Re: [Freesurfer] Difference between recon-all -autorecon2-wm and recon-all -autorecon2-wm -autorecon3

Hi Ye -autorecon3

should always be run after any of the autorecon2 steps. If it's not on the tutorial, that is a mistake

cheers Bruce On Tue, 2 Jul 2013, ye tian wrote:

Dear Freesurfers, I just realize that in the tutorial example of "geometric accuracy", recon-all -autorecon2-wm is used to recreate the final surfaces; while in "lateral ventricle", recon-all -autorecon2-wm -autorecon3 is used. However, the modification steps look the same to me -- fill in the "hole" of white matter in wm.mgz.

Why do they use different commands after all? What's the difference between -autorecon2-wm and -autorecon2-wm -autorecon3?

Thank you very much!

Sincerely, Ye