Hey thanks, I haven't worried about multi threading typically since I just run more brains simultaneously. On my computer, I have sufficient 64 gigs RAM (64 gigs) and 24 CPU/cores (not sure which) to run 20 recon-all scripts simultaneously at full speed. Would I still benefit from the multi threading? I am a little confused about cores vs cpus
I created a copy of the recon-all script that stops at calabel step, and am running that now. - Josh On Thu, Mar 28, 2013 at 12:58 PM, Natalie Han <zh...@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 <fis...@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 <jki...@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. >> >> >
_______________________________________________ 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.
