Thanks Greg! Unfortunately when I install CMTK from the Fiji CMTK GUI, the cmtk folder in the /bin/cmtk is always empty. I have another cmtk installed independently under /usr/bin and it functions under the command lines in the user guide, but it does not have munger.  I reinstalled my Fiji but the problem remains.

Is there any way to by pass the cmtk installed by the GUI and use the one under /usr/bin, but still use the GUI for input and configurations?Thanks!

Best,
Dan