Hi David

what does the aseg look like in those cases? That is, is it the hippo/amygdala stuff failing or is the root cause further back in the stream (something that caused a bad aseg)

cheers Bruce On Thu, 20 Jun 2019, David S Lee wrote:

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Hello FreeSurfer Experts,  I wanted to re-post this question (posted June 4th), yet did not receive your guidance:

I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version.

• 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but

in the volumetric output, there are values for the regions.

• 2 subjects' medical nuclei masks are located in the Putamen region (more

superior/detached from the rest of the amygdala).

I found the exact same inquiry RE: AAA region posted on April 30, 2019, but I did not see any response.

What would be your recommended course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions?

Thank you for your time,

-- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115