Re: [Freesurfer] control point and aseg edit

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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