Please see below;<br><br><div class="gmail_quote">On Tue, Jun 30, 2009 at 11:49 AM, Fijoy Vadakkumpadan <span dir="ltr"><<a href="mailto:fijoy@jhu.edu">fijoy@jhu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all,<br>
<br>
I have a template image and a subject image, each containing 5<br>
intensities, including the 0 intensity for the background. I would<br>
like to use the Landmarker to perform multichannel LDDMM to register<br>
the two images. I looked at the window that pops up after I press the<br>
"Multichannel" button in the Landmarker, and I was wondering if<br>
someone could please clarify the following:<br>
<br>
1. How many channels should I use? Should I use 4 channels, one for<br>
each nonzero intensity that the images have?</blockquote><div><br>> If I understand it correctly, you have segmented data. For example, if we do gray matter - white matter segmentation, you may get ONE IMAGE in which outside is 0, gray matter is 1, white matter is 2, and ventricle 3. For a template and a subject, you have two of these images. You can submit these two images to the "single-channel" LDDMM. <br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
2. The pop up window asks for a list of template images and a list of<br>
subject images. How many template and subject images should I create?<br>
How do I create them?</blockquote><div><br>> You can use the multi-channel if you have the following situation;<br>> Suppose you have the above segmented image based on T1-weighted image.<br>> Then you create SECOND segmentation map using a FA map. For example, use FA>0.25 and create another map in which white matter is 1 and outside is 0.<br>
> Now you have TWO segmentation maps for the template and for the subject (total 4 images).<br>> In this case, you use the "multi-channel" LDDMM. For the template, you choose T1-based and FA-based segmentation maps and for the subject, you choose T1-based and FA-based segmentation maps.<br>
> Then LDDMM will do; Template T1 - Subject T1 mapping as well as Template FA - Subject FA to get one solution that satisfies the two matching simultaneously.<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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3. If I should have more than 1 template image, how do I load multiple<br>
template images into the Landmarker?</blockquote><div><br>> First, open the template T1 using the Open icon in the top menu.<br>> Once you get a viewing window, use the Open icon in the right column of the viewing window to open template FA.<br>
> Go back to the Open icon in the top menu and open the subject T1<br>> Once you get another viewing window for the subject, use the Open icon in the right column of the subject viewing window to open subject FA.<br>
> Go to "multi-channel" LDDMM. You can find T1 and FA are listed for Template and also for the subject.<br><br>Hope this clarifies your question.<br><br></div>Susumu</div><br>