How to debug your data

This tool allows one to display in a common 3D space all the objects used by COMMIT (DWI data, streamlines etc...) in order to spot possible inconsistencies between the conventions of COMMIT and the software that generated the data, e.g. flip in some axes in the DWI data or in the peaks, spatial shift of the streamlines, whether the affine transformation was already applied to the data etc.

Warning

Please note that this tool is very rudimental and is released only for debugging purposes.

Synopsis

COMMIT_debugger \
    <dwi> \
    <scheme> \
    [-p <peaks> ] \
    [-f <tracts>] \
    [-m <map>]

• dwi: DWI data (4D NIFTI file);
• scheme: corresponding acquisition scheme (Camino format);
• peaks: major directions of the hindered water pools in each voxel (4D NIFTI file);
• tracts: tractogram to generate the restricted contributions of the tracts in each voxel (.TRK file); NB: no .TCK support for now
• map: background map; default is a b0 computed from the DWI data.

A dropdown menu will appear with right-click of the mouse.

Install dependencies

You need to install the following libraries:

• CMake to allow cross-platform compilation;
• Niftilib for reading/writing NIFTI files;
• Blitz++ for efficient manipulation of multi-dimensional arrays;
• OpenGL and GLUT for 3D visualization.

Please follow the corresponding documentation to install these libraries on your platform. Our code was successfully tested on Linux (Ubuntu 14.04) and OSX (10.9 up to 10.15) systems.

OSX with homebrew

If your're using homebrew, then the following should work:

brew tap brewsci/science
brew install cmake
brew install blitz
brew install niftilib

The OpenGL and GLUT libraries are already provided by the operating system.

UBUNTU with apt-get

To be done...

Compile, build and install

Open the terminal and type:

cd extras
mkdir build
cd build
ccmake ..

Hit c (twice) and then g. This will create the required makefiles for the compilation. Once back to the terminal, type:

make
make install

This will install the binaries into the /usr/local/bin folder. This installation path can be changed by rerunning ccmake .. and then modifying the CMAKE_INSTALL_PREFIX parameter to suit your custom needs.