MRtrix, FSL, ANTS, ... on the Windows subsystem for Linux


Windows 10 users, rejoice! Using the Windows subsystem for Linux, you can now basically hit start, type bash, and you’re in a Linux environment; Ubuntu to be precise. Here’s some info to install this feature first: .

After that, you can literally copy the MRtrix installation instructions for Linux ( ), as if you are on Ubuntu. That’s because you are effectively on Ubuntu, including apt-get and everything that comes with it! Everything but the graphical side of MRtrix runs. For mrview (and shview), you’ll still need the MSYS2 approach as before. But both systems can access your entire Windows filesystem; so you’ll just need to have 2 terminals open (bash on Ubuntu on Windows for all processing, and MinGW opened in the same path/folder, just for quick mrview purposes).

FSL can be installed, just as on Ubuntu, from Neurodebian via the instructions on and and .

ANTS can be downloaded for Ubuntu from or compiled from source using the instructions on (I checked and did the latter).

Installing all of this, all MRtrix scripts will run successfully (including dwipreproc, dwibiascorrect with both -fsl and -ants options, and 5ttgen).

More random info on the WSL:

Installing using Windows Subsystem for Linux
Mrtrix3 configuration problem on Windows Subsystem for Linux (WSL)
5ttgen: [ERROR] Script cannot run in FSL mode on Windows