MRtrix 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
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run.command(): Fix app cleanup with exitOnError=False
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README.md

MRtrix

Build Status

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 address all MRtrix3-related queries there. You can use you 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