Hi Anastasia,
It turns out that I was NOT able to run the original bedpostx on our
cluster, so thank you for pointing me in the right direction! In case other
users experience a similar problem, this is what we did to get the ball rolling
on our grid:
We found the "fsl_sub_seychelles" and "fsl_sub" scripts where the
default q-names were identified. We modified the files (changing long and
short.q to reflect the naming convention used here) and ran the original
bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx
function SEEMED to have launched fine, but we hit another snag...
The program finished far too quickly for it to have worked properly (an
hour, tops), and when I try to run the next "-prep" step I get the following
error, which confirms that suspicion:
_+_+_+_+_+_+_+_+_+_+_
"Loading BEDPOST parameter samples from
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Wed Nov 9 16:18:53 PST 2011
Word too long."
+_+_+_+_+_+_+_+_+_+_+_
I have to confess I'm not familiar with the "word too long" error. In
any case, bedpostx seems to fail to produce the requisite files for -prep
(mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for
creating such a file, I'm including my "ls" output for our dmri.bedpostX path.
_+_+_+_+_+_+_+_+_+_+_+
"[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancel logs mean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt mean_f1samples.nii.gz merged_f1samples.nii.gz monitor
dmri.bedpostX.nii.gz mean_f2samples.nii.gz merged_f2samples.nii.gz
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz merged_ph1samples.nii.gz xfms
[vhasfcbuckls@paris dmri.bedpostX]$"
+_+_+_+_+_+_+_+_+_+_
Do you have any advice for getting passed this step? We are fairly in
the dark with this function over here, so any help / hints you can provide
would be wonderful. Please let me know if you need more information.
Thanks again for your help and patience,
~Shannon B.
-----Original Message-----
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2
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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