yes, it will recognize and use the control points. autorecon2-cp is a subset of autorecon2 so no need to rerun it.
cheers Bruce
On Fri, 2 Mar 2012, Martijn Steenwijk wrote:
Okay :-). Last question then, how about skull strip correction. If I understood well, it is advisable to first add control points and then correct the skull strip. Will the option set -autorecon2 -autorecon3 (as indicated in the wiki to be runned after manual skull strip correction) also recognize the existence of the control points, or is it then needed to run -autorecon2-cp again?
Best, Martijn
On Fri, Mar 2, 2012 at 2:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Martin
yes, you are right, that is a typo. And rerunning autorecon2 is sufficient since it is a superset of autorecon2-cp (and will detect the existence of control points, and use them) cheers BruceOn Fri, 2 Mar 2012, Martijn Steenwijk wrote:
Dear all, On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp? Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3? Best, MartijnThe 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.