do you want it to regenerate the aseg? If not, then a). If so, then you would just run autorecon2 (instead of autorecon2-cp)

cheers
Bruce

On Thu, 14 Sep 2017, miracle ozzoude wrote:

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

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