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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
