[Freesurfer] Pial boundary overshoot

Dear Freesurfer experts,

I have run recon-all on brains atrophied by a neurodegenerative disease. as you can see in the attached images, the pial boundary seems to have overshot and contains mostly arachnoid space, and the white matter boundary (yellow) includes substantial amounts of cortical gray matter.

This is the case in all slices in three of the most atrophied brains. Do you have any suggestion as to what I can do to get these brains analyzed properly? Would perhaps changing the threshold for white matter intensity with control points help? I have manually adjusted the talairach, but it has not improved this issue.

Thank you for your help!

Victor