Hi Yi,<br><br>1) I recommend you to do AIR first from two reasons. First one is a practical reason. Our LDDMM requires that the matrix and pixel sizes of the two images are identical. After AIR, even if the input images have different dimensions, the output will have the same dimension. This is handy. Second one is more important. Let me use fitting of a X-Y plot for analogy. When you use linear fitting, no matter which software you use, the results are almost identical. This is because the energy landscape of linear fitting usually has a very simple "one-valley" shape, meaning the results always converge at the same solution. On the other hand, when you are using non-linear fitting, you are required to provide initial values, which are close to the real solution. Usually you first do linear solution and then use the result as the initial value for the subsequent non-linear fitting. This is because the energy landscape of non-linear fitting has a complicated "multi-valley" shape. If your initial values are far away from the real solution, the fitting is trapped by a local minima. <br>
<br>Non-linear warping is very similar. You are required to bring two brains as close as possible before you start non-linear warping.<br><br>When you adopt AIR+LDDMM, you have to transform the image twice, including tensor reorientation. Landmarker can combine transformation matrices so that you can do multiple transformation at once to avoid multiple interpolation. <br>
<br>Xin, can we combine AIR matrix and LDDMM matrix?<br><br>2) We usually don't use non-linear AIR. So we don't have much experience with it. Yes, it should do tensor reorientation if you apply the transformation to a tensor file.<br>
<br> <br><br><div class="gmail_quote">On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang <span dir="ltr"><<a href="mailto:yj3@duke.edu">yj3@duke.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;">
<div bgcolor="#ffffff">
<div><font face="Arial">Dear All,</font></div>
<div><font face="Arial"></font> </div>
<div><font face="Arial">I have two questions about
LDDMM:</font></div>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">1. if I have a template image and a subject image and
I want to register these two by LDDMM eventually, 1). should I use LDDMM to
register these two directly or 2). should I use AIR linear to affine transform
them first, and then LDDMM the updated subject image? In the 2<sup>nd</sup>
case, I need to reorient tensors twice, once by the AIR transformation matrix
and once by the LDDMM transformation matrix, right?</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">I am asking this question because for some other
registration software I have used, it seems the elastic transformation works
better after affine registering the images first.</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">Or maybe LDDMM covers rigid and affine transformation
well already so we can do #1?</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">2. How does the nonlinear AIR compensate/compare with
LDDMM? Can the nonlinear AIR transformation be applied to reorient
tensors?</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">Thank you very much!</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;"> </span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">Best,</span></p>
<p style="margin: 0in 0in 0pt;"><span style="font-family: Arial;">Yi</span></p></div>
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