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Hi FreeSurfer Developers,
I have a major problem with the reconstruction of the pial surface.
The issue is the opposite to the one relate to the brainmask: the reconstruction excludes part of the gray matter.
In attachment an example of the output after running -autorecon2-wm -noaseg, and the recon-all.log if needed.
Does anyone have any thoughts on how to fix it?
FreeSurfer version: v5.3.0 up to 'recon-all -s <subjid> -autorecon2-inflate1 -noaseg -cc-crs <x> <y> <z> -pons-crs <x> <y> <z>', v6.0.0 for manual editing on the wm and 'recon-all -s <subjid> -autorecon2-wm -noaseg -cc-crs <x> <y> <z> -pons-crs <x> <y> <z>'.
Thank you.
Best wishes,
Alessia Sepe
MSc | PhD Fellow
KU Leuven
Laboratory for Neuro- and Psychophysiology Department of Medicine ON II Herestraat 49, 3000 Leuven
