[Freesurfer] Recommended workflow

Greetings to all,

I have several pathological subjects, which need substantial editing involving removing of dura reminders, filling WM due to the lesions, and adding control points due to the WM atrophy. I ran "recon-all -all" first to have initial reconstruction, which helps me to focus on correcting the earlier mentions problems. I have corrected brainmask, wm, and created control points, and now I wonder if re-running "recon-all -autorecon2-cp -autorecon3" would be sufficient to get correct results, or should better run separately "recon-all -autorecon2-cp" followed by "recon-all -autorecon2-wm -autorecon3"?

Thanks in advance,

Martin