Dear Dough,

 

No worries, this was helpful too. Probably, I will test it on a subset of subjects and compare the two for possible discrepancies.

 

Thank you,

Sneha

 

 

sorry, did not see this before I responded. Ignore what I said

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)

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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

 

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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

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