Hi Florian - Tracula has certain expectations for what aparc+aseg labels each tract goes through or next to, and it'll skip areas that don't match those expectations. If the voxels in the lesions get labeled in the aparc+aseg, e.g. as white-matter hypointensities instead of white matter, you can switch those voxels to the white matter label, and then tracula will treat them like the rest of white matter. I should probably add an option for trac-all to be able to do that in the next version.

For now, you can change those voxels in mri/aparc+aseg.mgz (first keep a copy of the original file under another name for all other intents and purposes!) and then rerun trac-all. You can skip the trac-all steps before -masks, that's the step where it grabs the aparc+aseg to use in subsequent steps.

Hope this helps, a.y

On Wed, 16 Apr 2014, Florian Borsodi wrote:

Dear Freesurfer TRACULA Experts,

We are trying to run TRACULA on patients with lesions and found out, that TRACULA had problems tracking streamlines trough the lesions, which is understandable. The problem is, if TRACULA gets lost in the lesions, the whole streamline is not considered, even if the streamline until the lesion might be correct!

Is there any possibility to hand TRACULA lesionmasks, so that the regions with lesions are ignored? If not, is there a possibility to maintain the lost streamlines, or at least parts of it?

Thank you in advance for your help.

With kind regards,

Florian Borsodi, Lukas Pirpamer Department of Neurology Medical Universtiy of Graz