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.
>
>
>
>
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