<div>sorry about that. the zip and unzip files are executable and gmail doesn't allow me send it, for security reason</div>
<div>Siewmin<br><br></div>
<div class="gmail_quote">On Wed, Jul 15, 2009 at 10:36 AM, jinsong tang <span dir="ltr"><<a href="mailto:tangjinsonghn@yahoo.com.cn">tangjinsonghn@yahoo.com.cn</a>></span> wrote:<br>
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<div>I will try it again. The internet explorer cannot display the webpage in the office. I will try it at home.</div>
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<div>Thanks,</div>
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<div>Jinsong<font face="Tahoma" size="2">
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<b><span style="FONT-WEIGHT: bold">发件人：</span></b> Siewmin Gan <<a href="mailto:siewmin.gan@gmail.com" target="_blank">siewmin.gan@gmail.com</a>><br><b><span style="FONT-WEIGHT: bold">收件人：</span></b> "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a>><br>
</div><b><span style="FONT-WEIGHT: bold">已发送：</span></b> 2009/7/15(周三), 下午10:07:32<br><b><span style="FONT-WEIGHT: bold">主题：</span></b> [Mristudio-users] Re: 回复： Re： LDDMM questions<br></font><br></div>
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<div>Hi Jinsong, click on the link I sent you. I just downloaded it and it's fine. </div>
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<div>Siewmin<br><br></div>
<div class="gmail_quote">On Wed, Jul 15, 2009 at 9:32 AM, jinsong tang <span dir="ltr"><<a href="mailto:tangjinsonghn@yahoo.com.cn" target="_blank" rel="nofollow">tangjinsonghn@yahoo.com.cn</a>></span> wrote:<br>
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<div>Dear Siewmin and venkateswaran,</div>
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<div>Thank you for your kindly help. But I cannot download the attachments. Would you please sent it again.</div>
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<div>Best,</div>
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<div>Jinsong<br> <br></div>
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<b><span style="FONT-WEIGHT: bold">发件人：</span></b> Siewmin Gan <<a href="mailto:siewmin.gan@gmail.com" target="_blank" rel="nofollow">siewmin.gan@gmail.com</a>><br><b><span style="FONT-WEIGHT: bold">收件人：</span></b> "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org" target="_blank" rel="nofollow">mristudio-users@mristudio.org</a>><br>
<b><span style="FONT-WEIGHT: bold">已发送：</span></b> 2009/7/14(周二), 下午10:35:12<br><b><span style="FONT-WEIGHT: bold">主题：</span></b> Re: [Mristudio-users] Re： LDDMM questions<br></font>
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<div><br>Hi, This is from Xin. It works.<br> <a href="https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ" target="_blank" rel="nofollow">https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ</a>.<br><br>Siewmin<br>
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<div class="gmail_quote">On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang <span dir="ltr"><<a href="mailto:tangjinsonghn@yahoo.com.cn" target="_blank" rel="nofollow">tangjinsonghn@yahoo.com.cn</a>></span> wrote:<br>
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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 lang="EN-US" style="FONT-SIZE: 11pt"><font face="Times New Roman">Jinsong </font></span><font face="Tahoma" size="2">
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<b><span style="FONT-WEIGHT: bold">发件人：</span></b> Xin Li <<a href="mailto:xli16@jhmi.edu" target="_blank" rel="nofollow">xli16@jhmi.edu</a>><br><b><span style="FONT-WEIGHT: bold">收件人：</span></b> Yi Jiang <<a href="mailto:yj3@duke.edu" target="_blank" rel="nofollow">yj3@duke.edu</a>><br>
<b><span style="FONT-WEIGHT: bold">抄送：</span></b> "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org" target="_blank" rel="nofollow">mristudio-users@mristudio.org</a>><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>
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<div><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" target="_blank" rel="nofollow">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" target="_blank" rel="nofollow">yj3@duke.edu</a>>, "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org" target="_blank" rel="nofollow">mristudio-users@mristudio.org</a>>, Xin Li <<a href="mailto:xli16@jhmi.edu" target="_blank" rel="nofollow">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" target="_blank" rel="nofollow">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" target="_blank" rel="nofollow">Mristudio-users@mristudio.org</a><br>> > <br>> > Unsubscribe, send a blank email to:<br>> > <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank" rel="nofollow">Mristudio-users-unsubscribe@mristudio.org</a><br>
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