Thanks for all the help, Nick. While trying to run rebuild_gca_atlas.csh, I keep getting error re: a missing command, specifically: "pbsubmit: Command not found." I am using freesurfer v. 4.0.2 on a centos linux box. Is this of major concern? Any simple way to troubleshoot it?
Best, jamie. > Jamie, > > The script would contains lines like this: > > set SUBJECTS=(subj1 subj2 subj3 subj4) > set ONE_SUBJECT=(subj3) > > > When rebuilding the atlas of 40 subjects on our cluster, where each > subject gets its own node, it takes about 2 days. so on a single > machine, about 80 days. > > Nick > > > > > On Wed, 2009-04-08 at 16:32 -0500, Jamie Hanson wrote: >> > so that it just runs the command locally. note that this script submits >> > multiple subjects to multiple nodes, so if you have 30 subjects, and you >> > dont use a cluster, it will take much much much longer to complete. >> >> Hi Nick- >> >> I am working on that script right now. One quick question about this, >> is there an example of the subjects.csh file (to specify files for >> training?). I understand I need to set for ONE_SUBJECT variable, but I >> wasn't sure how the other SUBJECTS should be specified (and couldn't >> find any other examples on-line or in my version of freesurfer). >> >> RE: computation load / time... It sounds like 2 days w/ multiple >> nodes... We don't do any job queue / cluster batching system, so for a >> single machine, what is a rough ball-park for completion time? >> >> Thanks much! >> jamie. >> >> >> >> >> > Nick >> > >> > >> > On Tue, 2009-04-07 at 12:16 -0500, Jamie Hanson wrote: >> >> Hi Freesufer folks- >> >> >> >> I was just about to start constructing a custom aseg atlas and I >> >> wondered if there were any recommendations for any of the optional >> >> flags? Any parameters yield better results (especially for specific >> >> brain regions)? I was focused on improving amygdala segmentation for >> >> my structural images (hence my asking). >> >> >> >> Best, >> >> jamie. >> >> >> >> >> >> >> >> >> > >> > >> >> >> > > -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: [email protected] Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
