I'm not sure it matters, but if you put it at the end nothing will reset it

On Thu, 14 Sep 2017, miracle ozzoude wrote:

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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