Important notes - please read first

  • When installing or using MRtrix3, always use the ‘MinGW-w64 Win64 shell’; it will not work with the ‘MSYS2 shell’ or ‘MinGW-w64 Win32 shell’.

  • Some of the Python scripts provided with MRtrix3 are dependent on external software tools (e.g. FSL or ANTs). If these packages are not available on Windows, then the corresponding MRtrix3 scripts also cannot be run on Windows. A virtual machine may therefore be required in order to use these particular scripts; though MRtrix3 may still be installed natively on Windows for other tasks.

  • These instructions have changed for version 3.0.1, and no longer make use of a dedicated MRtrix3 pacman package repository. If you had used our previous recommendations and find that pacman -Syu warns that the mrtrix3 repo cannot be found, you can fix this by editing the /etc/pacman.conf file to remove these lines:

    SigLevel = Optional TrustAll
    Server =

Install MSYS2

Note: skip this step if MSYS2 is already installed on your system.

At the time of writing, we recommend the use of MSYS2 to run MRtrix3 on Microsoft Windows. It provides a complete Unix-like terminal environment, including the bash shell, and allows applications to be compiled to Windows-native code using the MinGW compiler. This is particularly important if you plan to use the MRtrix3 GUI components, mrview and shview, since these generally won’t work otherwise (at least not reliably or with full performance).

  • Download and install the most recent 64-bit MSYS2 installer (the filename should be of the form msys2-x86_64-*.exe), and follow the installation instructions from the MSYS2 wiki.

  • Start the ‘MinGW-w64 Win64 Shell’ from the start menu

  • Update the system packages, as per the instructions for the MSYS2 installer:

    pacman -Syu

    Close the terminal, start a new ‘MinGW-w64 Win64 Shell’, and repeat as necessary until no further packages are updated.

    Note: at time of writing, this MSYS2 system update may give a number of instructions, including: terminating the terminal when the update is completed, and modifying the shortcuts for executing the shell(s). Although these instructions are not as prominent as they could be, it is vital that they are followed correctly!

Managing MSYS packages with pacman

Once installed, additional packages can be installed and managed using the pacman command that comes bundled with MSYS2. If you need to find out more about how to use the pacman utility, there are plenty of resources available online, e.g. the Arch Linux page, or this Lifewire tutorial.

Install MRtrix3

  • Start the ‘MinGW-w64 Win64 Shell’ from the start menu

  • Download and install the latest MRtrix3 package. This can be accomplished by copy/pasting the following commands into the terminal (use Shift-Insert to paste into the terminal):

    pkg=$(curl -s | grep browser_download_url.*.tar.zst | awk '{print $2}' | tr '"' ' ' | sort -n | tail -n 1 )
    echo $pkg
    curl -L $pkg -O
    pacman -U $(basename $pkg)

    These commands perform the following steps:

    • figure out URL of most up to date package
    • print out the URL to check it is as expected (this should report something like
    • download the package
    • install the package using pacman

    If necessary, this can also be done by downloading the package directly from the latest release page on the MRtrix3 GitHub repository (the relevant file should be called mingw-w64-x86_64-mrtrix3-X.Y.Z-n-x86_64.pkg.tar.xz), and installing it using the pacman -U command (see links above for instructions on how to use pacman).

Upgrading MRtrix3

To update, simply run the install procedure again.