users > No reformatted files produced from Fiji/CMTK registration
Jun 28, 2019  08:06 AM | Zane Aldworth
No reformatted files produced from Fiji/CMTK registration
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!

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TitleAuthorDate
No reformatted files produced from Fiji/CMTK registration
Zane Aldworth Jun 28, 2019
Greg Jefferis Jun 28, 2019
Zane Aldworth Jun 28, 2019
Greg Jefferis Jun 29, 2019
Zane Aldworth Jun 29, 2019
Greg Jefferis Jun 30, 2019