Sounds right, since my fsl_sub is missing that part! I have fsl version 5.0.9 running, with the fsl_sub that came with it. Where is your version of fsl_sub from?
On Fri, May 6, 2016 at 1:01 PM, Joseph Orr <[email protected]> wrote: > Sounds like you might be using an old version of fsl_sub. You should have > a section in fsl_sub that starts with "$command V1.0beta" that has the > following options for fsl-sub: > > -T <minutes> Estimated job length in minutes, used to auto-set > queue name > This is helpful if you don't set a FSL default queue. > -q <queuename> Name of FSL defualt queue possible values for > <queuename> > are "verylong.q", "long.q" and "short.q". See below for > details. > -Q <queuename> Name of Wash U Queue to use, one of (dque, dque_HT, > dque_smp) > -a <arch-name> Architecture [e.g., darwin or lx24-amd64] > -p <job-priority> Lower priority [0:-1024] default = > 0 > -M <email-address> Who to email, default = none > -j <jid> Place a hold on this task until job jid has > completed > -t <filename> Specify a task file of commands to execute in > parallel > -N <jobname> Specify jobname as it will appear on queue > -n <nCPUs> Number of CPUs per node that job will use (default > = 1) > -R <RAM> Max total RAM to use for job (integer in MB) > -l <logdirname> Where to output logfiles > -m <mailoptions> Change the notification mail options, see qsub for > details > -F Use flags embedded in scripts to set SGE queuing > options > -v Verbose mode. > > -R is the MB of RAM you are allocating for the job. You may run in to > problems with other FSL tools with large HCP datasets, basically for > fslmerge and fslmaths commands you'll need to modify to allocate more RAM. > > -- > Joseph M. Orr, Ph.D. > Assistant Professor > Department of Psychology > Texas A&M University > College Station, TX > > On Fri, May 6, 2016 at 9:45 AM, Sarah Heilbronner < > [email protected]> wrote: > >> Hi Stam, >> >> Thanks for thinking this through with me! I added what you suggested, but >> I'm getting an error saying that -R is in invalid option. And when I look >> inside fsl_sub, I don't see any -R flags. Any ideas? >> >> for reference, that line is now: >> preprocid=`${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 >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
