Uuummm it’s hard to tell with single slices, but a lot of it is the alveus. There’s also a cyst in one of the cases.
From: Tricia Merkley <tmerkle22@yahoo.com>
Date: Friday, October 17, 2025 at 18:41
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal segmentation
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Hello FreeSurfers,
In visually reviewing the output of the hippocampal subfield segmentation, there are a few subjects that show gaps in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen.
Some also appear to include more than the hippocampus in the boundaries. Please see the attached examples. This was run with FS version freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Any idea why this may happen? Should we be concerned about the validity of the segmentation, or does it accurately represent the neuroanatomy for these individuals (normal variation vs. pathology)?