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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