Hi Jeff,<div><br></div><div>I think you can submit up to 4 or 5 channel LDDMM through DiffeoMap.</div><div><br></div><div>When you use more channels, the more memory it takes and could take longer time for calculation. So you want to use the channels wisely. For example, b0 and trace have very similar contrasts and won't improve the registration that much. FA+Trace+b0 could put more weight on Trace/b0 contrasts but other than that, the result should not be much different from FA+Trace. DWI may provide some additional information and could improve the results. What we often do is to submit 1/0 binary masking data for the ventricle. This improves the registration a lot especially for patients with very enlarged ventricles. This method, however, requires some additional work to define ventricles.</div>
<div><br>Addition three channels of color images (red, green, and blue) is another option. This theoretically allows us to match red fibers to red fibers, green to green, and blue to blue, further improving the registration, but there are a couple of things that require attentions. First, strictly speaking, the fiber color can change due to transformation. Therefore, we need to generate new color maps after each finite transformation. This algorithm is not implemented in the current DiffeoMap. Second, red-to-red matching sounds good for core white matter regions but for peripheral white matter regions where R, G, B are mixed in a complex and in-reproducible manner, you may not want to force red-to-red matching.</div>
<div><br></div><div>So, it is not an easy task to find if addition of new contrasts really improve registration in a reproducible way. It could also depend on the amount and nature of the anatomical abnormality of your patient group. So I would encourage you to give some testing. Oh, one thing I want to add is, if you use the color maps with the current DiffeoMap algorithm, you may get some unhappy reviewers when you submit a paper, although, I believe one of the original papers in this topic by C.F. Westin used this type of simplified version of color-to-color registration.</div>
<div><br></div><div><br><div class="gmail_quote">On Mon, Jul 30, 2012 at 4:42 PM, Jeff Sadino <span dir="ltr"><<a href="mailto:jsadino.queens@gmail.com" target="_blank">jsadino.queens@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<div><br></div><div>I am wondering why we only submit the FA and the Trace images. It seems like we could submit the FA, Color, DWI, and Trace images. I see that the information from these images come from the same "primary channel", but in my testing, the more images I submit, the better registration I get. Is there anything wrong with submitting all four of these channels?</div>
<div><br></div><div>Thank You,<br>Jeff Sadino</div>
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