qianchne/mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density

MRtrix

Please visit the official website for MRtrix to access the documentation for MRtrix3, including detailed installation instructions.

Getting help

Support and general discussion is hosted on the MRtrix3 Community Forum. Please also look through the Frequently Asked Questions on the wiki section of the forum. You can address all MRtrix3-related queries there, using your GitHub or Google login to post questions.

Quick install

1. Install dependencies by whichever means your system uses. These include: Python (>=2.6), a C++ compiler with full C++11 support (g++ 4.9 or later, clang++), Eigen (>=3.2.8), zlib, OpenGL (>=3.3), and Qt (>=4.8, or at least 5.1 on MacOSX).

2. Clone Git repository and compile:

    $ git clone https://github.com/MRtrix3/mrtrix3.git
    $ cd mrtrix3/
    $ ./configure
    $ ./build
   

3. Set the PATH:

   • Bash shell:

     run the set_path script provided:

       $ ./set_path
     

     or edit the startup ~/.bashrc or /etc/bash.bashrc file manually by adding this line:

       $ export PATH=/<edit as appropriate>/mrtrix3/bin:$PATH
     

   • C shell:

     edit the startup ~/.cshrc or /etc/csh.cshrc file manually by adding this line:

       $ setenv PATH /<edit as appropriate>/mrtrix3/bin:$PATH
     

4. Test installation:

   Command-line:

    $ mrconvert
   

   GUI:

    $ mrview
   

Keeping MRtrix3 up to date

1. You can update your installation at any time by opening a terminal in the mrtrix3 folder, and typing:

    git pull
    ./build
   

2. If this doesn't work immediately, it may be that you need to re-run the configure script:

    ./configure
   

   and re-run step 1 again.

Building a specific release of MRtrix3

You can build a particular release of MRtrix3 by checking out the corresponding tag, and using the same procedure as above to build it:

git checkout 3.0_RC3
./configure
./build

Contributing

Thank you for your interest in contributing to MRtrix3! Please read on here to find out how to report issues, request features and make direct contributions.