Dear Jonathan, the munger script is fussy about the naming of your input images. The floating images (but not the template) must end in 01.nrrd 02.nrrd etc to denote the channel. See http://flybrain.mrc-lmb.cam.ac.uk/dokuwi... (linked from the Fiji CMTK gui GitHub page) for further details.

In terms of the munger command line switches

-c 01 is the default and can be omitted but
-r 02 will only reformat channel 2, whereas you probably want
-r 0102 so that you can check that the nc82 registration In channel 1 worked ok.

All the best, Greg.