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:
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.htm...
http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-...
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!
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