Hm, this looks uniformly bad. Have you checked that the gradient
directions are correct? You can check that by looking at the eigenvectors
from the tensor fit that's done as part of the preprocessing. Although
tracula doesn't use tensors for tractography, it's a quick way to check
that your inputs are correct.
In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and
display dtifit_V1 as lines. Then make sure that the lines follow the basic
anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal
tract (I-S).
On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
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.wat...@childrens.harvard.edu>
Indeed. It's actually really easy to set up, too.
________________________________________
From: Anastasia Yendiki [ayend...@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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
behalf of Joana Braga Pereira [jbragapere...@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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