Dear freesurfer experts,

I am analysing some MP2RAGE images on freesurfer and found an error I am unable to correct. 

After the recon-all finished successfully, I looked at the T1 and brainmask images on freeview and I noticed a skullstripping error on the brainmask volume. On one side of the brain there was also skull (and other non brain parts), and on the other half there was a lot of missing cortex. 

I tried to change the watershed threshold but this didn't work, I also tried to put control points but most of them were ignored since they were outside of the estimated pial surface. 

What would be the best way to correct this problem?

Regards,

DK