New "-z 3" for uncompressed 3D volumes (old SPM)

README.md

@@ -200,6 +200,7 @@ This requires a compiler that supports c++11.
  - [Dcm2Bids](https://github.com/cbedetti/Dcm2Bids) uses dcm2niix 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).
   - [dcm2niir](https://github.com/muschellij2/dcm2niir) R wrapper for dcm2niix/dcm2nii.
   - [divest](https://github.com/jonclayden/divest) R interface to dcm2niix.
   - [sci-tran dcm2niix](https://github.com/scitran-apps/dcm2niix) docker.

console/main_console.cpp

@@ -98,14 +98,14 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
     if (opts.isGz) gzCh = 'y';
     #ifdef myDisableZLib
 		if (strlen(opts.pigzname) > 0)
-			printf("  -z : gz compress images (y/n, default %c)\n", gzCh);
+			printf("  -z : gz compress images (y/n/3, default %c) [y=pigz, n=no, 3=no,3D]\n", gzCh);
 		else
-			printf("  -z : gz compress images (y/n, default %c) [REQUIRES pigz]\n", gzCh);
+			printf("  -z : gz compress images (y/n/3, default %c)  [y=pigz(MISSING!), n=no, 3=no,3D]\n", gzCh);
     #else
     	#ifdef myDisableMiniZ
-    	printf("  -z : gz compress images (y/i/n, default %c) [y=pigz, i=internal:zlib, n=no]\n", gzCh);
+    	printf("  -z : gz compress images (y/i/n/3, default %c) [y=pigz, i=internal:zlib, n=no, 3=no,3D]\n", gzCh);
 		#else
-		printf("  -z : gz compress images (y/i/n, default %c) [y=pigz, i=internal, n=no]\n", gzCh);
+		printf("  -z : gz compress images (y/i/n/3, default %c) [y=pigz, i=internal, n=no, 3=no,3D]\n", gzCh);
 		#endif
     #endif
 
@@ -133,7 +133,8 @@ int invalidParam(int i, const char * argv[]) {
 		|| (argv[i][0] == 'o') || (argv[i][0] == 'O')
 		|| (argv[i][0] == 'h') || (argv[i][0] == 'H')
 		|| (argv[i][0] == 'i') || (argv[i][0] == 'I')
-		|| (argv[i][0] == '0') || (argv[i][0] == '1') || (argv[i][0] == '2'))
+		|| (argv[i][0] == '0') || (argv[i][0] == '1')
+		|| (argv[i][0] == '2') || (argv[i][0] == '3') )
 		return 0;
 
 	//if (argv[i][0] != '-') return 0;
@@ -256,7 +257,10 @@ int main(int argc, const char * argv[])
             } else if ((argv[i][1] == 'z') && ((i+1) < argc)) {
                 i++;
                 if (invalidParam(i, argv)) return 0;
-                if ((argv[i][0] == 'i') || (argv[i][0] == 'I') ) {
+                if ((argv[i][0] == '3') ) {
+                    opts.isGz = false; //uncompressed 3D
+                	opts.isSave3D = true;
+                } else if ((argv[i][0] == 'i') || (argv[i][0] == 'I') ) {
                     opts.isGz = true; //force use of internal compression instead of pigz
                 	strcpy(opts.pigzname,"");
                 } else if ((argv[i][0] == 'n') || (argv[i][0] == 'N')  || (argv[i][0] == '0'))

console/nii_dicom_batch.cpp

@@ -1342,6 +1342,10 @@ unsigned long mz_crc32(unsigned long crc, const unsigned char *ptr, size_t buf_l
  #define MZ_UBER_COMPRESSION 9
 #endif
 
+#ifndef MZ_DEFAULT_LEVEL
+ #define MZ_DEFAULT_LEVEL 6
+#endif
+
 void writeNiiGz (char * baseName, struct nifti_1_header hdr,  unsigned char* src_buffer, unsigned long src_len, int gzLevel) {
     //create gz file in RAM, save to disk http://www.zlib.net/zlib_how.html
     // in general this single-threaded approach is slower than PIGZ but is useful for slow (network attached) disk drives
@@ -1359,7 +1363,7 @@ void writeNiiGz (char * baseName, struct nifti_1_header hdr,  unsigned char* src
     strm.opaque = Z_NULL;
     strm.next_out = pCmp; // output char array
     strm.avail_out = (unsigned int)cmp_len; // size of output
-    int zLevel = Z_DEFAULT_COMPRESSION;
+    int zLevel = MZ_DEFAULT_LEVEL;//Z_DEFAULT_COMPRESSION;
     if ((gzLevel > 0) && (gzLevel < 11))
     	zLevel = gzLevel;
     if (zLevel > MZ_UBER_COMPRESSION)
@@ -2184,12 +2188,18 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis
 			char pathoutnameADC[2048] = {""};
 			strcat(pathoutnameADC,pathoutname);
 			strcat(pathoutnameADC,"_ADC");
-			nii_saveNII(pathoutnameADC, hdr0, imgM, opts);
+			if (opts.isSave3D)
+				nii_saveNII3D(pathoutnameADC, hdr0, imgM, opts);
+			else
+				nii_saveNII(pathoutnameADC, hdr0, imgM, opts);
 		}
 #endif
 		imgM = removeADC(&hdr0, imgM, numADC);
 #ifndef HAVE_R
-        returnCode = nii_saveNII(pathoutname, hdr0, imgM, opts);
+		if (opts.isSave3D)
+			returnCode = nii_saveNII3D(pathoutname, hdr0, imgM, opts);
+		else
+        	returnCode = nii_saveNII(pathoutname, hdr0, imgM, opts);
 #endif
     }
 #endif
@@ -2821,7 +2831,9 @@ void setDefaultOpts (struct TDCMopts *opts, const char * argv[]) { //either "set
     opts->isPhilipsFloatNotDisplayScaling = true;
     opts->isCrop = false;
     opts->isGz = false;
-    opts->gzLevel = -1;
+    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;

console/nii_dicom_batch.h

@@ -23,7 +23,7 @@ extern "C" {
 #endif
 
     struct TDCMopts {
-        bool isGz, isFlipY,  isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackSameSeries, isCrop;
+        bool isSave3D,isGz, isFlipY,  isCreateBIDS, isSortDTIbyBVal, isAnonymizeBIDS, isOnlyBIDS, isCreateText, isIgnoreDerivedAnd2D, isPhilipsFloatNotDisplayScaling, isTiltCorrect, isRGBplanar, isOnlySingleFile, isForceStackSameSeries, isCrop;
         int isVerbose, compressFlag, gzLevel; //support for compressed data 0=none,
         char filename[512], outdir[512], indir[512], pigzname[512], optsname[512], indirParent[512];
 #ifdef HAVE_R