> 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.
> Jamie,
>
> Included in the $FREESURFER_HOME/bin directory is a script called
> 'rebuild_gca_atlas.csh' that we use to rebuild our atlas. You will need
> to read and understand this script as some edits to it will need to be
> made. It contains descriptive text within the file.
>
> The script is intended to run on our cluster (collection of processor
> nodes), so you would have to change lines like this:
>
> if ($RunIt) pbsubmit ${PBCONF} -c "$cmd"
>
> to:
>
> if ($RunIt) $cmd
>
> 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.
>
> 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: jamielarshan...@gmail.com
Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/
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