Hi Dana, 

I am also using CMTK on windows, but I am using WSL https://docs.microsoft.com/en-us/windows/wsl/about. I think that might be easier than trying to use Cygwin as Greg suggested. At least it was easier for me. With WSL you can just install the linux version of CMTK. I followed these instructions:
https://www.nitrc.org/forum/forum.php?th...
making sure to enable to optional tools during ccmake to install munger
https://www.nitrc.org/forum/message.php?...

You wont have the GUI this way, but once you have a munger script that runs it is very easy to modify it to run whatever new data you want to register.