Hi Liz,

I cannot say for sure without seeing the posteriors, but that totally looks like it is part of the alveus – which we leave out of the hippo subfield segmentation.

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 Lizbeth Ayoub <lizbeth.ayoub@utoronto.ca>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, September 16, 2020 at 23:41
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal segmentation -quality check

External Email - Use Caution

Hi everyone,

I am in the process of checking my hippocampal segmentations. I am finding that the hippocampal mask is often underestimating certain grey matter areas perhaps pertaining to the hippocampus? For example, the area pointed by the red arrow, here below, was initially covered by the apart + aseg hippocampal mask. Would the FS voxel space mask of the hippocampus pass quality check or would you say that a part of the hippocampal grey matter would be missing ?

Thank you for your helpful insight,

Liz