Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours.
recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8
cheers, Natalie
On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Josh,
yes, I think that's correct.
Bruce On Thu, 28 Mar 2013, Joshua Lee wrote:
In fact, couldn't I stop after calabel if all I want is the aseg.mgz?
Josh
On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jkilee@ucdavis.edu wrote: Hi All,
Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge.
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.