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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
