Merge commit 'v1.0.20170818-8-gdd1d994' into debian

* commit 'v1.0.20170818-8-gdd1d994':
  Fix for rordenlab#124

README.md

@@ -197,7 +197,9 @@ This requires a compiler that supports c++11.
 
 ## Links
 
- - [Dcm2Bids](https://github.com/cbedetti/Dcm2Bids) uses dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
+  - [Dcm2Bids](https://github.com/cbedetti/Dcm2Bids) uses dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
+  - [bidskit](https://github.com/jmtyszka/bidskit) uses dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
+  - [DAC2BIDS](https://github.com/dangom/dac2bids) uses dcm2niibatch to create [BIDS](http://bids.neuroimaging.io/) datasets.
   - [heudiconv](https://github.com/nipy/heudiconv) can use dcm2niix to create [BIDS](http://bids.neuroimaging.io/) datasets.
   - [nipype](https://github.com/nipy/nipype) can use dcm2niix to convert images.
   - [pydcm2niix is a Python module for working with dcm2niix](https://github.com/jstutters/pydcm2niix).

console/nii_dicom.cpp

@@ -2697,6 +2697,7 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
 #define  kComplexImageComponent (uint32_t) 0x0008+(0x9208 << 16 )//'0008' '9208' 'CS' 'ComplexImageComponent'
 #define  kPatientName 0x0010+(0x0010 << 16 )
 #define  kPatientID 0x0010+(0x0020 << 16 )
+#define  kAnatomicalOrientationType 0x0010+(0x2210 << 16 )
 #define  kBodyPartExamined 0x0018+(0x0015 << 16)
 #define  kScanningSequence 0x0018+(0x0020 << 16)
 #define  kSequenceVariant 0x0018+(0x0021 << 16)
@@ -2765,6 +2766,9 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
 #define  kCoilSiemens  0x0051+(0x100F << 16 )
 #define  kImaPATModeText  0x0051+(0x1011 << 16 )
 #define  kLocationsInAcquisition  0x0054+(0x0081 << 16 )
+//ftp://dicom.nema.org/MEDICAL/dicom/2014c/output/chtml/part03/sect_C.8.9.4.html
+//If ImageType is REPROJECTION we slice direction is reversed - need example to test
+// #define  kSeriesType  0x0054+(0x1000 << 16 )
 #define  kDoseCalibrationFactor  0x0054+(0x1322<< 16 )
 #define  kIconImageSequence 0x0088+(0x0200 << 16 )
 #define  kDiffusionBFactor  0x2001+(0x1003 << 16 )// FL
@@ -3054,6 +3058,13 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
             case kPatientName :
                 dcmStr (lLength, &buffer[lPos], d.patientName);
                 break;
+            case kAnatomicalOrientationType: {
+            	char aotTxt[kDICOMStr]; //ftp://dicom.nema.org/MEDICAL/dicom/2015b/output/chtml/part03/sect_C.7.6.2.html#sect_C.7.6.2.1.1
+                dcmStr (lLength, &buffer[lPos], aotTxt);
+                int slen = (int) strlen(aotTxt);
+				if((slen < 9) || (strstr(aotTxt, "QUADRUPED") == NULL) ) break;
+                printError("Anatomical Orientation Type (0010,2210) is QUADRUPED: rotate coordinates accordingly");
+            	break; }
             case kPatientID :
                 dcmStr (lLength, &buffer[lPos], d.patientID);
                 break;

console/nii_dicom_batch.cpp

@@ -1509,10 +1509,18 @@ int nii_saveNII(char * niiFilename, struct nifti_1_header hdr, unsigned char* im
     	return EXIT_FAILURE;
     }
     #define  kMaxPigz 3758096384
+    //https://stackoverflow.com/questions/5272825/detecting-64bit-compile-in-c
+    #if UINTPTR_MAX == 0xffffffff
+	#define  kMaxGz 2147483647
+	#elif UINTPTR_MAX == 0xffffffffffffffff
+	#define  kMaxGz kMaxPigz
+	#else
+	compiler error: unable to determine is 32 or 64 bit
+	#endif
     #ifndef myDisableZLib
-    if  ((opts.isGz) &&  (strlen(opts.pigzname)  < 1) &&  ((imgsz+hdr.vox_offset) >=  2147483647) ) { //use internal compressor
-		printWarning("Saving uncompressed data: internal compressor limited to 2Gb images.\n");
-		if ((imgsz+hdr.vox_offset) <  3758096384)
+    if  ((opts.isGz) &&  (strlen(opts.pigzname)  < 1) &&  ((imgsz+hdr.vox_offset) >=  kMaxGz) ) { //use internal compressor
+		printWarning("Saving uncompressed data: internal compressor limited to %d bytes images.\n", kMaxGz);
+		if ((imgsz+hdr.vox_offset) <  kMaxPigz)
 			printWarning(" Hint: using external compressor (pigz) should help.\n");
     } else if  ((opts.isGz) &&  (strlen(opts.pigzname)  < 1) &&  ((imgsz+hdr.vox_offset) <  2147483647) ) { //use internal compressor
         writeNiiGz (niiFilename, hdr,  im, imgsz, opts.gzLevel);