Hmmm.  That doesn't seem to change the output, assuming I correctly understand the input format.  In my case I have only a single channel, with one reference brain and (at least initially) a single floating brain that I wish to register, so my input is currently:
filestem_01.nrrd (the reference brain)
otherfilestem_01.nrrd (the brain to be registered)

I've selected only to reformat channel 01, run the command, and still only get the Registration directory as an output.  Should I expect a Reformat directory, as in the classic gui?  Or are the reformatted/registered brains saved in some other manner?

Also, are there equivalent commands to e.g. "--class-ref label", "dof2mat", or "reformatx" in the gui, or is that functionality not supported here?

Thanks!