My first answer was a bit quick as I had to go give a talk, and I had
a feeling there'd be some follow up. Anyway, you can use the
Deformations utility (via the Batch system, looming in the SPM
Utilities options) to set up the following job to generate an inverse
deformation field.
Composition
. Inverse
. . Composition
. . . Imported _sn.mat
. . . . Parameter File [Your sn.mat file]
. . . . Voxel sizes [NaN NaN NaN]
. . . . Bounding box [NaN NaN NaN; NaN NaN NaN]
. . Image to base inverse on [Your subject's image]
Save as [some file name]
Apply to [nothing needed]
Output destination [up to you]
Interpolation [not needed]
This will generate a y_*.nii image file that has the same first three
dimensions as your subject's image. You can then read off where voxel
i,j,k is mapped to in MNI space by:
Nii = nifti('y_blah.nii');
Y = Nii.dat;
[Y(i,j,k,1,1), Y(i,j,k,1,2), Y(i,j,k,1,3)]
Best regards,
-John
On 25 April 2012 11:54, Zhijiang Wang <[log in to unmask]> wrote:
> Dear John,
>
> Greath thanks for your so valuable information.
>
> But, would you please say it more in detail?
>
> Thanks millions!
>
>
> Best wishes,
>
> Ross Wang
>
> --------------------------------------------
>
> PhD Candidate
>
> Room 407, East Segment, Material Science Building,
>
> The International WIC Institute,
>
> Brain Informatics,
>
> College of Computer Science and Technology,
>
> Beijing University of Technology,
>
> Beijing, China.
>
>
> δΊ 2012-4-25 18:25, John Ashburner ει:
>
> If the transform is nonlinear, then the Affine part will not give you
> the exact location. To map a point in native space to some location
> in MNI space, you'll need the inverse of the mapping from MNI space to
> native space (which is the one used for generating the normalised
> images). You can write out the inverse of the deformation via the
> Deformations Utility, and simply read off the appropriate values from
> the Nx x Ny x Nz x 1 x 3 volume.
>
> Best regards,
> -John
>
> 2012/4/25 Zhijiang Wang <[log in to unmask]>:
>
> Dear all SPMers,
>
> We all know individual images can be normalized to MNI template.
>
> But, there is a question.
> I have a physical coordinate (x1,y1,z1) mm for a voxel, so what's its MNI
> coordinate when its belonged individual image is normalized to MNI space?
>
> I found there is a variable "Affine" in "*seg_sn.mat",
> is it right to do (x1, y1, z1, 1) * Affine ?
>
> Thanks!
> --
>
> Best wishes,
>
> Ross Wang
>
> --------------------------------------------
>
> PhD Candidate
>
> Room 407, East Segment, Material Science Building,
>
> The International WIC Institute,
>
> Brain Informatics,
>
> College of Computer Science and Technology,
>
> Beijing University of Technology,
>
> Beijing, China.
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