[Simnibs-discuss] Recurring poor GM segementation/surface with charm pipeline

[Daniel McCalley]

Hi all,

I've noticed that in many (almost all) of the scans I've put through the charm pipeline have returned really nice surface segmentations of the scalp, bone, WM, etc. However, the grey matter surface typically appears very poor (loses detail in sulci/gyri).

I've tried headreco and charm for 3 separate anatomical scan acquisitions and got the same result consistently (photo attached).

I suspect something in the despiking/cleaning tetrahedra step in charm may be causing this, but I'm not sure. Any pointers or things to try for troubleshooting?

Best,

Dan McCalley, Ph.D.
Postdoctoral Scholar, Padula BRAVE lab
Stanford University
School of Medicine, Psychiatry and Behavioral Sciences
(he/him)
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