Hi Moji:

1. Absolutely. You can use standard FreeSurfer tools for extracting masks from a segmentation, resample them to whatever space, etc.

2. A lot of people have been making this question, so we’re now writing a bunch of merged segmentations to the mri directory of the subjects for convenience. If none of these groupings satisfies you, it is always possible to use standard FreeSurfer tools to do this.

3. Yes, the new atlas includes the nuclei of the amygdala (Saygin, Kliemann et al, NeuroImage, 2017).

Features 2 and 3 will be available in the dev version in the next few days; stay tuned!

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Aghajani, Moji" <m.aghajani@vumc.nl>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 23 August 2017 at 12:14
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal and amygdalar subregional segmentation

Dear Freesurfer Developers,

I have some questions regarding hippocampal and amygdalar subregional segmentation in the latest Freesurfer version:

1) Can one use the segmentation outputs as ROI masks, register those to native space functional image, and extract functional time courses in order to perform seed-based subregional functional connectivity analyses?

2) How sensible do you deem it to assess the functional connectivity profiles of all the subregions? Would you argue against grouping some of the subregions into a larger subregion and assess connectional profiles. For instance combining CA 1 to 4 into a CA subgroup? Or the Subiculum and Pre- Parasubiculum into one subgroup? I am asking this because most literature on hippocampal subregional connections focuses on the major subregions (CA, Dentate Gyrus, Subiculum), with very limited knowledge on connectivity profiles of smaller individual subregions. 

3) Is it already possible to segment the amygdala subregions as well with this new pipeline? On the Freesurfer website the following is stated: “In addition to the hippocampal subregions, it also simultaneously segments the nuclei of the amygdala”. However, the page also states that this functionality will soon be available in the dev version, so I am not sure whether the amygdala subregional segmentation pipeline is already in place? If not, is there a preliminary release date known already? 

Thanks for your time and effort!