How to check NIFTI image is in the right orientation/position with Python

Question

I am new here. Currently learning about medical imaging data on Python and wondering if it is possible to identify the NIFti image is in the right orientation and how to do the transformation. I looked up online and found some algorithm to 'rotate' the imaging data (in JPG format mainly) via affine transformation by certain angle but there's no documentation on how to do it on nifti image instead and save it as a new nifti image via nibabel.

To illustrate what I meant. I would like to learn how to change this image 1 into this image

avivd avivd · Accepted Answer · 2021-02-25T16:16:26

for your first question, you should check the orientation of your NIfTI image and then rotate it in the direction that you want.

for checking orientation we use nibabel aff2axcodes https://nipy.org/nibabel/reference/nibabel.orientations.html#nibabel.orientations.aff2axcodes

for the rotation we will use nibabel.orientations.flip_axis https://nipy.org/nibabel/reference/nibabel.orientations.html#nibabel.orientations.flip_axis

'''

def check_orientation(ct_image, ct_arr):
"""
Check the NIfTI orientation, and flip to  'RPS' if needed.
:param ct_image: NIfTI file
:param ct_arr: array file
:return: array after flipping
"""
x, y, z = nib.aff2axcodes(ct_image.affine)
if x != 'R':
    ct_arr = nib.orientations.flip_axis(ct_arr, axis=0)
if y != 'P':
    ct_arr = nib.orientations.flip_axis(ct_arr, axis=1)
if z != 'S':
    ct_arr = nib.orientations.flip_axis(ct_arr, axis=2)
return ct_arr

'''

Note that in your case you need to flip only the z axis, but try to use the function above and change to your situation in order to check your data.

The last thing is to save the new NIfTI scan (NumPy array) as nii image. In order to do it, use Nifti1Image to create nii object, and then nibabel.save to save it to a file.

'''

    new_nifti = nib.Nifti1Image(***ct_arr***.astype(np.float), nii_original_scan.affine)
    nib.save(new_nifti, f'***path to new scan***.nii.gz')

'''

ct_arr- is your numpy array (make sure is in float type). The second argument is the original NIfTI scan after loading.

in the save function- make sure you add in the file name the suffix .nii or .nii.gz

Hope it's clear :)

How to check NIFTI image is in the right orientation/position with Python

1 Answers