We outline the steps for installing MRtrix3 for Windows using MSYS2. Please consult windows_trouble_shooting if you encounter any issues with the configure, build or runtime operations of MRtrix3.
Some of the Python scripts provided with MRtrix3 are dependent on external software tools (for instance FSL). 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.
To install MRtrix3, you will need the following:
- a C++11 compliant compiler
- Python version >= 2.6
- The zlib compression library
- Eigen version 3.2 (do not install the beta version)
- Qt version >= 4.7 [GUI components only]
All of these dependencies are installed below by the MSYS2 package manager.
To run the GUI components of MRtrix3 (
shview), you will also need:
- an OpenGL 3.3 compliant graphics card and corresponding software driver
When following the instructions below, use the ‘MinGW-w64 Win64 shell’; ‘MSYS2 shell’ and ‘MinGW-w64 Win32 shell’ should be avoided.
Install and update MSYS2¶
Download and install the most recent 64-bit MSYS2 installer from http://msys2.github.io/ (msys2-x86_64-*.exe).
Run the program ‘MinGW-w64 Win64 Shell’ from the start menu.
Update the system packages:
Future versions of MSYS2 will drop
update-core. If your version came without
update-core, it is probably safe to skip this step.
Close the shell and start ‘MinGW-w64 Win64 Shell’
Update the other packages:
Install MRtrix3 dependencies¶
From the ‘MinGW-w64 Win64 Shell’ run:
pacman -S git mingw-w64-x86_64-python3 mingw-w64-x86_64-python3-numpy pkg-config mingw-w64-x86_64-gcc mingw-w64-x86_64-eigen3 mingw-w64-x86_64-qt5 Sometimes ``pacman`` may fail to find a particular package from any of the available mirrors. If this occurs, you can download the relevant package from `SourceForge <https://sourceforge.net/projects/msys2/files/REPOS/MINGW/x86_64/>`__: place both the package file and corresponding .sig file into the ``/var/cache/pacman/pkg`` directory, and repeat the ``pacman`` call above.
Set up git and download MRtrix3 sources¶
Configure global settings for Git in the ‘MinGW-w64 Win64 Shell’:
git config --global user.name "John Doe" git config --global user.email firstname.lastname@example.org git config --global push.default upstream
Clone the MRtrix3 repository:
git clone https://github.com/MRtrix3/mrtrix3.git
Configure the MRtrix3 install:
cd mrtrix3 ./configure
If this does not work, examine the ‘configure.log’ file that is generated by this step, it may give clues as to what went wrong.
Build the binaries:
Set up MRtrix3¶
Set your PATH in the shell startup file:
echo "export PATH=$(pwd)/release/bin:$(pwd)/scripts:$PATH" >> ~/.bashrc
Note that although the scripts provided with MRtrix will appear in your path, many of these will not work on a Windows installation due to their dependency on FSL; a virtual machine with both MRtrix3 and FSL installed would be required to run these scripts in this scenario.
Close the terminal and start another one to ensure the startup file is read
mrviewto check that everything works
You may also want to have a look through the mrtrix_config_options, and set anything you think might be required on your system.
Keeping MRtrix3 up to date¶
You can update your installation at any time by typing:
git pull ./build
If this doesn’t work immediately, it may be that you need to re-run the configure script:
and re-run step 1 again.
Compiling external projects with
ln -s command actually creates a copy of the
target, not a symbolic link. By doing so, the build script is unable
to identify the location of the MRtrix libraries when trying to compile
an external module.
The simplest way around this is simply to invoke the build script of the main
MRtrix3 install directly. For example, if compiling an external project called
myproject, residing in a folder alongside the main
mrtrix3 folder, the
build script can be invoked with:
# current working directory is 'myproject': ../mrtrix3/build
If you really want a symbolic link, one solution is to use a standard Windows
command prompt, with Administrator priveleges: In the file explorer, go to
C:\Windows\system32, locate the file
cmd.exe, right-click and
select ‘Run as administrator’. Within this prompt, use the
command (note that the argument order passed to
mklink is reversed
with respect to
ln -s; i.e. provide the location of the link, then
the target). Make sure that you provide the full path to both link and
mklink C:\msys64\home\username\src\my_project\build C:\msys64\home\username\src\MRtrix3\build
msys64 should be able to interpret the softlink path correctly