Get transformations of motion-corrected slices

The commands reconstruct, svr, and register allow us to save the motion-corrected slices to a folder by setting parameter --output-slices as follows

nesvor reconstruct \
    ...... \
    --output-slices folder-to-save-slices \
    ......

The slices and the corresponding masks would be saved to separate .nii files in the folder.

$ ls folder-to-save-slices -rt | head
0.nii.gz
mask_0.nii.gz
1.nii.gz
mask_1.nii.gz
2.nii.gz
mask_2.nii.gz
3.nii.gz
mask_3.nii.gz
4.nii.gz
mask_4.nii.gz

The transformation of each slice after motion correction can be obtained from the affine matrix in the .nii file.

>>> import nibabel as nib
>>> nib_image = nib.load('folder-to-save-slices/0.nii.gz')
>>> nib_image.affine
array([[ 1.08141804e+00, -7.78946728e-02, -2.63444871e-01, -1.09909004e+02],
   [-9.95342284e-02,  4.51498836e-01, -1.81252944e+00, -3.23390656e+01],
   [ 1.30065709e-01,  9.93161798e-01,  8.03327262e-01, -1.97971268e+02],
   [ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00, 1.00000000e+00]])