Thank you for your answer.
I'm not sure I understand your question right,
but I just processed the file using following procedures.
1. recon-all -autorecon1 -nuintensitycor-3T (because mine was 3T)
2. skullstripping brain mask using gcuts
3. adding control points (only on the left hemisphere)
4. recon-all -autorecon2-cp
and this figure was made by a commnad line, [tkmedit wm.mgz -aux brain.mgz -surfs].
Best,
EK.

2012/10/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
what was the name of the file that you transferred?

On Wed, 10 Oct 2012, EK Kim wrote:

I already uploaded this problem 2 days ago, reprocessing the subject to make
sure about control points.
However when I added the control points to the left hemisphere,
the right hemisphere surface was changed severely. 
I used the command line, recon-all -autorecon2-cp -s subjectID.
Could you tell me why does it occur and how to deal with it?


Best,

EK 




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.