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: https://msdn.microsoft.com/en-us/commandline/wsl/install_guide .
After that, you can literally copy the MRtrix installation instructions for Linux ( http://mrtrix.readthedocs.io/en/latest/installation/linux_install.html ), 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
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
FSL can be installed, just as on Ubuntu, from Neurodebian via the instructions on http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux and http://neuro.debian.net/pkgs/fsl-complete.html and http://neuro.debian.net/debian/extracts/fsl/README.Debian .
ANTS can be downloaded for Ubuntu from https://github.com/stnava/ANTs/releases or compiled from source using the instructions on https://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/ (I checked and did the latter).
Installing all of this, all MRtrix scripts will run successfully (including
dwibiascorrect with both
-ants options, and
More random info on the WSL: