Dear FSL-List,
I have the opportunity to use a Cluster for my BedpostX Analysis to
speed up the processing time.
With a little (actually quite a big) help from the admin I was
successful setting up fsl on the cluster.
One question though from the admin that I want to forward here:
> In the output directory, diffusion.bedpostX, there is a file called
> commands.txt containing:
> /global/home/phillips/software/fsl/fsl414/bin/
> bedpostx_single_slice.sh /global/home/phillips/software/fsl/run/
> diffusion 2 1 1000 125 0 25 0
> /global/home/phillips/software/fsl/fsl414/bin/
> bedpostx_single_slice.sh /global/home/phillips/software/fsl/run/
> diffusion 2 1 1000 125 0 25 1
> ...
> continuing from 0 to 56.
> Are all these commands independent? Could you have set up this job
> so that you call bedpostx_single_slice.sh yourself instead of
> getting bedpostX to do it for you?
> In that case, the whole thing could have been done as 56 separate
> jobs - that would have been finished in an hour and a half.
I know that the suggested sge_cluster environment handles splitting up
the jobs for every single slice by just running the bedpostx command.
I suppose that this is handled at the beginning of the bedpostx program
if [ "x$SGE_ROOT" = "x" ] ; then
if [ -f /usr/local/share/sge/default/common/settings.sh ] ; then
. /usr/local/share/sge/default/common/settings.sh
elif [ -f /usr/local/sge/default/common/settings.sh ] ; then
. /usr/local/sge/default/common/settings.sh
fi
fi
In our case we don't use sge to run the cluster. Would it then be
reasonable to use <fslsplit data.nii.gz diff_slices/data_slice_ -z>
and then run bedpostx_single_slice.sh ?
Any word of caution before we try that?
Thanks, Michael
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