Yes, it does look from the images like the L-R and A-P directions are
swapped. So you can switch around the x and y columns of you gradient
table and rerun the preprocessing and check the eigenvectors again. It may
be some other combination of swaps that needs to be done, but the x and y
looks like the most likely to me. For sure the gradient table is wrong.
On Thu, 5 Sep 2013, Joana Braga Pereira wrote:
Thanks!
I've uploaded those files as well as dmrirc and bvecs and bvals.
Let me know what you think.
2013/9/5 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
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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