Hi Stam,
Thanks for thinking this through with me! I added what you suggested, but
I'm getting an error saying that -R is in invalid option. And when I look
inside fsl_sub, I don't see any -R flags. Any ideas?
for reference, that line is now:
preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -R 10000 -m as -N bpx_preproc -l
${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}
${gflag}`
Thanks,
Sarah
On Fri, May 6, 2016 at 10:53 AM, Stamatios Sotiropoulos <
[email protected]> wrote:
> Hi
>
> If the problem is in fslslice, this is likely a memory problem. Depending
> on how strict your queueing software is and what are the memory limits for
> each queue, it may kill or not the preproc job if it thinks it asks too
> much memory. Notice that the HCP data are an order of magnitude larger than
> conventional data and this may cause such problems. All you need to do is
> change the amount of memory requested when queuing bpx_preproc.
>
> In the $FSLDIR/bin/bedpostx script, the line to modify (e.g. by adding
> fsl_sub -T 60 -R 10000…) would be the following:
>
> preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l
> ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}
> ${gflag}`
>
>
> By the way the “ -rician “ flag should be “ --rician"
>
> Hope this helps
> Stam
>
>
> On 6 May 2016, at 14:56, Sarah Heilbronner <[email protected]>
> wrote:
>
> Hello,
>
> I've been trying to run bedpostx on a single subject's HCP preprocessed
> diffusion data (I haven't made any changes from the initial download) on
> our cluster. I've run it a number of different ways, and always seem to get
> the same error:
> /software/fsl/5.0.7/fsl/bin/bedpostx_preproc.sh: line 77: 97699
> Killed
> ${FSLDIR}/bin/fslslice ${subjdir}/data
>
> Seems to be encountering a problem with the fslslice line inside
> bedpostx_preproc.
>
> For reference, I'm using the latest version of FSL. I'm entering this
> command:
> bedpostx subject#/T1w/Diffusion -n 3 -model 2 -g -rician
>
> I've also tested some variations, like without grad_dev/g, etc, always
> getting the same error message. Any help?
>
> Thanks,
> Sarah Heilbronner
> University of Rochester
>
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>
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