Merge tag 'v1.0.20170923' into debian

* tag 'v1.0.20170923': (43 commits)
  Increment version for new release
  Update dcm_qa submodule.
  Update dcm_qa submodule.
  Kludge for GEIIS violations https://www.nitrc.org/forum/message.php?msg_id=22370
  Fix file permissions
  Use ReconMatrixPE variable and update some inline comments
  @xjqian & @mharms tags BaseResolution, PhaseResolution, VendorReportedEchoSpacing, DerivedVendorReportedEchoSpacing rordenlab#130
  mharms suggestions for  rordenlab#130
  Partial fix for rordenlab#132
  Fix for rordenlab#131 (comment)
  bandwidthPerPixelCorrected from Dr. Junqian (Gordon) Xu rordenlab#130
  Add PhaseOversampling to BIDS
  BIDS Interpolation2D, RectangularFOV, improve ReadoutTime rordenlab#130
  TotalReadoutTime iPAT vs partial Fourier: rordenlab#130
  Move AsciiCsa to end of BIDS
  Eliminate AppVeyor compiler warnings
  Remove EchoTrainDuration and EPIFactor: rordenlab#127
  BIDS cleanup
  Reorder items in BIDS as suggested by Michael Harms
  Report Partial Fourier in BIDS json
  ...

README.md

@@ -15,8 +15,11 @@ This software should run on macOS, Linux and Windows without requiring any other
 
 ## Versions
 
-21-Aug-2017
+23-Sept-2017
+ - Swap [phase-encoding direction polarity](https://github.com/rordenlab/dcm2niix/issues/125) for Siemens images where PE is in the Column direction.
  - Sort diffusion volumes by [B-value amplitude](https://www.nitrc.org/forum/forum.php?thread_id=8396&forum_id=4703) (use "-d n"/"-d y" to turn the feature off/on).
+ - BIDS tag [TotalReadoutTime](https://github.com/rordenlab/dcm2niix/issues/130) handles partial fourier, Phase Resolution, etc (Michael Harms).
+ - Additional [json fields](https://github.com/rordenlab/dcm2niix/issues/127).
 
 18-Aug-2017
  - Better BVec extraction for  [PAR/REC 4.1](https://www.nitrc.org/forum/forum.php?thread_id=8387&forum_id=4703).

console/CMakeLists.txt

@@ -25,9 +25,11 @@ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-dead_strip")
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     # using GCC
-    add_definitions(-Wno-unused-result)
-    if (${CMAKE_CXX_COMPILER_VERSION} VERSION_GREATER 4.7)
-        add_definitions(-fno-diagnostics-show-caret)
+    if (${CMAKE_CXX_COMPILER_VERSION} VERSION_GREATER 4.4.7)
+        add_definitions(-Wno-unused-result)    # available since GCC 4.5
+    endif()
+    if (${CMAKE_CXX_COMPILER_VERSION} VERSION_GREATER 4.7.4)
+        add_definitions(-fno-diagnostics-show-caret)    # available since GCC 4.8
     endif()
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
     # using Intel C++

console/jpg_0XC3.cpp

@@ -125,17 +125,21 @@ unsigned char *  decode_JPEG_SOF_0XC3 (const char *fn, int skipBytes, bool verbo
     unsigned char *lRawRA = (unsigned char*) malloc(lRawSz);
     size_t lSz = fread(lRawRA, 1, lRawSz, reader);
     fclose(reader);
-    if ((lSz < lRawSz) || (lRawRA[0] != 0xFF) || (lRawRA[1] != 0xD8) || (lRawRA[2] != 0xFF)) {
+    if ((lSz < (size_t)lRawSz) || (lRawRA[0] != 0xFF) || (lRawRA[1] != 0xD8) || (lRawRA[2] != 0xFF)) {
         abortGoto("JPEG signature 0xFFD8FF not found at offset %d of %s\n", skipBytes, fn);//signature failure http://en.wikipedia.org/wiki/List_of_file_signatures
     }
     if (verbose)
         printMessage("JPEG signature 0xFFD8FF found at offset %d of %s\n", skipBytes, fn);
     //next: read header
     long lRawPos = 2; //Skip initial 0xFFD8, begin with third byte
     //long lRawPos = 0; //Skip initial 0xFFD8, begin with third byte
-    unsigned char btS1, btS2, SOSss, SOSse, SOSahal, SOSpttrans, btMarkerType, SOSns = 0x00; //tag
-    uint8_t SOFnf, SOFprecision;
-    uint16_t SOFydim, SOFxdim; //, lRestartSegmentSz;
+    unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; //tag
+    unsigned char SOSpttrans = 0;
+    unsigned char SOSss = 0;
+    uint8_t SOFnf = 0;
+    uint8_t SOFprecision = 0;
+    uint16_t SOFydim = 0;
+    uint16_t SOFxdim = 0;
     // long SOSarrayPos; //SOFarrayPos
     int lnHufTables = 0;
     const int kmaxFrames = 4;
@@ -186,7 +190,7 @@ unsigned char *  decode_JPEG_SOF_0XC3 (const char *fn, int skipBytes, bool verbo
                     DHTnLi = DHTnLi +  l[lFrameCount].DHTliRA[lInc];
                     if (l[lFrameCount].DHTliRA[lInc] != 0) l[lFrameCount].MaxHufSi = lInc;
                     if (verbose) printMessage("DHT has %d combinations with %d bits\n", l[lFrameCount].DHTliRA[lInc], lInc);
-                    
+
                 }
                 if (DHTnLi > 17) {
                     abortGoto("Huffman table corrupted.\n");

console/main_console.cpp

@@ -77,6 +77,7 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
     printf("  -b : BIDS sidecar (y/n/o(o=only: no NIfTI), default %c)\n", bidsCh);
     if (opts.isAnonymizeBIDS) bidsCh = 'y'; else bidsCh = 'n';
     printf("   -ba : anonymize BIDS (y/n, default %c)\n", bidsCh);
+    printf("  -c : comment stored as NIfTI aux_file (up to 24 characters)\n");
     if (opts.isSortDTIbyBVal) bidsCh = 'y'; else bidsCh = 'n';
     printf("  -d : diffusion volumes sorted by b-value (y/n, default %c)\n", bidsCh);
     #ifdef mySegmentByAcq
@@ -113,13 +114,15 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
     printf(" Defaults stored in Windows registry\n");
     printf(" Examples :\n");
     printf("  %s c:\\DICOM\\dir\n", cstr);
+    printf("  %s -c \"my comment\" c:\\DICOM\\dir\n", cstr);
     printf("  %s -o c:\\out\\dir c:\\DICOM\\dir\n", cstr);
     printf("  %s -f mystudy%%s c:\\DICOM\\dir\n", cstr);
     printf("  %s -o \"c:\\dir with spaces\\dir\" c:\\dicomdir\n", cstr);
 #else
     printf(" Defaults file : %s\n", opts.optsname);
     printf(" Examples :\n");
     printf("  %s /Users/chris/dir\n", cstr);
+    printf("  %s -c \"my comment\" /Users/chris/dir\n", cstr);
     printf("  %s -o /users/cr/outdir/ -z y ~/dicomdir\n", cstr);
     printf("  %s -f %%p_%%s -b y -ba n ~/dicomdir\n", cstr);
     printf("  %s -f mystudy%%s ~/dicomdir\n", cstr);
@@ -195,6 +198,9 @@ int main(int argc, const char * argv[])
                     	opts.isAnonymizeBIDS = true;
                 } else
                 	printf("Error: Unknown command line argument: '%s'\n", argv[i]);
+            } else if ((argv[i][1] == 'c') && ((i+1) < argc)) {
+                i++;
+                snprintf(opts.imageComments,24,"%s",argv[i]);
             } else if ((argv[i][1] == 'd') && ((i+1) < argc)) {
                 i++;
                 if (invalidParam(i, argv)) return 0;

console/nifti1_io_core.cpp

@@ -86,19 +86,19 @@ int isSameFloat (float a, float b) {
 
 ivec3 setiVec3(int x, int y, int z)
 {
-    ivec3 v = {x, y, z};
+    ivec3 v = {{x, y, z}};
     return v;
 }
 
 vec3 setVec3(float x, float y, float z)
 {
-    vec3 v = {x, y, z};
+    vec3 v = {{x, y, z}};
     return v;
 }
 
 vec4 setVec4(float x, float y, float z)
 {
-    vec4 v= {x, y, z, 1};
+    vec4 v= {{x, y, z, 1}};
     return v;
 }