Hi Bruce,<div><br></div><div>It&#39;s version 5.1. Thanks for the suggestion about the second problem (surface not following wm). For the white matter hypointensity problem (surface follows wm volume, but wm is incorrect; this occurs in several places on multiple subjects), will we just have to delete this manually from wm.mgz in every case? I can upload a recon with the problem if this would help.<br>


<br>thanks,</div><div>Nicole</div><div><br></div><div><br><div class="gmail_quote">On Mon, Jul 9, 2012 at 1:39 PM, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@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 Nicole<br>
<br>
what version are you running? It&#39;s hard to diagnose from just the images. In general, if the surface doesn&#39;t follow the wm.mgz it means there was a topological defect that was corrected in that region. You can find it and fix it be editing the wm. If you can&#39;t find it, upload it and send us the coords you are looking at and we&#39;ll find it and show you.<br>



<br>
cheers<br>
Bruce<div><div><br>
<br>
<br>
On Mon, 9 Jul 2012, Nicole Senecal wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
I&#39;ve been having two variants of problems with wm.mgz, using version5.1. One<br>
can be seen in the attached screenshot FI137 - areas that are not white<br>
matter are designated as &quot;white matter hypointensities&quot; on wm.mgz, and<br>
create problems with both surfaces. This has happened in a number of our<br>
subjects, in multiple locations throughout each brain. Is this something we<br>
just need to delete manually on each subject, or is there a more efficient<br>
way to deal with this?<br>
<br>
The second is seen in the screenshots of MP860 wm. An area that is not white<br>
matter, and is not designated as white matter on wm.mgz, is still created as<br>
a white matter surface. This hasn&#39;t happened as often as the above, but we<br>
don&#39;t know how to get rid of an inaccurate wm surface if it&#39;s not on wm.mgz.<br>
<br>
Thanks for your help,<br>
Nicole<br>
<br>
<br>
--<br>
Nicole Senecal<br>
Neuroscience Graduate Group<br>
Kable Lab<br>
3720 Walnut St., Room C37<br>
Philadelphia, PA  19104<br>
Lab phone:  <a href="tel:215-746-4371" value="+12157464371" target="_blank">215-746-4371</a><br>
<br>
<br>
<br>
<br>
</blockquote>
<br>
<br></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Nicole Senecal<br>Neuroscience Graduate Group<br>Kable Lab<br>3720 Walnut St., Room C37<br>Philadelphia, PA  19104<br>Lab phone:  <a href="tel:215-746-4371" value="+12157464371" target="_blank">215-746-4371</a><br>

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