If you only made edits to the aseg, then you can run: recon-all -s subject_name -autorecon2-aseg -autorecon3 which omits some stages that don't need to be redone (but which would otherwise be included if you use the -autorecon2 flag).
If you in addition added control points, then you would run recon-all -s subject_name -autorecon2-cp -autorecon3 which includes the stages needed to handle the aseg edits as well. cheers, -MH On Fri, 2011-11-25 at 22:49 +0100, Tetiana Dadakova wrote: > Hi Maria, > > Yes, you are editing aseg.mgz. After saving the segmentation, you should run > <recon-all -s subject_name -autorecon2 -autorecon3>. > If you also added some control points, then you should run > <recon-all -s subject_name -autorecon2-cp -autorecon3> > > Best wishes, > Tanja. > > On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski > <[email protected]> wrote: > > > > Hi, > > > > I am a relatively new user of Freesurfer and have a couple questions. > > I have gone through the tutorials and I am now at the point where I check > > the segmentation. > > If I open my subject in tkemdit > > (tkmedit your_subject_name brainmask.mgz -surfs -aseg) and use the edit the > > segmentation and then press "save segmentation", I am editing the aseg.mgz > > file, correct? After doing that, what parts of recon-all would I need to > > run again? > > Thanks, > > Maria > > -- > > Maria Jalbrzikowski, M.A. > > University of California, Los Angeles > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
