Thank you Dr. Mori,<div><br></div><div>Yes, my lesions are mostly surgical resections. The second question was mostly a comparison between different alpha maps in LDDMM and SPM normalization on lesioned brains. In SPM a T1 can be normalized (either directly or through segmentation) on a MNI template and the transformation matrix can be applied to any volume (i.e. BOLD, FA, Tensors). I was wondering whether this method maybe worst or better on lesioned data compared to LDDMM.</div>
<div><br></div><div>Best regards.</div><div>Dorian<br><br><div class="gmail_quote">2012/12/1 susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
You need to mask anatomically equivalent regions in both the patients and the atlas, which is difficult. <div>I assume your "lesions" mean surgically removed tissues. Is it correct? If you can assume that the anatomical deformation around the lesions is small (like the partial moon), you can register the patient image to the atlas by affine (either automatically or landmark-driven) and transfer the lesion locations to the atlas manually, I think. In stead of affine, you may be able to use low-elasticity LDDMM (alpha = about 0.01).</div>
<div><br></div><div>I didn't quite get your second question. Using LDDMM (DiffeoMap), you can control the elasticity by alpha value. 0.01 and larger give low elasticity. 0.005 is recommended for normal brains. 0.001-0.002 is used when anatomical difference is large.</div>
<div><br></div><div>When you want alpha smaller than 0.005, cascading alphas are recommended (e.g. three consecutive LDDMM with 0.01-0.005-0.002) to avoid being trapped by a local minima. Using this cascading-alpha approach, you can also obtain the intermediate results; results with low elasticity (alpha = 0.01), medium alpha (alpha = 0.01/0.005).</div>
<div><br></div><div>In DiffeoMap, you can use up to 3 cascading alphas.<div><div class="h5"><br><br><div class="gmail_quote">On Fri, Nov 30, 2012 at 7:54 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">Thank you for answering Dr. Mori,<div><br></div><div>Would it be feasible to mask only the lesion on the patient or does it have to be on both patient and atlas?</div>
<div><br></div><div>Has anybody compared a T1 normalization on SPM and applying the matrix to DTI to a low elasticity normalization in DTIstudio?</div>
<div><br></div><div>Best regards.</div><div>Dorian </div><div><br><br><div class="gmail_quote">2012/11/30 susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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"><div><div>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>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>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><font color="#888888"><div>Dorian P</div>
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