Hi, Just to add to Romain's email, that preproc and postproc jobs in bepostx are the most demanding memory-wise. So you should be able to get away by simply increasing the amount of memory requested for the preproc and postproc, which normally do not take more than a few minutes to run.
Cheers Stam On 21 Oct 2013, at 13:24, romain valabregue <[email protected]> wrote: > Hello > > I also get similar problem : the diffusion data are quite to big. I had to > repeat the bedpostx 2 or 3 times in order to make it complete. > So I guess it depend of the load of each node. It was not killed by the sge > for any ressource limit, but it was kill by the processor because of memory > issue I guess (so I could not see it on the cluster log file) > > I had a similar problem when trying to do probtrackx. (the jobs were kill by > the cluster) The solution was just to ask a big amount of memory (qsub -l > mem=12gb) so that the cluster will only run one or two probtrack process on > the same node. > > I do not know how to change fslsub so that bedpostx add the extra argument to > qsub (ie : -l mem=...) > You can also use qalter as suggest by Colin, but then you have to be quick to > make the qalter during the preproc step, before each element of the array > start. > > > Cheers > > Romain > > > Le 17/10/2013 00:24, Huang Su-Chun a écrit : >> You are right, the missing slices mainly located in the middle of the brain. >> So I guess the problem comes from our grid engine.... >> >> I tried use -nf=3, but the process fails all the time. I guess it too >> demanding for the computer >> >> Thank you, >> >> >> Su >> >> >> 2013/10/16 Glasser, Matthew <[email protected]> >> Do you know that your cluster is not killing some of the jobs? Which slices >> are missing? If it is mainly the middle ones, I'd suspect that they are >> exceeding some limit for the cluster. >> >> For HCP data you can successfully model 3 fibers (--nf=3) and should use the >> -g option with FSL 5.0.5. I'd leave fudge and bi at their defaults unless >> you have a reason to change them. --model=2 is correct. >> >> Peace, >> >> Matt. >> >> From: Huang Su-Chun <[email protected]> >> Date: Wednesday, October 16, 2013 4:27 PM >> To: Matt Glasser <[email protected]> >> Cc: Stamatios Sotiropoulos <[email protected]>, >> "[email protected]" <[email protected]> >> >> Subject: Re: [HCP-Users] BedpostX failed >> >> It happened on subject 100307 and 105115. I am running the job in a grid >> engine. >> The command line I use is listed below: >> >> bedpostx >> /NAS_II/Public-Data/Parcellation/Q2_released_data/105115/105115_Diffusion_preproc/T1w/Diffusion >> --nf=2 --fudge=1 --bi=1000 --model=2 >> >> Thank you, >> >> Su >> >> >> >> 2013/10/15 Glasser, Matthew <[email protected]> >> What subject is this? >> >> What command line did you call bedpostx with? >> >> Are you running this on your local machine or in some cluster environment? >> >> Note that a new version of FSL was just released with improvements to >> bedpostx that you need to correctly process HCP data (not fixing missing >> slices, but correcting for the effects of gradient nonlinearities on the >> bmatrix), so I highly recommend you update. >> >> Peace, >> >> Matt. >> >> From: Huang Su-Chun <[email protected]> >> Date: Tuesday, October 15, 2013 6:12 PM >> To: Stamatios Sotiropoulos <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] BedpostX failed >> >> Hi Stam, >> >> I checked the bedpostX results and it didn't have the same number of slices >> as the input data. It caused problem when I want to to probabilistic >> tracking. And this missing slices problem happens quite a lot! >> >> Thank you, >> >> Su >> >> >> 2013/10/15 Stamatios Sotiropoulos <[email protected]> >> Hi >> >> Is it just the message that worries you? Have you checked whether bedpostx >> results have the same number of slices as the input data? Notice that the >> diffusion data are transferred to T1 space and lots of inferior/superior >> slices may be empty. >> >> Cheers >> Stam >> >> >> On 15 Oct 2013, at 04:47, Huang Su-Chun <[email protected]> wrote: >> >>> Hi dear experts, >>> >>> I am running bedpostX on the HCP diffusion data, however, it seems that >>> sometimes (60% of chance) the bedpostX ended before finishing all the >>> slices. Take the HCP data for example, it should have 145 slices, but the >>> betpostX stopped at slice 103 then show a message said "All slice >>> processed." >>> >>> Does anyone know where the problem might be? Thank you! >>> >>> Cheers, >>> >>> Su >>> >>> -- >>> Su-Chun Huang >>> Research Scientist >>> Integrated Brain Imaging Center >>> Department of Radiology >>> University of Washington >>> Seattle, WA 98195 >>> phone: 206-687-0113 >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> >> >> >> -- >> Su-Chun Huang >> Research Scientist >> Integrated Brain Imaging Center >> Department of Radiology >> University of Washington >> Seattle, WA 98195 >> phone: 206-687-0113 >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> >> >> >> -- >> Su-Chun Huang >> Research Scientist >> Integrated Brain Imaging Center >> Department of Radiology >> University of Washington >> Seattle, WA 98195 >> phone: 206-687-0113 >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> >> >> >> -- >> Su-Chun Huang >> Research Scientist >> Integrated Brain Imaging Center >> Department of Radiology >> University of Washington >> Seattle, WA 98195 >> phone: 206-687-0113 >> _______________________________________________ >> 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
