Dear Raj,

A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But this is a direction I’m still interested in, and which I’m planning to revisit in the future.

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Emily K Clarke <ekc23@duke.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 26 September 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Dr Rajendra Morey, M.D." <rajendra.morey@duke.edu>
Subject: [Freesurfer] amygdala segmentation atlas influence

External Email - Use Caution

Hello all,

I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help!

raj