Hi Akvile - I'm attaching a screenshot of the FA map and primary eigenvectors from your data set through the corpus callosum and cingulum areas. You'll see that the eigenvectors are not oriented correctly, which probably means that there's something wrong with the gradient directions in you bvecs file.

Looking at the eigenvectors from the tensor fit is important when troubleshooting - the FA alone doesn't tell the full story since it's invariant to rotation of the vectors.

Hope this helps, a.y

On Wed, 3 Oct 2012, A. Lukose wrote:

Dear Anastasia,

Thank you very much for your reply. I have uploaded the requested directories (in a zip file tracts.zip) of one subject (I have run several, but all of them look the same). Thank you very much in advance!

Kind regards, Akvile Lukose

On 27/09/2012 18:34, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:

...

Hi Akvile - Sorry for the late response, I was out of town for a bit.

At first glance it looks like all the tracts are stuck where they're initialized. This might happen occasionally for a tract if initializing it is tricky (i.e., if the subject is not well aligned to the atlas, if the brain mask has a hole, etc), which is why the reinit option exists. But I've never seen it happen to all tracts, so something's fishy here.

If you upload all the tracula-related directories for this subject (dmri, dlabel, dpath, scripts), I'll take a look.

http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

a.y

On Thu, 13 Sep 2012, Akvile Lukose wrote:

...

Hello Freesurfers,

I ran into a problem running TRACULA that I couldn't solve myself, and I would really appreciate if you could have a look.

I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with 16GB RAM.

I extracted the bvals and bvecs with the dcm2nii converter and adjusted the format to what FS expects (scans acquired on a non-Siemens scanner).

I attach the dmrirc file as well.

First, I had a memory problem (cannot alloc memory) during the ­prep stage. The new compiled update from here (http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula )helped and ­prep stage finished without any errors.

I was not able to run bedpostx from dmrirc configuration file. I could work around it by running bedpostx directly on dmri directory (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html) . Then I had a problem with symlinks, I created them manually and after that it worked fine, I had all the output files as listed here (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html).

-path worked also without any errors, but I keep getting very short thin tracks (all tracks) (snapshot attached). There is nothing wrong with the aparc+aseg.mgz. I tried rerunning every stage after I added option "set reinit=1" (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html) , but unfortunately it didn't help.

Do you have any ideas how to fix it? Thank you very much in advance!

Kind regards,

Akvile Lukose

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