Hi Anastasia,
I checked the brain mask and it looks good. We are using FSLv4.1.4. I
take it that we are due for an upgrade? Is there a minimum version number that
we should be using in order for bedpostx to run smoothly?
Thanks again,
~SB
-----Original Message-----
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2
Hi Shannon - Which version of FSL do you have? Older versions didn't use
to save the mean_dsamples.nii.gz, but that was a while ago.
How quickly it runs depends on the size of the brain mask, so I'd check
that that's ok too.
a.y
On Wed, 9 Nov 2011, Shannon Buckley wrote:
> 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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