Hi Moises, Thanks for the reply!
I also want to know a couple other things - is Sun Grid Engine (SGE) a particular requirement to ensure bedpostx internally splits the slices among all available CPU cores? Or will something like Torque and Maui also be fine? The system administrator in my college says that we already have Torque and Maui and so it’ll be much quicker to have that set up for me. If Torque and Maui will also be fine, could you also share the relevant changes that we’d have to make to any files/anything else to successfully and quickly run bedpostx for HCP diffusion data? And on a slightly different note, what kind of memory usage should I anticipate when I run this for HCP diffusion data? Regards, Karthik From: Moises Hernandez Fernandez [mailto:mois...@fmrib.ox.ac.uk] Sent: Friday, January 27, 2017 3:37 PM To: Gopalakrishnan, Karthik <gkart...@gatech.edu> Cc: Glasser, Matthew <glass...@wustl.edu>; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Running bedpostx on HCP diffusion data I mean information inside the mask, (nodif_brain_mask) Moises. On 27 January 2017 at 20:17, Gopalakrishnan, Karthik <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> wrote: Thanks Moises and Matt! Just to clarify, doesn’t HCP diffusion data (<subject>/T1w/Diffusion/data.nii.gz) have something like 145 slices, not 90? Regards, Karthik From: Glasser, Matthew [mailto:glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, January 26, 2017 5:49 AM To: Moises Hernandez Fernandez <mois...@fmrib.ox.ac.uk<mailto:mois...@fmrib.ox.ac.uk>>; Gopalakrishnan, Karthik <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Running bedpostx on HCP diffusion data One should use 3 fibers for HCP data however. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Moises Hernandez Fernandez <mois...@fmrib.ox.ac.uk<mailto:mois...@fmrib.ox.ac.uk>> Date: Thursday, January 26, 2017 at 4:44 AM To: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Running bedpostx on HCP diffusion data Hi Karthik, It depends on your processor and on the parameters that you use. One large slice of HCP diffusion data takes about 4 hours on a single CPU core (modern processors have several cores) using the default parameters (2250 MCMC iterations, 2 fibres estimation). HCP data has about 90 slices with diffusion information, although some of them are small and are processed in few minutes. If you have a queue system, such as SGE, you can send each slice to a different CPU core. Moises. On 25 January 2017 at 23:29, Gopalakrishnan, Karthik <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> wrote: Hi, I want to run bedpostx on HCP diffusion data – what is the estimated time for successfully running it for a HCP subject in a regular computer without a GPU? Also, what are the recommended hardware specs to run bedpostx on HCP data? Thanks! Karthik _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
