Thank you for your answer!

No, I haven't copy+pasted anything, so that shouldn't be the problem. I have also used epiunwarp and reformatx from the same source. When trying the describe function, all I get is "File does not exist".

Thanks for the advice about running Cygwin tools in Windows. I tried running the whole EPI unwarping in the Windows command line using the Cygwin-CMTK (with Cygwin binaries added to the path), and it worked! So I think that will probably be my solution, given that I am able to modify the path in MeVisLab.

Best,
Ingrid