Dear Freesurfer users,<div><br></div><div>Thank you Dr.Stevens for suggestions. I reran -autorecon2 but still it didn&#39;t fix the pial surface. I edited wm.mgz again by adding more control points AND more white matter voxels using the &#39;edit voxel brush&#39; but still, after reran the whole second recon step, pial surface failed to include the added wm voxels in. Pls see the attachment. Does anyone encounter the same thing before? Thank you for advice!</div>
<div><br></div><div>Min<br><br><div class="gmail_quote">On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens <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;">Hi Min,<br>
We&#39;ve learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2 and see if it fixes everything.<br>
Allison<div><div></div><div class="h5"><br>
<br>
On Thu, 31 Mar 2011, Min Liu wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Freesurfer users,<br>
<br>
My first run of recon1&amp;2 left some white and grey matter at temporal pole<br>
region excluded. So I edited the wm.mgz by adding a bunch of control points<br>
intending to get more white matter and expand the pial surface (please see<br>
the coronal slice in the attachment where the control points were placed).<br>
Then I ran the command &#39;recon-all -autorecon2-cp -subjid XX&#39; WITHOUT<br>
&#39;-autorecon3&#39;. From my understanding, Freesurfer would recalculate the<br>
wm.mgz as well as the white matter and pial surfaces in temporal pole<br>
according to the control points. However, I got wm.mgz corrected and pial<br>
surface wrong (as the attached graph indicated).<br>
<br>
Did I do something wrong? Why wm.mgz got fixed while pial surface not?<br>
Thanks for help in advanced!<br>
<br>
Veronica<br>
<br>
</blockquote>
<br>
<br></div></div>
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