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