Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598