Dear Paul,

maybe this is implicit, but to assure:

you have also to include -autorecon3.

Therefore the full command is:

recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial

Antonin

Yes, I think so

> On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
> 
> Hello, 
>  I ran the entire recon pipeline with T2 option and then added control 
> points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the 
> pial surface or not? Thanks.  
> Paul
>