Purposes

The main purposes of the build on comic1 are

to allow the use of the "special" Midas Analyze images in the Dementia Research Center, by setting the vox_offset to 0 when reading in the images;
to avoid potential crashes when using the gcc4/g++4 compilers on comic1, by using the default gcc/g++ compiler;
to have the latest build from Kelvin after he has left the Dementia Research Center.

Location

The source/build/installation are in "comic1:/home/kkleung/work/NifTK-14.03-kelvin".

CMake options

The basic CMake options are listed below:

 BUILD_COMMAND_LINE_PROGRAMS      ON
 BUILD_COMMAND_LINE_SCRIPTS       ON
 BUILD_NIFTYREC                   OFF
 BUILD_NIFTYREG                   OFF
 BUILD_NIFTYSEG                   OFF
 BUILD_NIFTYSIM                   OFF
 BUILD_PROTOTYPE                  ON
 BUILD_SUPERBUILD                 ON
 BUILD_TESTING                    OFF
 BUILD_UTILITIES                  OFF
 CMAKE_BUILD_TYPE                 Release
 CMAKE_INSTALL_PREFIX             /home/kkleung/work/NifTK-14.03-kelvin/install
 NIFTK_Apps/NiftyIGI              OFF
 NIFTK_Apps/NiftyMIDAS            OFF
 NIFTK_Apps/NiftyView             OFF
 NIFTK_BUILD_ALL_APPS             OFF
 NIFTK_USE_COTIRE                 OFF
 QT_QMAKE_EXECUTABLE              /home/kkleung/work/qt/install/bin/qmake
 VTK_USE_SYSTEM_FREETYPE          OFF

Some of the CMake advanced options are listed below:

 BUILDNAME                        Linux-x86_64-gcc--dev-7e26ab50-Rel
 BUILD_ITKFFTW                    ON
 CMAKE_CXX_FLAGS_RELEASE          -O3 -DNDEBUG -mfpmath=sse -msse2
 CMAKE_C_FLAGS_RELEASE            -O3 -DNDEBUG -mfpmath=sse -msse2

"-mfpmath=sse -msse2" is used to allow consistent floating point results across platforms/architectures.

Various manual patches

MITK warning as error

This is turned off by adding the following in "build/MITK-src/CMake/mitkMacroCreateModule.cmake".

 set(MODULE_WARNINGS_AS_ERRORS 0)

ITK vox_offset

The vox_offset is set to 0 for 2-file Nifti images (including Analyze images) by modifying one line in the file "build/ITK-src/Modules/ThirdParty/NIFTI/src/nifti/niftilib/nifti1_io.c".

   if( is_onefile ){
     ioff = (int)nhdr.vox_offset ;
     if( ioff < (int) sizeof(nhdr) ) ioff = (int) sizeof(nhdr) ;
   } else {
     // ioff = (int)nhdr.vox_offset ;
     ioff = 0 ;
   }

niftkTransformation

The compilation causes comic1 to run out of memory. The 2D cases have been removed to reduce the memory requirement.

niftkMacroFixupCommandLineApps.cmake

To speed up the installation, the fixup_bundle in "source/CMake/niftkMacroFixupCommandLineApps.cmake" is commented out.

    # This is slow, we have to validate apps one at a time.
    foreach(APP ${_install_APPS})
      set(_full_app_path "${CMAKE_INSTALL_PREFIX}/bin/${APP}")

      #install(CODE "
      #  include(BundleUtilities)
      #  fixup_bundle(\"${_full_app_path}\"   \"\"   \"${_library_dirs}\")
      #  " COMPONENT Runtime)

    endforeach()

The libraries are manually copied to the installation after "make install".