Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana




2013/9/2 Watson, Christopher <Christopher.Watson@childrens.harvard.edu>
Indeed. It's actually really easy to set up, too.
________________________________________
From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapereira@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
>
>
>


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