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 > > > _______________________________________________ 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.
