Thanks for the pointers, Chris. I'd call it an "opportunity for FSL customization" rather than an "FSL problem" per se :o)
On Mon, 2 Sep 2013, Watson, Christopher wrote: > This is an FSL problem. You can try the FSL list, and check out some links: > https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge > http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html > http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira > [jbragapere...@gmail.com] > Sent: Monday, September 02, 2013 9:53 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q" > > Dear Anastasia and FreeSurfers, > > I was preprocessing some data using tracula and found this error after > running trac-all -bedp -c dmrirc: > > INFO: SUBJECTS_DIR is /data-02/joana/Last > INFO: Diffusion root is /data-02/joana/tracula/ > Actual FREESURFER_HOME /usr/local/freesurfer-5.3 > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri > subjectdir is /data-02/joana/tracula/XXX/dmri > Making bedpostx directory structure > Queuing preprocessing stages > Unable to run job: Job was rejected because job requests unknown queue > "short.q". > Exiting. > Queuing parallel processing stage > Unable to run job: Job was rejected because job requests unknown queue > "long.q". > Exiting. > Queuing post processing stage > Unable to run job: denied: "60" is not a valid object name (cannot start with > a digit) > Job was rejected because job requests unknown queue "long.q". > Exiting. > > Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. > Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the > queued tasks. > > You will get an email at the end of the post-processing stage. > > > So far no slices have been processed. Does anyone know how to solve it? > > Thanks! > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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.
