The matrix that is shown is the voxel-to-voxel affine transform. Even
though the registration may be rigid, this transform is often not,
simply because non-isotropic voxels or different voxel sizes between the
images.
In order to figure out what the rigid-body parameters were, you would
need to have known what was returned by spm_get_space before you ran the
coregistration.
The matrix that is displayed is from:
Q = inv(VF.mat\spm_matrix(x(:)')*VG.mat);
Where VF.mat and VG.mat are the matrices that represent the original
"voxel-to-world" mappings of the images, and x are the parameters.
After running spm_coreg, the orientation of the source image (and any
"other" images) is updated by modifying its header. This changes the
voxel-to-world mapping, so that SPM considers the images to be in
alignment (try the images with the Check Reg button).
The columns displayed are: x translation, y translation, z translation,
rotation about x axis, rotation about y axis, rotation about z axis and
finally, the value of the objective function.
Best regards,
-John
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Helen
Sent: Wednesday, January 24, 2007 5:15 PM
To: [log in to unmask]
Subject: [SPM] spm_coreg
Dear SPM,
I am a new user in SPM for spatial normalization. Currently I am
trying
to find the six parameters for the rigid body transformation. There are
two ways I had explored, spm_coreg and coregister in GUI. The result
from spm_coreg and the one from the unix window by running GUI are the
same. However in GUI, the output dindow print out the transformation
matrix. How Xo, Yo, Zo transformed to X1, Y1, Z1. So I use spm_imatrix
to convert the matrix into parameters. But I get 12 parameters for
affine
transformation. I wonder if the GUI is using affine tranformation or
rigid body transformation. I wonder if the result is due to the fact
that
spm_imatrix is under the affine model. And I would like to know if
there
are any other spm matlab command that can transform the matrix of
coregister from GUI output window to six parameters of rigid body
transformation?
Another question is about the output of spm_coreg. Is there any way
to
find out which value represents x-shift, y-shift, z-shift, pitch, row
and
yaw? And what unit they are in (mm, voxel or other unit for shifts and
degree or radian for roation)?
Thank you so much.
Helen
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