On Fri, Mar 2, 2012 at 2:37 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
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
Bruce
On 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,
Martijn
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