Hi Anastasia, I am operating on 5.1... I'm glad to know that there is such a huge difference in versions; and that there's so much gain in upgrading. I will look at the fsl_sub_mgh script, and I'll post back what I figure out (if anything), if other people are interested. Otherwise, it's vox clamantis en deserto...
Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 1:02 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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. If you received this >> e-mail in error or from someone who was 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. >> >> >> >> ______________________________**______________________________** >> _____________________ >> _ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the >> intended recipient. >> It may contain confidential information which is legally privilegedor >> 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. >> >> 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<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. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> Susie Kuo >> >> Mediocrity knows nothing higher than itself, but talent instantly >> recognizes >> genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear >> >> -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*
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