Registration an MRI image to another coordinate system

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1

I have a NIFTI image that I want to register to another coordinate system (I am not sure if registration
is the correct technical term here) using a given affine transformation matrix.

The affine matrix of NIFTI image is

array([[ -1.,  -0.,  -0.,   0.],
       [ -0.,  -1.,  -0., 239.],
       [  0.,   0.,   1.,   0.],
       [  0.,   0.,   0.,   1.]])

And the target affine matrix is:

array([[ -1.,  -0.,  -0.,   0.],
       [ -0.,   1.,  -0., 239.],
       [  0.,   0.,   1.,   0.],
       [  0.,   0.,   0.,   1.]])

The difference between the two matrices is the (2,2) element.

A snippet of a slice in the z-direction for the MRI image is:

image
image928×848 41 KB

And my code to do the registration is:

  nifti = nilearn.image.resample_img(nifti, target_affine=target_affine, target_shape=nifti.shape,
                             interpolation='nearest')

However, the resulting NIFTI image is all zeros. Based on my understanding, the new NIFTI image should be flipped around the second dimension but I think my understanding is off.

  1. What causes the registered NIFTI image to be zero?
  2. How to fix this problem?
2

Nilearn resampling fails for such transformation. I am not sure what the reason is. I had to use AFNI program 3dresample.

3

Thank you for sharing. How did you use 3dresample in your case?