Hi Donald – TRACULA doesn’t use deterministic ROIs, instead it assigns a 
probability to any ROI to be the one that the specific tract intersects or 
neighbors at a specific position along that tract’s trajectory. These prior 
probabilities are computed from the training subjects that make up the TRACULA 
atlas (where atlas here refers to a set of individuals rather than an average 

For what you’re looking for, find the files: 

There is one file for each tract. The 0_0_0 in the file name means that you’re 
looking at the ROIs that tract goes through (rather than the tract’s left, 
right, etc neighbors - there are other files for those). In each of these 
files, each line corresponds to a different position along the tract. Since 
you’re interested in the endpoints, you want to look at the first and the last 
line. The ID numbers in that file correspond to ROIs as specified in 

Hope this helps,

 on behalf of "Krieger, Donald N." <krieg...@upmc.edu<mailto:krieg...@upmc.edu>>
Reply-To: Freesurfer support list 
Date: Wednesday, February 14, 2018 at 10:19 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI

Dear List,

I need a list of Freesurfer ROIs which are typical endpoints for each standard 
pathway used in tracula.
I think this information is likely included in the default tracula atlas which 
I have been unable to find although I do not need spatial coordinates but 
rather just the list of ROI names for each pathway.
If this information is contained in publications, I would like to cite them.

I hope this is clear and thank you for any help you can provide.

Best - Don

Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh

Freesurfer mailing list

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.

Reply via email to