Hi Allison,<div><br></div><div>But when I run -autorecon-cp it complains that the option does not exist. I&#39;m using FS5.1.. </div><div><br></div><div><div>msteenwj@lnx-rad-03 freesurfer51 % recon-all -subjid P102_corr -autorecon-cp</div>
<div>ERROR: Flag -autorecon-cp unrecognized.</div><div>-subjid P102_corr -autorecon-cp</div><div>Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux</div><div><br></div><div>
recon-all -s P102_corr exited with ERRORS at Fri Mar  2 14:23:15 CET 2012</div><div><br></div><div>For more details, see the log file</div><div>To report a problem, see <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting">http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a></div>
</div><div><br></div><div>Best,</div><div>Martijn<br><br><div class="gmail_quote">On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens Player <span dir="ltr">&lt;<a href="mailto:astevens@nmr.mgh.harvard.edu">astevens@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"><div bgcolor="#FFFFFF"><div>Hi Martijn,</div><div>autorecon-cp is correct, we start the process a bit earlier now. But even better, regardless of what edits you make, you can rerun with &quot;recon-all -make all&quot; and it will start at the earliest needed step. (Although running from autorecon2 after the skullstrip fix is correct as well).</div>
<div>Allison</div><div><div></div><div class="h5"><div><br>On Mar 2, 2012, at 6:11 AM, Martijn Steenwijk &lt;<a href="mailto:martijnsteenwijk@gmail.com" target="_blank">martijnsteenwijk@gmail.com</a>&gt; wrote:<br><br></div>
<div></div><blockquote type="cite"><div>Dear all,<div><br></div><div>On <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction</a> it is indicated that -autorecon-cp should be added if control points are added. Shouldn&#39;t this be -autorecon2-cp?</div>

<div><br></div><div>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?</div>

<div><br></div><div>Best,</div><div>Martijn</div>
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