In general, lesions (severe intensity changes) or severe anatomical changes (e.g. missing tissues or tumor) are very difficult to deal with, when you are using a transformation-based analysis.<div><br></div><div>When you use transformation with low elasticity (e.g. linear transformation), the transformation could be less affected because the registration would be mostly driven by the brain outlines. So, if your lesions (intensity changes) do not accompany anatomical deformation, you may be able to compare patients and controls.</div>
<div><br></div><div>As the elasticity increases, the transformation would be more affected by the lesions. Of course, if the lesions are small, they may not cause much problems but I assume you have large lesions.</div><div>
<br></div><div>If you are studying, for example, stroke and interested in anatomical changes of contralateral hemisphere (or the brainstem), you can mask-out the ipsilateral hemisphere for both patients and the atlas. We have done this type of analyses before.</div>
<div><br></div><div>Sorry that I could give you only a generic answer. This is an issue that the whole community faces.<br><br><div class="gmail_quote">On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<div><br></div><div>I am interested on normalizing lesioned brains with a dual channel Diffeomap procedure. The normalization will be done on MNI existing template of Diffeomap. Lesions typically come from surgical resections.</div>
<div><br></div><div>Does this procedure work well on lesioned brains or shall I need some mask for Diffeomap to avoid normalizing the lesioned area?</div><div><br></div><div>Any comment is welcome. I couldn't find much about the topic on previous posts and articles.</div>
<div><br></div><div>Thank you.</div><span class="HOEnZb"><font color="#888888"><div>Dorian P</div>
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