[Mristudio-users] LDDMM questions
Xin Li
xli16 at jhmi.edu
Tue Jul 14 10:10:47 EDT 2009
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
> >
> > _______________________________________________
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> > Mristudio-users at mristudio.org
> >
> > Unsubscribe, send a blank email to:
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> >
> >
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