Okay :-). Last question then, how about skull strip correction. <div><br></div><div>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?</div>
<div><br></div><div>Best,</div><div>Martijn<br><br><div class="gmail_quote">On Fri, Mar 2, 2012 at 2:29 PM, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu">fischl@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Martin<br>
<br>
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)<br>
<br>
cheers<br><font color="#888888">
Bruce</font><div><div></div><div class="h5"><br>
On Fri, 2 Mar 2012, Martijn Steenwijk wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
On <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction" target="_blank">http://surfer.nmr.mgh.<u></u>harvard.edu/fswiki/<u></u>RecommendedReconstruction</a> it is indicated that -autorecon-cp should be added if control points are added. Shouldn&#39;t this be<br>

-autorecon2-cp?<br>
<br>
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<br>
call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3?<br>
<br>
Best,<br>
Martijn<br>
<br>
<br>
</blockquote>
<br>
<br></div></div><div><div></div><div class="h5">
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