It looks like it is missing WM extending into the temporal pole. If it is not in the filled.mgz, then edit the wm.mgz and/or add control points in the WM in that region.

On 12/1/2022 11:34 AM, Alessia Sepe wrote:

External Email - Use Caution

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer