[Mristudio-users] LDDMM questions

Tue Jul 14 10:44:49 EDT 2009

Hi Jinsong,

I am attaching the executable AIR files which i obtained form Xin Li longtime ago. 

venkateswaran

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of jinsong tang
Sent: Tue 7/14/2009 10:30 AM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: [Mristudio-users] Re: LDDMM questions

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 
________________________________

???: Xin Li <xli16 at jhmi.edu>
???: Yi Jiang <yj3 at duke.edu>
??: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>
???: 2009/7/14(??), ??10:10:47
??: 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
>  >
>  > 
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