I have used: recon-all -s -subcortseg
which runs through step 11 (-calabel), with the understanding re: accuracy that Bruce pointed out. -Julie On 7/7/10 8:07 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > Hi Salem, > > yes, you can run any individual options in recon-all. See the -help output > and run it through step 11 if you want. Note that we do use the surfaces to > improve the aseg accuracy at the very end, so you'll be giving that up. > > cheers > Bruce > On > Wed, 7 Jul 2010, Hannoun wrote: > >> >> >> Hi, >> >> I am a new user of freesurfer. Is it possible to do just the volumetric >> processing stages without the surface processing stages? >> >> In fact what I want is to segment the subcortical structures. >> >> Is there a command line for this purpose only or should we run all the >> recon-all steps? >> >> Thank you for your help >> >> Salem >> >> >> >> >> >> > _______________________________________________ > 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
