Indeed, they look like they're oriented A-P in the corpus callosum and L-R
in the cinglulum, when it should be the opposite obviously. This'd mean
you'd have to swap things in the gradient table. It's hard to tell for
sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1
volumes for me here, I'll look at them:
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
Hi Anastasia,
Thanks! I checked dtifit_FA and did the overlay with V1.
They don't look ok to me (see attached picture). Any suggestions on how to
solve this? Perhaps by modifying
any of the previous steps?
Thanks!
2013/9/5 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
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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