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
