Hi Jamie,
pbsubmit is the command we use to put a job into our batch cluster queue.
Do you have a cluster you can use?
cheers,
Bruce
On Tue, 14 Apr 2009, Jamie Hanson wrote:
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.
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