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) http://www.jeiglesias.com
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