How to Convert from FreeSurfer Space Back to Native Anatomical Space

Question: I have successfully run a subject's data through FreeSurfer. FreeSurfer creates volumes in 1mm3, 2563 space, but I want the FreeSurfer results in the space of my original anatomical. How do I do this?

The exact command you use depends on what you want to convert, an image (like brain.mgz) or a segmentation (like aseg.mgz).

For an image:

cd $SUBJECTS_DIR/subject
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz

"rawavg.mgz" is a file created by FreeSurfer and is in the native space of your anatomical. The output is brain-in-rawavg.mgz and will be in the native space of the anatomical.

For a segmentation (aseg.mgz, aparc+aseg.mgz, wmparc.mgz, etc):

cd $SUBJECTS_DIR/subject
mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz

After running these two commands, tkmedit should show the aseg overlaid properly on the brain

tkmedit -f brain-in-rawavg.mgz -seg aseg-in-rawavg.mgz