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.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 > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.