Hi Farhad,
I'd be happy to help you with this problem. This appears to be a topological defect. You can edit the white matter volume (wm.mgz) by using the recon edit button to remove the section of white matter that is connecting the gyri. After making the edits and saving the volume, you can re-run recon all with the following command: recon-all -autorecon2-wm -autorecon3 -subjid <subject name>. By editing the white matter volume, both the white matter and pial surfaces will be regenerated. I recommend looking at the following link for additional information.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
If you have any further questions, feel free to ask.
Morgan ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Farhad Ghaseminejad [a.farhadgt@gmail.com] Sent: Thursday, August 31, 2017 1:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] rh.white and rh.pial surface manual edit
Hello FreeSurfer experts,
I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached.
https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=shar...
Best, Farhad