Hi, There is nothing to solve — that is the expected behavior around the hippocampus/amygdala.
See this FAQ: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt hestructuresthere.HowcanIfixthis.3F
cheers, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 7/6/16, 4:47 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Barbara Kreilkamp" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of bakk.hbg@googlemail.com> wrote:
Dear Freesurfers,
Unfortunately I am having a problem with recon-all segmentation in some of my participants.
It seems that part of the brain is cut off in the medial part of the Temporal lobes (please see attachment), around the region where the hippocampus is.
I am unable to place WM region control points, as the algorithm does not have seemed to miss white matter, rather only gray matter of the hippocampus.
I've seen on your website that also there the cortical surface does not include the hippocampus, so I wonder if this is intentional? Problem is that the surface here grasps some of the hippocampus but not all of it.
What is the best way of solving this?
Thanks very much.
Best wishes,
Barbara
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