Hi Shannon - Does the original bedpostx run fine on your cluster? You'd probably have to edit that to get it to work, it's not made to work on every possible cluster. Bedpostx_seychelles is the modified version that tracula calls that I've modified from the original FSL version so that it runs on our clusters.
In either case, trac-all is meant to always be run from the command line, whether you're on a personal computer (where is runs jobs serially) or a cluster (where it submits them as jobs using qsub). But probably some editing will be needed as I said.
Hope this helps, a.y On Wed, 2 Nov 2011, Shannon Buckley wrote:
Hi Anastasia, I am trying to run Tracula for the first time in our lab and I’m getting errors during step 2 that seem to involve how the program wants to be launched via grid. I’ve attached the configuration file I’m using and the error message is below... ____________________________________________________________________________ $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh Using Freesurfer version 5.1. Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ Sessions Directory is /home/vhasfcbuckls/sessions INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 ln -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_ mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n ii.gz ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/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. ____________________________________________________________________________ Although we DO have a grid, I am trying to test the program for feasibility purposes, just on my own system’s terminal, since we aren’t sure how results will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI @ b=1000, with 1 b0 image). We are very interested in performing tractography in T1-space… I am open to running this over the grid, if that’s really the best way to do it, but the problem is that I don’t see anywhere to specify the name of the queue that should be used for launching the program. Can you please tell me how to launch this without using the so-called long.q and short.q? We typically launch jobs to our grid using our “bash.linux.q”, but I haven’t been able to locate a place in the configuration file, or any switches to use in the cmd line, to specify that this queue should be used. I tried specifically launching Tracula’s step 2 onto our bash.linux.q via the cmd line using “qsub”, but received the same old error I had been getting. I checked the data independently using “bedpostx_preproc.sh”, and it appears that all the required data are set up properly. As far as I can tell, the only issue we have is this inability to use the long.q and short.q… What do you think? I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in case you need someone to chime-in with any specific information about how our Linux systems are set-up. Thanks very much for your time, Shannon T. Buckley SRA III - Supervisor CIND, UCSF 4150 Clement St. (114M) San Francisco, CA 94121 Phone: (415) 221-4810 x4251 Fax: (415) 386-3954
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