[Mristudio-users] Re： LDDMM questions

[Siewmin Gan]

Hi, This is from Xin. It works.
 https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ.

Siewmin

On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang
<tangjinsonghn at yahoo.com.cn>wrote:

> Hello, Dear all,
>
> 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
> 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.
>
> Best regars,
>
> Jinsong
> ------------------------------
> *发件人：* Xin Li <xli16 at jhmi.edu>
> *收件人：* Yi Jiang <yj3 at duke.edu>
> *抄送：* "DTI Studio, ROI Editor, Landmarker Questions/Support" <
> mristudio-users at mristudio.org>
> *已发送：* 2009/7/14(周二), 下午10:10:47
> *主题：* Re: [Mristudio-users] LDDMM questions
>
> Yi,
>
> Landmarker can combine AIR matrix and LDDMM matrix. The button for this
> function is right below the button for multichannel remote LDDMM.
>
>
> Xin
>
>
>
> ----- Original Message -----
> From: susumu mori <susumu at mri.jhu.edu>
> Date: Tuesday, July 14, 2009 2:21 am
> Subject: Re: [Mristudio-users] LDDMM questions
> To: Yi Jiang <yj3 at duke.edu>, "DTI Studio, ROI Editor, Landmarker
> Questions/Support" <mristudio-users at mristudio.org>, Xin Li <xli16 at jhmi.edu
> >
>
>
> > Hi Yi,
> >
> >  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.
> >
> >  Non-linear warping is very similar. You are required to bring two
> > brains as
> >  close as possible before you start non-linear warping.
> >
> >  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.
> >
> >  Xin, can we combine AIR matrix and LDDMM matrix?
> >
> >  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.
> >
> >
> >
> >  On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang <yj3 at duke.edu> wrote:
> >
> >  >  Dear All,
> >  >
> >  > I have two questions about LDDMM:
> >  >
> >  >
> >  >
> >  > 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 2nd case, I need to
> reorient
> >  > tensors twice, once by the AIR transformation matrix and once by
> > the LDDMM
> >  > transformation matrix, right?
> >  >
> >  >
> >  >
> >  > 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.
> >  >
> >  >
> >  >
> >  > Or maybe LDDMM covers rigid and affine transformation well already
> > so we
> >  > can do #1?
> >  >
> >  >
> >  >
> >  > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the
> >  > nonlinear AIR transformation be applied to reorient tensors?
> >  >
> >  >
> >  >
> >  > Thank you very much!
> >  >
> >  >
> >  >
> >  > Best,
> >  >
> >  > Yi
> >  >
> >  > _______________________________________________
> >  > Mristudio-users mailing list
> >  > Mristudio-users at mristudio.org
> >  >
> >  > Unsubscribe, send a blank email to:
> >  > Mristudio-users-unsubscribe at mristudio.org
> >  >
> >  >
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
> ------------------------------
> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/be2a5e92/attachment.html