Re: [Freesurfer] where to start recon-all after edits

Hi, If the surfaces are 'done' and we update/edit the the aseg.mgz with recon-all -surfsegedit and then run recon-all -autorecon2-cp -autorecon3 to update the .stats, this also creates new wm and pial surfaces that may be different to those used for -surfsegedit. Is that right? As another alt

Re: [Freesurfer] where to start recon-all after edits

Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -

Re: [Freesurfer] where to start recon-all after edits

Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method des

Re: [Freesurfer] where to start recon-all after edits

Yes, if this is in the long, you also need to add the -long …. stuff Martin > On Apr 28, 2015, at 12:46 AM, prasser wrote: > > Thanks for your response, not sure if I've quite got it yet. > > So, after the surfaces are done and we update/edit the the aseg.mgz with say, > > recon-all -surfseg

Re: [Freesurfer] where to start recon-all after edits

Repost. On Mon, 27 Apr 2015 21:46:02 -0700 prasser wrote Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autoreco

Re: [Freesurfer] where to start recon-all after edits

Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl

Re: [Freesurfer] where to start recon-all after edits

I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr

Re: [Freesurfer] where to start recon-all after edits

Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-no

Re: [Freesurfer] where to start recon-all after edits

Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .sta

Re: [Freesurfer] where to start recon-all after edits

Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki

[Freesurfer] where to start recon-all after edits

Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfe