Hi Frederick,
freesurfer always transforms your input data into 256 cubed. It does,
however, store information on this transform, so you can get your data
back into the original space if you want to.
Let's say you wanted to get Freesurfer's segmentation back into original
space. You could cd into your subject's mri subdirectory and do:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg_in_raw_space.mgz
Cheers,
Johannes
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