Hi Ingrid -

There have recently been folks who've had similar issues because they copy-and-pasted command lines from a text editor, and in the process their "space" characters were changed to something other than ASCII space (e.g., some Unicode space). That led to failure of the command, but was virtually impossible to tell from looking at the command line, because the Unicode space and ASCII space appear exactly the same.

Can you rule out that this is happening to you? (In general, if you type your command, not paste it, then you should be okay.)

Another possible source of problems is that CMTK will generally compress Nrrd files using libz compression. Since libz is not a standard library on native Windows, it needs to be built along with CMTK (a source version of it is actually bundled with CMTK's source code.) If you wrote a file with a CMTK tool build with libz support, then a tool built without that support would not be able to read the resulting files. So if, say, you ran epiunwarp from a Cygwin build but tried to read the file with a native Windows reformatx binary. then that might fail. If you are using epiunwarp/reformatx from the same source, then you should be safe, though, since either all tools in a build have libz support, or none do.

Finally - I think you *should* actually be able to run Cygwin tools from inside MeVisLab, even on Windows. A Cygwin binary is a perfectly valid Windows binary; it simply depends on the cygwin.dll to provide Cygwin functionality. So as long as you have cygwin.dll installed (and, perhaps, in your search path) you should have no problem running Cygwin binaries from the Windows shell or any other program, just like you would a native Windows tool.

Hope this helps.

Best,
Torsten