The output of TRACULA is a probability distribution that tells you how likely each voxel is to be part of the tract that you’re looking at. Voxels with low probability values are not very likely to be part of the tract. Setting the threshold in freeview to 20% means that you only want to display the voxels that have probability values greater than 20% of the voxel with the greatest probability to be part of this tract.

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Daumail, Loic Jean" <LDAUMAIL@mgh.harvard.edumailto:LDAUMAIL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, July 20, 2018 at 10:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Question about Freeview, 20% threshold

Dear FreeSurfer experts,

I am currently using TRACULA( from freeSurfer 6.0), and on the freeview visualization of merged files of the probability distributions of the tracts, I don't understand the thing about the "20% threshold".

Indeed, on the tracula tutorial, it is written that the tracts are displayed in a way that they are at 20% of their maximum threshold. However, what does this mean? Is it the 20% of the most probable paths for each tracts? The adjustment bar on the side of the screen permits to vary this threshold, but when we reduce the level of the threshold, the size of the tracts increase, which seems in contradiction with the previous statements... I then suppose that my guess must be wrong?

Thank you for your time and consideration!

Sincerely,

Loïc