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_m
ask.bbr.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.ni
i.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
Tracula.sh
Description: Binary data
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