Dear Yixin,

Yes, give segmentHA_T1.sh a shot. You need to install the development version of FreeSurfer, though.

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

Research staff

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate

Computer Science and Artificial Intelligence Laboratory (CSAIL)

Massachusetts Institute of Technology

Lecturer on Radiology

Harvard Medical School

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yixin Ma <yixinma9@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 11 February 2019 at 10:01
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampus subfield division

External Email - Use Caution

Hi Freesurfer experts,

I'm writing to ask about the hippocampus subfield division again. Last time, I gave you an example of the subject that I failed to run the hippocampal subfield division, and you told me that you were able to run the hippocampus subfield on your laptop. I was using the older command of recon-all -all -s bert -hippocampal-subfields-T1. Should I try to use the newer version: segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible FreeSurfer upgrading is the reason that I failed to run a subject on my server recently (but I was able to run it before). Also, can I ask where can I find the file of segmentHA_T1.sh?

Thanks for your help.

Cheers,

Yixin