to correct the pial surface for incorrect assignment of head tissue, I edit the brainmask.mgz. Hope that's correct...
Thanks,
Torsten
On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote:
and which volume are you editing? On Tue, 4 Oct 2011, Torsten Ruest wrote:
Hi Bruce,
thanks for your quick reply. No I am editing using the following command:
tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white
Thanks,
Torsten
On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote:
what pial edits to you want to undo specifically? Was it just edits to the brain.finalsurfs.mgz volume?
On Mon, 3 Oct 2011, Torsten Ruest wrote:
Hi there,
I think there is an option to remove all edits that have been incorporated using recon2 -clean.
Is there a chance that I can selectively undo all incorporated pial edits (ie that have been incorporated by running "recon-all -subject TEST -autorecon2 > TEST-2.log")?
Thanks very much in advance,
Torsten
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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.
Hi Torsten, If you run: recon-all -all -clean-bm -s subjid
This should trask all the edits you made to the brainmask volume and make a new one to replace that. It will keep all your other edits. Allison
On Tue, 4 Oct 2011, Torsten Ruest wrote:
to correct the pial surface for incorrect assignment of head tissue, I edit the brainmask.mgz. Hope that's correct...
Thanks,
Torsten
On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote:
and which volume are you editing? On Tue, 4 Oct 2011, Torsten Ruest wrote:
Hi Bruce,
thanks for your quick reply. No I am editing using the following command:
tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white
Thanks,
Torsten
On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote:
what pial edits to you want to undo specifically? Was it just edits to the brain.finalsurfs.mgz volume?
On Mon, 3 Oct 2011, Torsten Ruest wrote:
Hi there,
I think there is an option to remove all edits that have been incorporated using recon2 -clean.
Is there a chance that I can selectively undo all incorporated pial edits (ie that have been incorporated by running "recon-all -subject TEST -autorecon2 > TEST-2.log")?
Thanks very much in advance,
Torsten
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Allison, that's great!
Torsten
On Tue, 2011-10-04 at 09:40 -0400, Allison Stevens wrote:
Hi Torsten, If you run: recon-all -all -clean-bm -s subjid
This should trask all the edits you made to the brainmask volume and make a new one to replace that. It will keep all your other edits. Allison
On Tue, 4 Oct 2011, Torsten Ruest wrote:
to correct the pial surface for incorrect assignment of head tissue, I edit the brainmask.mgz. Hope that's correct...
Thanks,
Torsten
On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote:
and which volume are you editing? On Tue, 4 Oct 2011, Torsten Ruest wrote:
Hi Bruce,
thanks for your quick reply. No I am editing using the following command:
tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white
Thanks,
Torsten
On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote:
what pial edits to you want to undo specifically? Was it just edits to the brain.finalsurfs.mgz volume?
On Mon, 3 Oct 2011, Torsten Ruest wrote:
Hi there,
I think there is an option to remove all edits that have been incorporated using recon2 -clean.
Is there a chance that I can selectively undo all incorporated pial edits (ie that have been incorporated by running "recon-all -subject TEST -autorecon2 > TEST-2.log")?
Thanks very much in advance,
Torsten
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Torsten Ruest