External Email - Use Caution

Thank you Matt for letting me know that.

John

For what it’s worth, we had problems with FreeSurfer 7.X with surface placement accuracy on HCP-Style data (i.e. 0.8-0.7mm isotropic T1w and T2w) and have continued to recommend using FreeSurfer 6 for the HCP Pipelines for now. We usually quote 2.6mm average cortical thickness for young adults, but it does depend on age.

Matt.

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Xiaojiang Yang xjyan...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cortical thickness on version 6 vs 7

External Email - Use Caution Dear Freesurfer developers,

I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7.

When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm.

According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm.

Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you!

John.