[Mristudio-users] how to save the transformation matrix from a landmarker based transformation

[Andreia Faria]

Hi Yi,

1. Your procedure to save the matrix is correct. The file (.dat) is small because it is just a 3x4 matrix.

2. In the current Landmarker version you can combine LDDMM and .air matrix but not .dat matrix (Xin, please correct me if I am wrong). But you can apply the .dat matrix you saved using the 'load transformation matrix' button, choosing the option 'translation, affine or rigid.

3. Yes, the landmarks are not used, the linear transformation (in the subject window) and LDDMM are based on the image intensity.

Please let me know if it is not clear.

Best regards,

Andreia.

 

----- Original Message -----
From: susumu mori <susumu at mri.jhu.edu>
Date: Tuesday, August 4, 2009 9:59 pm
Subject: Re: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation
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>, ANDREIA FARIA <afaria1 at jhmi.edu>


> Hi Yi,
>  
>  I believe you can save the matrix. Xin should know how to do it.
>  As for the matrix combination, I remember that we discussed about exactly
>  the same topic in my lab. I thought that answer was Yes, but don't exactly
>  remember how to do it. Andreia and Xin, do you know how to do it?
>  
>  On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang <yj3 at duke.edu> wrote:
>  
>  >  Dear All,
>  >
>  > I have tried to look through the online manual, but could not find 
> the
>  > answer.
>  >
>  > I tried to use the landmark based transformation (translation) from 
> the
>  > main menu of the Landmarker window. The result is pretty good. 
> However, I do
>  > not know how to save the transformation matrix. I tried to click 
> the "save
>  > transformation matrix" button in the subject window. It seems two 
> files was
>  > saved (.hdr? and .dat), but the file sizes were very small.
>  >
>  > I also want to combine the transformation matrix from the landmark 
> based
>  > translation with a AIR linear rigid, a AIR linear affine 
> transformation, and
>  > a LDDMM matrix. Can I do that? I do not know if the transformation 
> matrix
>  > from landmark based translation is a AIR format, or LDDMM raw 
> format, or a
>  > LDDMM vtk format, which was asked in the combine matrix window.
>  >
>  > The last question may be stupid: if there are defined landmarks in 
> the
>  > memory, when I click on AIR linear or multichannel LDDMM (not from 
> the main
>  > menu, but the buttons in the subject window), those landmarks were 
> not used
>  > in transformation, right?
>  >
>  > Thank you very much!
>  >
>  > Best,
>  > Yi
>  >
>  >
>  >
>  >
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