Hi! The following is what has happened:
$ dwifslpreproc dwi_45784336_unringed.mif dwi_45784336_preproc.mif -pe_dir AP -rpe_none
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc: [ERROR] Script cannot run on Windows due to FSL dependency
p.s.:The error doesn’t occur in the case of mrconvert, dwidenoise, and mrdegibbs.
Do you have FSL installed? Also, as a heads-up I recommend you also install ANTs which will be probably required in the next step - dwibiascorrect.
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,