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 <jepierc...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
