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 <pras...@zoho.com> 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 -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 > > <mailto: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 > > > > <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 <mailto:mreu...@nmr.mgh.harvard.edu>> > > wrote ---- > > Hi > > > > so take a look at > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData > > <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 > > <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 > > <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 <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 <mailto:freesur...@nmr.mgh>.h > > arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu <mailto:reu...@mit.edu> > > Web > > : http://reuter.mit.edu <http://reuter.mit.edu/> > > > > > > _______________________________________________ Freesurfer mailing list > > freesur...@nmr.mgh <mailto:freesur...@nmr.mgh>.h > > arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu <mailto:reu...@mit.edu> > > Web > > : http://reuter.mit.edu <http://reuter.mit.edu/> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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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