You can copy your edited brainmask.mgz to brain.finalsurfs.manedit.mgz then rerun the case from the beginning using: recon-all -all -clean-bm -s subjid

This will recreate the brainmask.mgz so no chunks of cerebellum are missing (and therefore cerebellum volume estimates won't be off). If you don't care about cerebellum and the aseg is still accurate everywhere else despite the missing cerebellum, you don't have to do this.

Make a backup copy of brain.finalsurfs.manedit.mgz somewhere else just in case it gets written over when you rerun. Allison

Date: Fri, 18 Nov 2011 11:55:49 -0800 (PST) From: Jordan Pierce jepierce87@yahoo.com To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cerebellum Edits

We've been manually editing brainmask.mgz to remove voxels that are included in the pial surface that shouldn't be, and recently found on the wiki that to remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz instead.  What is the reason for this difference? Do we need to redo edits that we've done only on brainmask.mgz?  We are going to be looking at cortical thickness.

Thanks,   Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer