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<DIV>Hello, Dear all,</DIV>
<DIV><BR>I am trying to use Landmarker with the AIR functions. I am using a 32bit windows XP. According to the instruction, I need to compile the AIR <BR>functions myself. However, I was not able to build those executable files. Are there anyone has those .exe files,and could share them with us.<BR><BR>Best regars,<BR><BR><SPAN style="FONT-SIZE: 11pt" lang=EN-US><FONT face="Times New Roman">Jinsong </FONT></SPAN><FONT size=2 face=Tahoma>
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<B><SPAN style="FONT-WEIGHT: bold">发件人：</SPAN></B> Xin Li <xli16@jhmi.edu><BR><B><SPAN style="FONT-WEIGHT: bold">收件人：</SPAN></B> Yi Jiang <yj3@duke.edu><BR><B><SPAN style="FONT-WEIGHT: bold">抄送：</SPAN></B> "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users@mristudio.org><BR><B><SPAN style="FONT-WEIGHT: bold">已发送：</SPAN></B> 2009/7/14(周二), 下午10:10:47<BR><B><SPAN style="FONT-WEIGHT: bold">主题：</SPAN></B> Re: [Mristudio-users] LDDMM questions<BR></FONT><BR>Yi,<BR><BR>Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM.<BR><BR><BR>Xin<BR><BR><BR><BR>----- Original Message -----<BR>From: susumu mori <<A href="mailto:susumu@mri.jhu.edu" ymailto="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</A>><BR>Date: Tuesday, July 14, 2009 2:21 am<BR>Subject: Re: [Mristudio-users] LDDMM questions<BR>To:
Yi Jiang <<A href="mailto:yj3@duke.edu" ymailto="mailto:yj3@duke.edu">yj3@duke.edu</A>>, "DTI Studio, ROI Editor, Landmarker Questions/Support" <<A href="mailto:mristudio-users@mristudio.org" ymailto="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</A>>, Xin Li <<A href="mailto:xli16@jhmi.edu" ymailto="mailto:xli16@jhmi.edu">xli16@jhmi.edu</A>><BR><BR><BR>> Hi Yi,<BR>> <BR>> 1) I recommend you to do AIR first from two reasons. First one is a<BR>> practical reason. Our LDDMM requires that the matrix and pixel sizes <BR>> of the<BR>> two images are identical. After AIR, even if the input images have different<BR>> dimensions, the output will have the same dimension. This is handy. Second<BR>> one is more important. Let me use fitting of a X-Y plot for analogy. <BR>> When<BR>> you use linear fitting, no matter which software you use, the results
<BR>> are<BR>> almost identical. This is because the energy landscape of linear fitting<BR>> usually has a very simple "one-valley" shape, meaning the results always<BR>> converge at the same solution. On the other hand, when you are using<BR>> non-linear fitting, you are required to provide initial values, which <BR>> are<BR>> close to the real solution. Usually you first do linear solution and <BR>> then<BR>> use the result as the initial value for the subsequent non-linear fitting.<BR>> This is because the energy landscape of non-linear fitting has a complicated<BR>> "multi-valley" shape. If your initial values are far away from the real<BR>> solution, the fitting is trapped by a local minima.<BR>> <BR>> Non-linear warping is very similar. You are required to bring two <BR>> brains as<BR>> close as possible before you start
non-linear warping.<BR>> <BR>> When you adopt AIR+LDDMM, you have to transform the image twice, including<BR>> tensor reorientation. Landmarker can combine transformation matrices <BR>> so that<BR>> 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<BR>> with it. Yes, it should do tensor reorientation if you apply the<BR>> transformation to a tensor file.<BR>> <BR>> <BR>> <BR>> On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang <<A href="mailto:yj3@duke.edu" ymailto="mailto:yj3@duke.edu">yj3@duke.edu</A>> wrote:<BR>> <BR>> > Dear All,<BR>> ><BR>> > I have two questions about LDDMM:<BR>> ><BR>>
><BR>> ><BR>> > 1. if I have a template image and a subject image and I want to register<BR>> > these two by LDDMM eventually, 1). should I use LDDMM to register <BR>> these two<BR>> > directly or 2). should I use AIR linear to affine transform them <BR>> first, and<BR>> > then LDDMM the updated subject image? In the 2nd case, I need to reorient<BR>> > tensors twice, once by the AIR transformation matrix and once by <BR>> the LDDMM<BR>> > transformation matrix, right?<BR>> ><BR>> ><BR>> ><BR>> > I am asking this question because for some other registration <BR>> software I<BR>> > have used, it seems the elastic transformation works better after affine<BR>> > registering the images first.<BR>> ><BR>> ><BR>> ><BR>> > Or maybe LDDMM covers
rigid and affine transformation well already <BR>> so we<BR>> > can do #1?<BR>> ><BR>> ><BR>> ><BR>> > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the<BR>> > nonlinear AIR transformation be applied to reorient tensors?<BR>> ><BR>> ><BR>> ><BR>> > Thank you very much!<BR>> ><BR>> ><BR>> ><BR>> > Best,<BR>> ><BR>> > Yi<BR>> ><BR>> > _______________________________________________<BR>> > Mristudio-users mailing list<BR>> > <A href="mailto:Mristudio-users@mristudio.org" ymailto="mailto:Mristudio-users@mristudio.org">Mristudio-users@mristudio.org</A><BR>> > <BR>> > Unsubscribe, send a blank email to:<BR>> > <A
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