Hi all,

I recently tried to use the CMTK gui from FIJI in order to register some brains.  While the process seemed to work well and generated a "Registration" directory (with affine and warp subdirectories), I did not see a directory for the reformatted images, nor indeed any reformatted images in the other directories.  I did find the "registration" output file, which I gather I could use to transform the original images if I wanted to install command line CMTK, but that seems to be a bit against the spirit the spirit of using a gui.
I did check (and uncheck and re-check) the box for reformat in the gui, and I performed the registration with affine & warp as well as affine only, with all output results being similar- registration folder produced, but no reformatted image.

Should I expect reformatted images as an output of FIJI/CMTK?

Also, assuming I can get the reformatted images, I have a couple of further options from command line CMTK that I would like to implement in the gui, but it seems that the syntax may need to be a bit different:
I'm registering labeled files instead of actual brains, so I need to add the "--class-ref label" and "--class-flt label" tags- is that the proper syntax? And would assume it goes to the "further registration params" field?
Similarly, I believe I read that the default similarity measure is nmi.  Is that the case, and if not can I just add "--nmi"?
What is the default interpolation method, and how could I change it to partial volume (assuming "--partial-volume" doesn't work)?
For the affine registration I see 9 degrees of freedom as output, but haven't seen a 12 degree of freedom output (i.e. no sheer elements in the "registration" output file).  Is there a way to do sheering or to specify the dof in the registration?
Finally, once the labelled files have been registered, I would like to apply the transformation matrices to both the original image stacks as well as to a traced neuron file.  Are there commands equivalent dof2mat and reformatx from the command line?

Thanks for any help!