Dear Bruce,

Thank you very much! Sincerely, Ye

On Tue, Jul 2, 2013 at 4:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

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

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