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 <fis...@nmr.mgh.harvard.edu> wrote ---- 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 <pras...@zoho.com> wrote ---- > > Thank you again for your reply. > > For editing aseg.mgz, as mentioned in > > https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme > ntations > > it does suggest using -autorecon2-noaseg, but from what I can see this does not > update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't > this command (as does -autorecon3) also re-create surfaces that would need to be > re-checked and re-edited if needed? > > Also, I think FS5.1 does not have the -autorecon2-noaseg flag. > > As an alternative, with completed wm/pial boundaries could we run > > recon-all -surfsegedit, > > then we would edit aseg as needed and then: > > recon-all -aparc2aseg -segstats -wmparc > > This will not change any surfaces but would update aseg.stats > aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc > > P > > > ---- On Mon, 20 Apr 2015 13:42:49 -0700 Martin > Reuter<mreu...@nmr.mgh.harvard.edu> wrote ---- > 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/OtherUsefulFlags > has details on the steps. > > Best, Martin > > > > On 04/20/2015 03:21 PM, Martin Reuter wrote: > > 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://freesurfer.net/fswiki/LongitudinalEdits > for a description of the different edits, and where they should be > done. > > About where to restart after making the edits, everything should be > done the same way as in the regular (cross sectional) processing. > So you specifically ask about: > - brainmask edits > - brainfinalsurf edits > - and manual aseg edits. > > I just looked at the description of those regular edits > http://freesurfer.net/fswiki/Edits > but sadly there it does not say where to start re-run either. I'll > try to find out and update that soon. > > I hope someone with editing experience can chime in and tell us. (I > changed the subject, so that it get's read). > > Cheers, Martin > > On 04/20/2015 09:44 AM, Bruce Fischl wrote: > > cheers > Bruce > > > On Mon, 20 Apr 2015, prasser wrote: > > Dear All, > I wanted to check that corrections to a Long pial > surface through edits > to brainmask.mgz and brain.finalsurfs.manedit.mgz > are followed by the > command: > recon-all -long tpN1 templateID -autorecon2-pial > -autorecom3 > > Is this correct? > > Also, after editing the Long aseg.mgz to correct > the volume of structures > what command should be run to have these edits > update the dependent files? > > Thanks, > > P > > > > > > _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.h > arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci > ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett > s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog > y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, > MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web > : http://reuter.mit.edu > > > _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.h > arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci > ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett > s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog > y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, > MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web > : http://reuter.mit.edu > _______________________________________________ > 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. 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