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 brain).
For what you’re looking for, find the files: $yoursubject/dlabel/mni/*_fsids_all_0_0_0.txt
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 $FREESURFER_HOME/FreeSurferColorLUT.txt.
Hope this helps, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Krieger, Donald N." <kriegerd@upmc.edumailto:kriegerd@upmc.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 14, 2018 at 10:19 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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