Hi Jeff, you can run recon-all with flags -autorecon1, -gcareg, -canorm, -careg, -careginv, -rmneck, -skull-lta and -calabel if you want to generate files upto aseg.mgz. Please refer to this wiki for more details about the flags.
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 Sita. On Mon, 1 Aug 2011, Jeff Eriksen wrote: > I would like to run FreeSurfer just up to the point it creates the aseg file, > and no further. I believe this would be steps 1 through 11. Is there any way > other than making a copy of the recon-all script and removing everything > after step 11. Not sure I know exactly where this is. > > -Jeff > _______________________________________________ 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.
