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:

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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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