Su - sge outputs "o" (output) and "e" (error) files for the job name/number. Those have info that may help and that you can pass to the admin.
you can specify the number of cores for an array job with qsub -t but you can also just run the bedpostx script and then limit the number of cores while the pre-processing stuff runs with qalter -t (or something like that) And ask your admin the right module and queue for fsl/5.0.5 and like matt says whether there is a time or other limit on your individual jobs. probably the sge e/o files will say if the job (slice) was killed due to a resource limit. Colin On 16 October 2013 23:24, Huang Su-Chun <[email protected]> wrote: > 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
