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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Hi,
I have a related question. Should the optic nerve included in the pial surface be considered a problem for the surfaces? The nerve also does create a small bump on the inflated surface as viewed in tksurfer.
If so, from which volume should the optic nerve be erased?
Thanks for your time.
Lars T. Westlye University of Oslo
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
Hi Lars,
Typically the optic nerve is not a problem - it's likely included in all our subjects. If you feel you need to edit it you will want to remove it from the brainmask.mgz volume, to affect where your pial surface is.
Jenni
-----Original Message----- From: Lars Tjelta Westlye [mailto:larstw@student.sv.uio.no] Sent: Monday, May 21, 2007 5:26 AM To: Jenni Pacheco Cc: 'Freesurfer Mailing List' Subject: RE: [Freesurfer] tkmedit
Hi,
I have a related question. Should the optic nerve included in the pial surface be considered a problem for the surfaces? The nerve also does create a small bump on the inflated surface as viewed in tksurfer.
If so, from which volume should the optic nerve be erased?
Thanks for your time.
Lars T. Westlye University of Oslo
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
freesurfer@nmr.mgh.harvard.edu
-
Jenni Pacheco -
Lars Tjelta Westlye