Hi Aaron
Yes, you won’t be able to get it to extend there. If it did it would miss all
sorts of internal boundaries in the hippocampus so I don’t think it would be
all that useful. Can you not just use the hippocampal subfield and amygdalar
nucleus models in addition to the surfaces?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Aaron Geller
Sent: Sunday, April 17, 2022 12:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] pial surface vs aseg in MTL
External Email - Use Caution
Thanks Bruce! I was not aware of this basic design decision.
If that is the case, will freesurfer disregard manual corrections to try to
force inclusion of the hippocampus?
I am using freesurfer to make cortical models for use with epilepsy surgery,
and as the MTL is a common implant target, having the pial surface respect
this structure is important.
Aaron
On Apr 17, 2022, at 9:59 AM, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Aaron Geller
Sent: Sunday, April 17, 2022 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] pial surface vs aseg in MTL
External Email - Use Caution
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.
<image001.png>
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
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