hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer
and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > wrote: > Hi Lea, > > > I wrote that script to simplify processing on our cluster which uses qsub > PBS for submission. I have never used SLURM so far. > > > There is two functions that you (or someone who knows this stuff) would > need to modify: > > def submit > > and > > def wait_jobs > > > The submit procedure basically issues a submit command (stored in pbcmd). > The examples there should help anyone who programs python to modify it for > a slurm submission. > > > The wait_jobs scripts runs a different command (here qstat and grep user) > to see how many jobs you are already running and waits until this number > sinks below maxjobs, then it continues submitting new jobs. If you don't > care about the number of submitted jobs (because your cluster does the > scheduling anyway), you can just write > > > " return" as the first line (before the " users = os....." line). > > > Still the submit block would have to be rewritten for slurm. > > > Best, Martin > > > > Am 17.02.2018 um 12:13 schrieb Backhausen, Lea: > > Dear FS experts, > > I am trying to do a longitudinal analysis of around 250 adolescents with > up to 4 data points each. Given the complexity I would like to use the > long_submit_jobs script which is described here: https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/Scripts > > Unfourtunately it does only run on launchpad and I would do the analyses > with SLURM using bash system. > Has anybody adopted the script so i will run with SLURM or does anybody > know where I should look to get information on this? > > I have little scripting experience so any help would be greatly > appreciated! > > Best, > > Lea Backhausen, B.Sc. > > Research assistant > > Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie > Tel. +49 (0)351 458-7166 <+49%20351%204587166> > Fax +49 (0)351 458-5754 <+49%20351%204585754> > > Universitätsklinikum Carl Gustav Carus > an der Technischen Universität Dresden > Anstalt des öffentlichen Rechts des Freistaates Sachsen > Fetscherstraße 74, 01307 Dresden > *MailScanner has detected a possible fraud attempt from "deref-web-02.de" > claiming to be* *http://www.uniklinikum-dresden.de* > <https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=http%3A%2F%2Fwww.uniklinikum-dresden.de%2F> > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. 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 . 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. > >
_______________________________________________ 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. 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 . 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.
