Hi @henry36911,
Yes, unfortunately running MRtrix on Windows via MSYS2 comes with limitations, one of which is that other 3rd party packages that some of the scripts rely on won’t work, because they’re simply not available on that platform. More information on that on the MSYS2 download page.
As to what you can do about it: if you’re running on Windows 11, you can install WSL2 with Wayland support, and then install a full-featured Ubuntu Linux environment with graphics support. That would then allow you to run both MRtrix (the linux version) along with FSL, ANTs, and any of the other required packages. See e.g. this post for further details. Note that this will eventually be our recommended route for installation on Windows (not yet though as this doesn’t work completely under Windows 10, and there are still many people running that OS).
All the best,
Donald.