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

[Xin Li]

Yi,

You can take a look at the .dat file by opening it using notepad. Just as Andreia said, it is a 3x4 matrix.

As Andreia said, the "combine matrix" function combines LDDMM map and .air file but not .dat matrix.


Xin




----- Original Message -----
From: Andreia Faria <afaria1 at jhmi.edu>
Date: Tuesday, August 4, 2009 11:43 pm
Subject: Re: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation
To: susumu mori <susumu at mri.jhu.edu>
Cc: 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. 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
>  >  >
>  >  >
>  >  >
>  >  >
>  >  > _______________________________________________
>  >  > Mristudio-users mailing list
>  >  > Mristudio-users at mristudio.org
>  >  > 
>  >  > Unsubscribe, send a blank email to:
>  >  > Mristudio-users-unsubscribe at mristudio.org
>  >  >
>  >  >