_dosage;
         double dateTime, acquisitionTime, acquisitionDate, bandwidthPerPixelPhaseEncode;
-        bool isDerived, isXRay, isMultiEcho, isSlicesSpatiallySequentialPhilips, isValid, is3DAcq, isExplicitVR, isLittleEndian, isPlanarRGB, isSigned, isHasPhase,isHasMagnitude,isHasMixed, isFloat, isResampled;
+        bool isSegamiOasis, isDerived, isXRay, isMultiEcho, isSlicesSpatiallySequentialPhilips, isValid, is3DAcq, isExplicitVR, isLittleEndian, isPlanarRGB, isSigned, isHasPhase,isHasMagnitude,isHasMixed, isFloat, isResampled;
         char phaseEncodingRC;
         char softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionAddress[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageType[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr],seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], birthDate[kDICOMStr], gender[kDICOMStr], age[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr], imageComments[kDICOMStr];
         struct TCSAdata CSA;

console/nii_dicom_batch.cpp

@@ -517,9 +517,6 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
 		case kMANUFACTURER_TOSHIBA:
 			fprintf(fp, "\t\"Manufacturer\": \"Toshiba\",\n" );
 			break;
-		case kMANUFACTURER_SEGAMI:
-			fprintf(fp, "\t\"Manufacturer\": \"Segami\",\n" );
-			break;
 	};
 	fprintf(fp, "\t\"ManufacturersModelName\": \"%s\",\n", d.manufacturersModelName );
 	if (!opts.isAnonymizeBIDS) {
@@ -2833,7 +2830,6 @@ void setDefaultOpts (struct TDCMopts *opts, const char * argv[]) { //either "set
     opts->isGz = false;
     opts->isSave3D = false;
     opts->gzLevel = MZ_DEFAULT_LEVEL; //-1;
-    printMessage(">>>>> %d\n",Z_DEFAULT_COMPRESSION);
     opts->isFlipY = true; //false: images in raw DICOM orientation, true: image rows flipped to cartesian coordinates
     opts->isRGBplanar = false; //false for NIfTI (RGBRGB...), true for Analyze (RRR..RGGG..GBBB..B)
     opts->isCreateBIDS =  true;