Noe need to rerun recon-all with T1+T2 ;-) the difference will be nearly inexistent. Cheers, /Eugenio
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Juan Eugenio Iglesias
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
External Email - Use Caution Hi all, 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?
Thank you very much!
-- Zehua Cui|崔泽华, Ph.D. Post-Doctoral Fellow Neurocognitive Development Lab 4094 Campus Drive, Biology/Psychology Building University of Maryland, College Park, MD 20742 Zoom Meeting ID: https://umd.zoom.us/j/8975314130https://secure-web.cisco.com/1_DD2JIMsdFxT6lsQdL9CaK--HcIDgdBd5U8PGauw5NHp6glWZ5KRHB7F_oYDbjxIKnIm-cAWApaxQ-R3Bkr-VH6Ts_DkyV17HsT5KGiQUKX5DzchLNmlIqNF2kcYBv5TkhytyviWyWP3pid61JnVr9tZxYJjvIBSj9H_QFqB_pbOiNl8T9bzJAvurbdP-pZZiAEOMcUZYH7828mZdx9ELsu7u7h-Rej4dWTejLCPX9fhKk5NW_vd0jDWA4f8d5WDEkYEDPbixfAW8YEv6mRXCGA9BKK0vGWI95qCL6BTL0UQMPrj_I1IT4rEHx7D_LWMgsFxANRIg1wRwa8f-5-eiQ/https%3A%2F%2Fumd.zoom.us%2Fj%2F8975314130 [https://secure-web.cisco.com/1s5TbjjXsVIGJuHa_oQEhFROpnmuKIL9rXfU-bRoi09ArXe...]