I used the expert option for control points and manually edited the aseg.presurf.mgz. Which is the proper flag to use in other to incorporate the respective changes? 

a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time

or 

b) recon-all -autorecon2-cp -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time

Thanks. 

Best, 
Paul