Hi,

While CMTK can work under windows with cygwin or pearl, I think the Munger script may use unix style path and commands, setting up your environment in linux or macOs would be the optimal solution. Or if you want to stay on windows install it under the Windows Subsystem Linux.

If you are unsure use one of these methods, whichever you find work best:

https://github.com/sandorbx/Fiji-CMTK-re...

https://github.com/jefferis/fiji-cmtk-gu...