Hi Sanna

They were kind of hand tuned ages ago, but I’m pretty sure that they get re-estimated by a procedure that adapts to the intensities in the input images. They were probably tuned for a specific class of T1-weighted scans (like FLASH), but the adaptive estimation usually works well on a broad variety of scans (like MP-RAGE, where you trade off higher noise for better contrast)

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lokhandwala, Sanna
Sent: Thursday, April 18, 2024 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Default intensity values for gray and white matter

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Dear FreeSurfer developers, 

I am interested in understanding where the freesurfer default intensity values for gray and white matter specifically come from within the recon-all command. I understand the default intensity of white matter (mean) is 110, white matter (low) is 90, white matter (high) is 125, gray matter (low) is 30, and gray matter (high) is 100. I know that the default parameters are meant to improve segmentation of the gray and white matter tissue but could you please tell me how/where these values come from? I’ve read the 2002 paper “Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain” and I saw that Figure 1 had varying distributions for gray and white matter intensity, but I did not see anything that explicitly stated how these default values were chosen.  

Your guidance is appreciated, 

Sanna Lokhandwala