Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is more reliable than using the whole white / gray matter to compute parameters. But it could be hacked, albeit it would be a bit less reliable. I’ll add this
to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to look at it any time soon…)
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2003@med.cornell.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, May 5, 2020 at 10:46
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] samseg with subfields
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg? If it is possible is it as reliable as from running regular routine with “-all” recon-all flag?
Thank you,
Sneha
From: Sneha Pandya
Sent: Thursday, April 30, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: samseg with subfields
Dear experts,
Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset?
Thank you,
Sneha