Re: [HCP-Users] BedpostX failed

[Glasser, Matthew]

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 <claire0...@gmail.com> Date: Wednesday, October 16, 2013 4:27 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: Stamatios Sotiropoulos <s...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <glass...@wusm.wustl.edu> 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 <claire0...@gmail.com> Date: Tuesday, October 15, 2013 6:12 PM To: Stamatios Sotiropoulos <s...@fmrib.ox.ac.uk> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <s...@fmrib.ox.ac.uk> 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 <claire0...@gmail.com> 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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users