We do not have a way to generate surfaces for hippocampus. You could
play with the subfields, eg, like
mri_binarize --i subfields.mgz --match M1 M2 ... --surf lh.hippo
--surf-smooth 2
This will build a surface around segments M1, M2, ...
you can then view with freeview
On 2/28/2023 8:42 AM, Khazar Ahmadi wrote:
External Email - Use Caution
Dear FS experts,
I’d like to delineate WM and pial surfaces in the hippocampus and
subsequently bin GM layers of it (like the approach that is commonly
used for laminar analyses in V1 or other sensory cortices). I think
the current output of recon-all does not contain WM/pial surfaces in
subcortical regions. Have tried running the FS hippocampal module. It
generates subfields (in .mgz format) and volume estimates but I cannot
find any surface-based output. Is there a way to obtain pial and WM
surfaces in this region? I have another question regarding
surface-based representation of the subfields. Based on the paper by
Sämann et al., 2020 (see the link below; Figure 6), I think it is
possible to have surface-based visualization of the subfields using
ENIGMA, but I could not find additional documentation on that. Any
ideas on how to obtain surface-based segmentation of the hippocampus
would be greatly appreciated.
Thanks a lot, and best wishes,
Khazar
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Khazar Ahmadi, PhD
Postdoctoral Researcher,
Institute of Cognitive Neuroscience,
Department of Neuropsychology, Ruhr University Bochum, Bochum,Germany
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