Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?<div>Caspar<br><br>On Thursday, October 3, 2013, Bruce Fischl  wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Caspar<br>
<br>
try putting control points in the white matter where the pial surface doesn&#39;t get out far enough.<br>
<br>
cheers<br>
Bruce<br>
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Freesurfer Experts,<br>
I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having<br>
trouble getting the pial surface to go all the way through the grey matter.<br>
Please see screenshot attached. These data were acquired with a surface coil<br>
and the grey matter varies a lot in intensity. Interestingly, the pial<br>
surface growing process fails where the grey matter is fairly dark. I have<br>
tried several rounds of normalizing using the N3 tool but that didn&#39;t change<br>
anything.<br>
Thanks for any advice on this, Caspar<br>
<br>
<br>
</blockquote>
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