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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jdtournier Merge pull request #1515 from MRtrix3/only_include_xmmintrin_if_used
only include xmmintrin.h header if actually used
Latest commit 2b8e7d0 Dec 13, 2018
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bin dwipreproc: Compatibility with FSL6.0.0 Dec 8, 2018
cmd dwiextract: Fix extraction based on TRT Nov 25, 2018
core only include xmmintrin.h header if actually used Dec 13, 2018
docs docs: update install instructions, notably for Windows Aug 13, 2018
icons final svg source cleanup Mar 1, 2017
lib/mrtrix3 dwipreproc: Search PATH for 'eddy_cpu' Dec 9, 2018
matlab write_mrtrix: update to output generic fields Jul 20, 2017
share/mrtrix3 labelconvert: Add lookup tables for HCP MMP Apr 10, 2018
src Streamline::calc_length(): Make no assumptions Dec 9, 2018
testing further updated test data for mrpad Nov 21, 2018
.gitignore add testing/src/project_version.cpp to .gitignore May 17, 2018
.gitmodules use submodule to host testing data Mar 29, 2016
.travis.yml TravisCI: try using git repo to fetch Eigen Dec 11, 2018
Doxyfile Doxyfile: update input folders to list 'core' rather than 'lib' Aug 25, 2017
LICENCE.txt use correct spelling for LICENCE.txt... Dec 11, 2015 README: fix stray tabs Jun 3, 2018
appveyor.yml add no-action appveyor,yml to allow testing to pass Aug 14, 2018
build fix and macro MRTRIX_MODULE -> MRTRIX_PROJECT May 11, 2018
check_syntax checK_syntax: Look for %zu in print calls Jul 9, 2018
configure bugfix for configure May 17, 2018
doxygen Major overhaul of version number handling - please update external co… Jan 7, 2014 Move scripts/ to generate_bash_compl… Feb 7, 2017 new icons and command to install mime types, icons and desktop applic… Oct 24, 2014
mrtrix-mime.xml Revert "signal handling: try SetConsoleCtrlHandler on Windows - doesn… Jan 18, 2017
mrtrix-mrview.desktop Revert "signal handling: try SetConsoleCtrlHandler on Windows - doesn… Jan 18, 2017
package_mrtrix package_mrtrix: option to set QT plugin path. defaults to search for it Jul 11, 2017
run_pylint run_pylint: fix to report correct version information Nov 26, 2018
run_tests run_test: find bug introduced in previous commit Mar 26, 2018
set_path Better detection of MinGW python Oct 24, 2017 build: add option -nopaginate May 10, 2018
update_dev_doc update_dev_doc: minor fix Apr 13, 2016


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
     $ 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:


     $ mrconvert


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


    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