Well, you could get this matrix for both images, an then matrix-divide them I guess?
 
V1=spm_vol('file1.nii')
V2=spm_vol('file2.nii')
 
V2.mat/V1.mat
 
When I remember the math well this matrix should map file1 to file2 in worldspace, if that is what you are after.
 
check 'help mrdivide' and 'help mldivide' to be sure, I just do this math from the head right now.
 
But when you want to map one image to another, why dont you use coregister > estimate in SPM, which is the normal way? You would not have to bother with matrix algebra altogether ...
 
Good luck,
 
Bas
--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
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Van: [log in to unmask] [mailto:[log in to unmask]] Namens Dan Golding
Verzonden: vrijdag 21 mei 2010 15:13
Aan: Neggers, S.F.W.
Onderwerp: Re: [SPM] Finding affine transformation parameters

Thanks, but would you mind explaining this in a bit more detail?

I'm don't quite see the difference in loading an image using spm_vol(spm_select) and using spm_vol('filename.nii') which is how I have been doing it. The .mat field gives information about the individual images, but not about how to transform one image to another which is what I am looking for. Unless I have misunderstood?

If you could please explain to me how I can coregister one nifti image to another, and get the affine transformation matrix describing that transformation, I would greatly appreciate it.

Thanks
Dan

On Fri, May 21, 2010 at 2:54 PM, Neggers, S.F.W. <[log in to unmask]> wrote:
V=spm_vol(spm_select);

V.mat


--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
             Room B.01.1.03
Mail     : Huispost B.01.206, P.O. Box 85500
            3508 GA Utrecht, the Netherlands
Tel       : +31 (0)88 7559609
Fax      : +31 (0)88 7555443
E-mail  : [log in to unmask]
Web    : http://www.neuromri.nl/people/bas-neggers
            http://www.neuralnavigator.com
--------------------------------------------------



> -----Oorspronkelijk bericht-----
> Van: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] Namens Dan Golding
> Verzonden: vrijdag 21 mei 2010 14:43
> Aan: [log in to unmask]
> Onderwerp: [SPM] Finding affine transformation parameters
>
> Hi,
>
> I would like to find the 12 parameters for an affine
> transformation between two nifti images. I have been looking
> into using spm_coreg and spm_matrix but I couldn't quite
> understand how to use them form their help. spm_coreg outputs
> 6 parameters, I'm not sure what these 6 are?
>
> Also is there a function that does the reverse of spm_matrix,
> i.e. one that can take an affine transformation matrix and
> split it into 3 rotations, 3 scalings etc...?
>
> Thanks
> Dan
>

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