ps: just wanted to add a clarification to my question. The two scenarios are: <div>Scenario A:</div><div>1. recon-all -s &lt;subject&gt; -autorecon1 -autorecon2 -autorecon3 </div><div>2. add control points </div><div>3. recon -all -s &lt;subject&gt; -autorecon2-cp -autorecon3</div>

<div><br></div><div><div>Scenario B:</div><div>1. recon-all -s &lt;subject&gt; -autorecon1 -autorecon2</div><div>2. add control points </div><div>3. recon -all -s &lt;subject&gt; -autorecon2-cp -autorecon3</div><div><br>
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<div>If Scenario B is permissible, the advantage is that, -autorecon3 is only run once thus saving </div><div>a few hours of computation. </div><div><br></div><div>Thanks</div><div>Mehul</div><div><br><div class="gmail_quote">

On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat <span dir="ltr">&lt;<a href="mailto:mpsampat@gmail.com" target="_blank">mpsampat@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

Hi Folks,<div>Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then  </div><div>run -autorecon2-cp and -autorecon3 again. </div><div><br></div><div>Recently, I was looking at the process flow table: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable</a> </div>


<div>and I have two questions: </div><div><br></div><div>1. From this table it seems like ?h.white is created in autorecon2 and ?h.pial is created in autorecon3. </div><div>However, when i run recon-all -s subj -autorecon1 -autorecon2 i see that ?h.pial is also already created.</div>


<div>Does this mean I am interpreting the process flow table incorrectly or is there an error in the table ? </div><div><br></div><div>2. Also if ?h.pial and ?h.white are already created at the end of autorecon2; then  can we add control </div>


<div>points at immediately after autorecon2 ? This way we would need to run autorecon3 only once and save resources.  </div><div><br></div><div>Or am I missing something and is it that one must run -autorecon2 and -autorecon3 and then add control points </div>


<div>and then run -autorecon2-cp and -autorecon3 again. </div><div><br></div><div>Thanks</div><span class="HOEnZb"><font color="#888888"><div>Mehul</div><div><br></div><div><br></div><div><br></div>
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