Just to add to what Greg is saying - if you do decide to try and run CMTK directly, there are several pieces of documentation that might help you:

https://www.nitrc.org/docman/index.php?g...

One of these is a general user guide covering mostly registration and reslicing. The other two deal with two very specific applications, unwarping of structural and echo-planar MRI.

Also, all CMTK tools will give you a summary of their available command line options when you call them with "--help"; in some cases, advanced options will only be shown with "--help-all", to keep the initial help output a little less cluttered.

Hope this helps.

Best,
  Torsten