Thank you for your kind suggestions.<div>I reprocessed the subject and this time I&#39;m sure about the control points.</div><div>However when I added the control points to the left hemisphere,</div><div>the right hemisphere surface was changed severely. </div>
<div>I used the command line, recon-all -autorecon2-cp -s subjectID.</div><div>Could you tell me why does it occur and how to deal with it?</div><div><br></div><div><br></div><div>Best,</div><div><br></div><div>EK </div><div>
<br><div class="gmail_quote">2012/9/25 Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@nmr.mgh.harvard.edu</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi EK<br>
<br>
make sure that you don&#39;t have any control points in any voxels that contain any GM. It looks like maybe you do in the region where you drew a red arrow, although it&#39;s impossible to tell for sure from those images.<br>

<br>
cheers<br>
Bruce<div><div class="h5"><br>
<br>
On Tue, 25 Sep 2012, EK Kim wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all expert,<br>
Hello, I have been trying to solve this WM/GM boundary error. <br>
The data I attached here have a lots of problems, especially WM/GM boundary<br>
was not detected in temporal areas.<br>
Using mri_cnr function, I calculated the gray/white CNR of the norm.mgz.<br>
<br>
------------------------------<u></u>---<br>
norm.mgz<br>
<br>
white = 97.3+-10.3, gray = 77.3+-14.8, csf = 55.6+-19.5<br>
gray/white CNR = 1.222, gray/csf CNR = 0.790<br>
lh CNR = 1.006<br>
<br>
white = 97.0+-11.2, gray = 76.9+-15.1, csf = 55.9+-19.3<br>
gray/white CNR = 1.139, gray/csf CNR = 0.737<br>
rh CNR = 0.938<br>
total CNR = 0.972<br>
------------------------------<u></u>----<br>
<br>
1. Does the low CNR affect the bad tissue segmentation results?<br>
How can I solve the problem? <br>
Is there a way to improve the low CNR value?<br>
<br>
2. How can I delete the continuous areas, indicated by red arrow  (axial,<br>
134)?<br>
<br>
<br>
I use freesurfer-Darwin-leopard-<u></u>i686-stable-pub-v5.1.0.<br>
<br>
<br>
Thank you for any comments or replies in advance.<br>
<br>
<br>
Best, <br>
<br>
EK<br>
<br>
<br>
</blockquote>
<br>
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