recon-all \

-skullstrip \

-s fs_output \

-clean-bm \

-wsthresh 100

But, I found too much brain tissue has been removed, particularly for the visual and motor cortex, please see below.

Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include more brain tissues. 

Looking forward to your reply. Thanks.

Best,

Cain