Hi Barbara
yes, this is intentional and shouldn't be a problem. The hippocampus has lots of internal structure that we don't model with the surfaces (but we do with the subfield stuff), but we exclude it from our analyses so you should be fine
cheers Bruce
On Wed, 6 Jul 2016, Barbara Kreilkamp 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