Thank you Bruce, So if I want to edit both cortex and subcortical structures, should the steps be the following:
1. edit wm.mgz 2. recon-all -autorecon2-wm -subjid 3. edit subcortical structures 4. recon-all -autorecon2 -autorecon3 -subjid ? Best wishes, Tanja. On Thu, May 5, 2011 at 2:40 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Tanja > > yes, there is really no visible extreme capsule white matter, I guess > because it is so thin. If you are trying to fix the surfaces you will want > to edit the wm.mgz though, not the aseg.mgz. > > cheers > Bruce > > On Thu, 5 May 2011, Tetiana Dadakova wrote: > >> Dear Bruce, >> >> For some of my subjects the segmentation of putamen "sticks" to the >> cortex (please look at attached image "before.jpg"). Therefore, I do >> some manual corrections that affect the cortex (please look at >> attached image "after.jpg"). >> >> How should I proceed after this kind of manual correction? >> >> Thank you, >> Tanja. >> >> On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >>> >>> Hi Tanja >>> unless the editing would change the cortex, you don't need to worry about >>> it >>> >>> Bruce >>> On Wed, 30 Mar 2011, Tetiana Dadakova wrote: >>> >>>> Dear FreeSurfer list, >>>> >>>> I am making some manual correction to subcortical structures using >>>> Edit Segmentation Tool. >>>> And my question is: how should I proceed after saving aseg.mgz? Should >>>> I re-run autorecon2 with some options? >>>> >>>> Thank you, >>>> Tanja. >>>> _______________________________________________ >>>> 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
