Hi Martin,
You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit
Hi,
I have a question about using tkmedit. Up until now, our group has been editing out the eye muscles after autorecon-1 and editing out the optic nerve after autorecon-2. I know on earlier versions of freesurfer it was highly recommended to do so because the program would sometimes crash otherwise. However, using the newer version, the program seems to know to not include eye muscles in the pial matter boundary, and the optic nerve does create a region of high curvature at that point, but it doesn't crash the program.
I was wondering, in your own analyses, did you do editing at each step (excluding situations that are obviously out of the norm), and would it be a bad thing not to edit those regions in the majority of cases?
Thanks, Martin Chang
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