Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
Hi David
what version are you running?
Bruce On Wed, 28 Dec 2011, David Groppe wrote:
Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
-David
On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David
what version are you running?
Bruce
On Wed, 28 Dec 2011, David Groppe wrote:
Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
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.
Try fixing the aseg and running from there forward
On Dec 28, 2011, at 9:05 PM, David Groppe david.m.groppe@gmail.com wrote:
Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
-David
On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David
what version are you running?
Bruce
On Wed, 28 Dec 2011, David Groppe wrote:
Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
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.
-- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/
You could also look at the filled.mgz to see if the hemis are separated and potentially make some edits. Then you would run:
recon-all -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -autorecon3 -s <subjID>
Lastly, you could set seed points for the corpus callosum using the -cc-crs flag.
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences https://surfer.nmr.mgh.harvard.edu/fswiki/Edits -See the "seed points, fill and cut" section
-Louis
On Wed, 28 Dec 2011, David Groppe wrote:
Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
-David
On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David
what version are you running?
Bruce
On Wed, 28 Dec 2011, David Groppe wrote:
Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
David Groppe -
Louis Nicholas Vinke