On Thu, Mar 28, 2013 at 12:58 PM, Natalie Han <zhan1@stanford.edu> wrote:

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.edu> wrote:

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.
>
>
>
>

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