If you do it in tkregister2, you can load the orig.mgz as the target and movable, apply the transformations you want, then save the registration matrix. Then use mri_vol2vol to actually resample the volume (either orig or aseg). When applying it to the aseg, you should make sure to use --interp nearest.
doug
Jordan Poppenk wrote:
Dear list,
I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method.
Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it.
Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)?
Thanks in advance for any help.
Cheers, Jordan
Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk
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