Hi Aaron

We explicitly exclude amygdala/hippocampus from the surface models since they aren’t neocortical. Hippocampus of course has some internal structure that could be modeled that way (and has been), but it is pretty tough to do without significantly higher res data than we usually require and would require a different algorithm than the pial surface one

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Aaron Geller
Sent: Sunday, April 17, 2022 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] pial surface vs aseg in MTL

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Hi-

A recurring issue with my recons is that the pial surface excludes the hippocampal formation and associated MTL grey matter structures.  A typical image is attached.

Aseg has clearly captured the location of these structures correctly, as indicated by the coloring in freeview, 

so I'm wondering: does freesurfer not use the aseg results when constructing the pial surface?  If not, can it be made to do so? Is there any workaround other than manual correction of each pial surface?

Interestingly, I have never seen freesurfer exclude the ventral midbrain (or thalamus), though it seems to be in an analogous situation.

Thanks,

Aaron