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 <sarah.heilbron...@gmail.com<mailto:sarah.heilbron...@gmail.com>> 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users