If you copy and paste this into MATLAB, I think it might do what you want.
It hasn't been extensively tested though, and is not the approved way of
spatially normalising in SPM.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
P = spm_select(2,'image','Select images.'); % Select the files to align.
VG = spm_vol(P(1,:)); % Get old-style handles for images
VF = spm_vol(P(2,:));
eoptions = struct('cost_fun','nmi',...
'sep', [4 2],...
'tol', [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01
0.01 0.001 0.001 0.001],...
'fwhm', [7 7],...
'params', [0 0 0 0 0 0]); % Settings for rigid alignment
params = spm_coreg(VG,VF,eoptions); % Run a rigid alignment
sep = 2; % Just work at the finer scale
eoptions.params = [params 1 1 1 0 0 0]; % Add the extra parameters: 3
zooms and 3 shears
params = spm_coreg(VG,VF,eoptions); % Run the full affine
alignment
R = inv(spm_matrix(params)) % Generate the matrix to
premultiply the moved image by
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Best regards,
-John
On 27 October 2017 at 02:19, Chao Suo <[log in to unmask]> wrote:
> Thanks for your explanation, John.
> Firstly, I agree with you that the coreg in SPM (6dof) is a bit rough. It
> is one of the steps to find a TMS stimulating point from MNI space to
> individual space.
> That is actually one of the reason we use flirt, which did 12 dof affine
> transform. So, svd(Xfm(1:3,1:3)) showed a scaling factor.
>
> I think there is a good point in the part your cited in fsl website. It
> seems the centre of mass of the volume was used as the centre. So I might
> need to find the additional transform matrix to make the shift, which could
> be the last puzzle.
>
> At the meantime, could you suggest how to do a 12dof affine "coreg" in
> spm? I'm thinking to re-do this step on SPM, if possible.
>
> Thanks,
>
> Chao
>
>
> On 26 October 2017 at 21:03, John Ashburner <[log in to unmask]> wrote:
>
>> My first point is that you won't get very good alignment if you just use
>> Coreg to get to MNI space, as it only does rigid alignment and doesn't
>> handle the different sized and differently shaped brains.
>>
>> I'm not quite sure what Mark J and the guys in FMRIB use for encoding
>> their transforms, so I can't say much here. What I do notice though is
>> that the Xfm does not encode a rigid body transform. Ignoring the
>> translations, the transform is decomposed into a rigid body rotation, some
>> isotropic zooms and another rigid body transform, which can be computed via
>> SVD. The zooms are:
>>
>> > svd(Xfm(1:3,1:3))
>>
>> ans =
>>
>> 1.0730
>> 1.0291
>> 0.9739
>>
>> This suggests that the matrix does not encode a rigid transform. If you
>> called FLIRT with 6 dof, then I really have no idea what the matrix encodes.
>>
>> I seems that FLIRT ignores things like the origin in the images, which
>> may account for the very different translations. According to
>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ :
>>
>> The FSL convention for transformation matrices uses an implicit centre of
>> transformation - that is, a point that will be unmoved by that
>> transformation, which is an arbitrary choice in general. This arbitrary
>> centre of the transformation for FSL is at the mm origin (0,0,0) which is
>> at the centre of the corner voxel of the image.
>>
>> When using the transformation parameters from FLIRT, there is an
>> additional complication in that the parameters are calculated in a way that
>> uses a different centre convention: the centre of mass of the volume. The
>> effect of this is that each of the three matrices above end up with an
>> adjustment in the fourth column (top three elements only) that represents a
>> shift between the corner origin and the centre of mass, while the rest of
>> the matrix (first three columns) is unaffected. Once that is done the
>> matrices are multiplied together, as indicated above, and you get your
>> final matrix.
>>
>>
>> Best regards,
>> -John
>>
>>
>>
>>
>>
>>
>>
>> On 26 October 2017 at 01:37, Chao Suo <0000171bf1c6344d-dmarc-reques
>> [log in to unmask]> wrote:
>>
>>> Dear SPM/FSL users,
>>>
>>> I have a question about the inconsistent transform matrix during linear
>>> corregister using SPM and FSL.
>>> For example, I have one image (Qform is A) coregistered to an MNI space
>>> using a standard MNI template using "Coregister: Estimate" function.
>>> The new image’s Qform is A’. The transform matrix (TE_spm) my understand
>>> is equal to A’*inv(A).
>>> I can use this matrix (TE_spm) to reorient the Image to the MNI space
>>> using the function Batch-> SPM-> Util -> reorient images
>>>
>>> When I use “flirt” in FSL toolbox, the output image is also aligned to
>>> MNI space. However, the output matrix (xfm) is way different with the
>>> TE_spm I generate.
>>> And it doesn’t work with the “reorient images” function in SPM. Further,
>>> as the function “flirt” will reslice (resample) the image by default, the
>>> Qform of A’ generated by flirt is re-set to the centre of the image matrix.
>>>
>>> My question is how to apply the xfm to reorient the input image A to MNI
>>> space? Also, is it possible to convert the xfm in FSL to the matrix that
>>> can be used in reorient image function?
>>> I have attached the matrix below, for more information.
>>>
>>>
>>> A=[ -0.9992 -0.0244 0.0314 97.7589
>>> -0.0244 0.9997 0.0008 -133.7938
>>> 0.0314 -0.0000 0.9995 -149.3965
>>> 0 0 0 1.0000]
>>>
>>> A’=[ -0.9995 -0.0092 0.0317 93.3496
>>> 0.0067 0.8845 0.4665 -176.7222
>>> 0.0323 -0.4665 0.8839 -58.0182
>>> 0 0 0 1.0000]
>>>
>>> TE_spm= [ 0.9999 0.0152 0.0003 -2.3183
>>> -0.0136 0.8844 0.4665 12.6318
>>> 0.0069 -0.4665 0.8845 11.0441
>>> 0 0 0 1.0000 ]
>>>
>>> Xfm = [1.015110314 0.001403876797 -0.03273563415 -2.95397524
>>> -0.0340642576 0.881267329 0.4458567806 -42.9856035
>>> 0.03133599993 -0.4915636726 0.9529941246 7.78935539
>>> 0 0 0 1 ]
>>>
>>>
>>> Thanks,
>>>
>>> Chao
>>
>>
>>
>>
>> --
>> Prof John Ashburner
>> Professor of Imaging Science
>> UCL Institute of Neurology
>> Queen Square
>> Wellcome Trust Centre for Neuroimaging
>> University College London
>> <https://maps.google.com/?q=London+12+Queen+Square,+London,+WC1N+3BG&entry=gmail&source=g>
>> 12 Queen Square, London, WC1N 3BG
>> <https://maps.google.com/?q=London+12+Queen+Square,+London,+WC1N+3BG&entry=gmail&source=g>
>> E: [log in to unmask] T: +44 (0)20 3448 4365 <+44%2020%203448%204365>
>> http://www.fil.ion.ucl.ac.uk/
>>
>
>
--
Prof John Ashburner
Professor of Imaging Science
UCL Institute of Neurology
Queen Square
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square, London, WC1N 3BG
E: [log in to unmask] T: +44 (0)20 3448 4365
http://www.fil.ion.ucl.ac.uk/
