On Tue, Jul 2, 2013 at 4:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.