Hello Bruce,

Yes, that is my end goal. I have a patient i edited the aseg to include left-cerebral white matter and also, want to normalize the intensity using expert option. Where should I place the "-canorm-usecps" flag ? After the command like " recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like "recon-all -autorecon2 -canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. Thank you.

Best, 
Paul 

On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
do you want the control points to be applied to the aseg? If so, you need to also specify -canorm-usecps


cheers
Bruce
On Thu, 14 Sep 2017, miracle ozzoude wrote:

Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert option for control point.
That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. 
Best, 
Paul

On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      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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