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.
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.
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jamie Hanson -
Nick Schmansky