Kazim,

I'm sorry, I have limited ability to help you here. I've never tried to do this in Windows or ever used WSL. run_mri_reface_docker.sh is bash code, so you can view and/or modify the source if some changes are needed for your WSL environment. 

In this line, 
File not found: C:/Users/kjafri/AppData/Local/Temp/tmp.hiSWIStylc/inputs/input
we are seeing a windows-style path: ("C:/") rather than a Linux-style path ("/c/"). The error is coming from inside the Docker, so we shouldn't be seeing a path like that. My best guess is that mktemp -d (line 56 of run_mri_reface_docker.sh) is not behaving appropriately for the WSL/MINGW/Linux-emulating environment. This probably means that you have an environment value $TMPDIR that contains something like "C:/" when inside WSL you want something like "/c/" (or nothing at all, and let it be the default). You appear to be using some sort of AI-based translation layer ("Gordon"), and it may be the culpret of making changes to your environment (TMPDIR) that aren't appropriate here. 

Chris