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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
