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]<mailto:[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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