Stuck on an issue?

While using transforms on the MNI152 template I noticed that the output of to_nibabel() was flipped along the vertical plane. While investigating the issue, I noticed, that this is caused by a wrong extraction of the q-form parameters (direction, origin) from ITK.

    ants_mni = ants.image_read('./MNI152.nii.gz')
    nii_mni = nib.load('./MNI152.nii.gz')

    ants_mni = ants_mni.to_nibabel()

    print(ants_mni.get_qform())
    print(nii_mni.get_qform())

results in:

[[  2.   0.   0. -90.]
 [  0.  -2.   0. 126.]
 [  0.   0.   2. -72.]
 [  0.   0.   0.   1.]]
[[  -2.    0.    0.   90.]
 [   0.    2.    0. -126.]
 [   0.    0.    2.  -72.]
 [   0.    0.    0.    1.]]

Using the ITK internal functions for exporting to nifti file format, everything works as expected:

    ants_mni = ants.image_read('./MNI152.nii.gz')
    ants.image_write(ants_mni, './ANTS_MNI152.nii.gz')

    ants_nii = nib.load('./ANTS_MNI152.nii.gz')
    nii_mni = nib.load('./MNI152.nii.gz')

    print(ants_nii.get_qform())
    print(nii_mni.get_qform())

[[  -2.    0.    0.   90.]
 [   0.    2.    0. -126.]
 [   0.    0.    2.  -72.]
 [   0.    0.    0.    1.]]
[[  -2.    0.    0.   90.]
 [   0.    2.    0. -126.]
 [   0.    0.    2.  -72.]
 [   0.    0.    0.    1.]]

Although this could be used a a quick work around, like in the from_nibabel() implementation, a Nifti/Nibabel class export, should no rely on using hard-drive exports, when all the necessary information could be retrieved while loading the file initially.