Hi all, Good news. I was able to submit the job to our cluster using the -s flag of the trac-all command. Once I did that, I just wrote a loop to go through my subjects and was good to go. --Matt
-----Original Message----- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 1:02 PM To: Susan Kuo Cc: Hoptman, Matthew; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] any way to parallelize Tracula? Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: > Hi Anastasia, > I apologize for jumping in here, but I have run bedpostx parallelized on a > cluster. Are there files that we can modify to run the script in parallel? I > noticed the '-prior' step is particularly long and cumbersome. Thank you! > > > Susie Kuo > NIH > > > On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > wrote: > > Hi Matt - Have you ever ran any parallelized FSL program (like > bedpostx) on your SGE cluster? Our scripts have built on the FSL > scripts, adding support for our PBS cluster, but in theory the SGE > functionality is still there, so it should be possible to make it > work. Of course practice is often somewhat more complicated than > theory... > > a.y > > On Thu, 16 May 2013, Hoptman, Matthew wrote: > > > Hi all, > I have access to a cluster computer. Is there any way to > parallelize tracula > using SGE without having to make a unique dmrirc for each > subject? If I could > pass subject numbers to the dmrirc that would be great, for > example. > > Thanks, > > Matt > > > > Matthew J. Hoptman, PhD > Research Scientist V > Nathan S. Kline Institute for Psychiatric Research > > Research Associate Professor in Psychiatry > NYU School of Medicine > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended recipient. > It may contain confidential information which is legally > privileged or otherwise > protected by law. 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PLEASE NOTIFY US > IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. > Thank you for > your cooperation. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended recipient. > It may contain confidential information which is legally privileged or > otherwise > protected by law. If you received this e-mail in error or from someone > who is not > authorized to send it to you, you are strictly prohibited from > reviewing, using, > disseminating, distributing or copying the e-mail. PLEASE NOTIFY US > IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. > Thank you for > your cooperation. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. 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