Ok, this seems to be the problem that I posted about earlier today. There is indeed an issue with the procedure, which is probably a result of recent changes in MSYS2.
I’ve just pushed a fix for this that’ll hopefully handle this more gracefully, but it’s not yet merged. In the meantime, the workaround I suggest is to replace:
$ ./configure
$ ./build
with:
$ /usr/bin/python ./configure
$ /usr/bin/python ./build
Other random notes:
I’m not sure what makes you say that…? The error message is about Eigen3, which is unrelated to Qt…
Yes and no. You can build MRtrix3 on WSL, but you can’t run mrview yet - see discussion e.g. here.