Hi Karthik,
I unfortunately don't have any experience myself with torque. However,
taking a quick look again at the code, it looks like the idea is to copy
the updated files under ${FSLDIR}/overlay and then you update the PATH
variable with the overlay directory as the first entry. This way any of
those files (updated for torque) will take precedence and be used.On Tue, Jan 31, 2017 at 6:36 PM, Gopalakrishnan, Karthik < [email protected]> wrote: > Thanks Niels and Moises! > > > > Niels, the documentation in the Github repo makes setting up the overlay > look pretty straight-forward. I did take a look at some of the code – it > looks like the fsl_sub script has been altered to use qsub for Torque. Do > you suggest deploying this overlay as-is? Or do you have any specific > change recommendations for these scripts? > > > > Moises, could you please tell me what kind of memory usage I should > anticipate when running this with HCP diffusion data after I set it up? > > > > Thanks a lot! > > > > Regards, > > Karthik > > > > *From:* Niels Bergsland [mailto:[email protected]] > *Sent:* Tuesday, January 31, 2017 4:19 AM > *To:* Gopalakrishnan, Karthik <[email protected]> > *Cc:* Moises Hernandez Fernandez <[email protected]>; > [email protected] > > *Subject:* Re: [HCP-Users] Running bedpostx on HCP diffusion data > > > > Hi Karthik, > You may find this useful for getting FSL scripts adapted for torque: > > > > https://github.com/octomike/fsl_overlay/ > > > > On Mon, Jan 30, 2017 at 11:30 PM, Gopalakrishnan, Karthik < > [email protected]> wrote: > > 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:[email protected]] > *Sent:* Friday, January 27, 2017 3:37 PM > *To:* Gopalakrishnan, Karthik <[email protected]> > *Cc:* Glasser, Matthew <[email protected]>; [email protected] > > > *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 <[email protected]> > 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:[email protected]] > *Sent:* Thursday, January 26, 2017 5:49 AM > *To:* Moises Hernandez Fernandez <[email protected]>; > Gopalakrishnan, Karthik <[email protected]> > *Cc:* [email protected] > > > *Subject:* Re: [HCP-Users] Running bedpostx on HCP diffusion data > > > > One should use 3 fibers for HCP data however. > > > > Matt. > > > > *From: *<[email protected]> on behalf of Moises > Hernandez Fernandez <[email protected]> > *Date: *Thursday, January 26, 2017 at 4:44 AM > *To: *"Gopalakrishnan, Karthik" <[email protected]> > *Cc: *"[email protected]" <[email protected]> > *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 <[email protected]> > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ > 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. > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > -- > > Niels Bergsland > Integration Director > Buffalo Neuroimaging Analysis Center > 100 High St. Buffalo NY 14203 > [email protected] > -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [email protected] _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
