Thanks for the interest in our tool, Sarah! With the smallest nuclei, it is possible that nucleus X has non-zero probability for a bunch of voxels, but does not win any of those voxels (i.e., there’s another label with larger probability). If that happens, the volume will be non-zero (as you have some volume coming from the non-zero probabilities) but no single label will be labeled as X.

Does this make sense?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sarah Skinner <seskinner@wisc.edu>
Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Friday, January 13, 2023 at 11:46 AM
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - Anterior Amygdala Area missing in FreeView

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Hi FreeSurfer Experts,

I'm attempting to QC the hippocampal/amygdala segmentation in FreeView. When looking at ?h.hippoAmygLabels-T1.v21.FS60.mgz I can see that a few subjects are either missing a mask of the anterior amygdaloid area (AAA) for a single hemisphere or the AAA is extremely small. However, in both circumstances the volumetric value for the AAA in the output (?h.amygNucVolumes-T1.v21.txt) looks normal. In the cases where no AAA mask is visible, if you check the box "Show existing labels only", the label "7010 Anterior-amygdaloid-area" does not even appear for that hemisphere. 

AAA is the only structure where this is occurring. There are other structures (such as the medial nucleus) that appear small in FreeView, but still have a normal volumetric value. However, no other structure is completely missing.

Note: In all of these cases aseg looks fine. And T1s were processed using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but we used freesurfer-darwin-macOS-7.1.0-20200511-813297b to run with hippocampal/amygdala segmentation (segmentHA_T1.sh).

Thank you for you time and help,

Sarah Skinner

Research Specialist
University of Wisconsin - Madison