From: Zehua Cui <zcui12@umd.edu>
Date: Wednesday, September 17, 2025 at 11:57 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Jade Dunstan <jdunstan@umd.edu>
Subject: [Freesurfer] hippocampal subfield segmentation

We want to use Freesurfer's automatic hippocampal subfield segmentation flag using a T1 and T2 (high resolution hippocampal T2 sequence that is focused on the Medial Temporal Lobe and does not have full coverage of the brain). We previously ran recon-all with just the T1. Is it essential for us to re-run recon-all with both the T1 and the T2 as input or can we simply run the subfields flag and specify the T1 and T2 (which we copied over into the recon-all output directory) there? Will it make a big difference for the resulting subfield volumes?