to_nibabel() produces wrong transforms

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.

[cookpa]

ITK uses LPS coordinates and NIFTI RAS. This is handled in the I/O, when ITK converts qform into a direction cosine matrix or writes a cosine matrix back out as a qform.

https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx

See methods SetImageIOOrientationFromNIfTI and SetNIfTIOrientationFromImageIO.

According to this page

https://nipy.org/nibabel/coordinate_systems.html

NiBabel always wants RAS coordinates so I think it should be safe to apply the same conversion steps in the to_nibabel and from_nibabel functions.

Some more on this:

https://itk.org/Doxygen/html/classitk_1_1ImageBase.html#a23ebc76de3b60bb1eeabf66cd4dabc48

This is the base ITK class that handles voxel to physical space conversion. It references this page

https://itk.org/Wiki/Proposals:Orientation#Some_notes_on_the_DICOM_convention_and_current_ITK_usage

[stnava]

consider https://github.com/ANTsX/ANTsPy/commit/1e73b82fd23a9c39d80918739991da41f290cd9d