Reorder Nifti file axes

Question

I have some 3D nifti files of dimension (50, 100, 50). I would like to flip the the y and z axes so that the dimension will be (50, 50, 100). What is the best way to go about doing this and how would I modify the associated affine with the file?

Currently, I am making the nifti file into a numpy array and swapping the axes like so

array = np.asanyarray(niiobj.dataobj)
img_after_resample_swapped_array = np.swapaxes(img_after_reample_array, 1, 2)

I'm confused as to the next step. I know I can use the function nib.Nifti1Image to make the numpy array into a nifti object, but how would I have to modify the affine to account for the axis change?

Thank you for any help.

@BelalHomaidan Unfortunately, don't have the liberty to do that. Is there anything I can answer for you? — intl
no thanks, I just wanted to see a sample to test with it, otherwise I can't help much. — Bilal

Dave Chen Dave Chen · Accepted Answer · 2020-06-25T14:14:09

If you use SimpleITK, there is a PermuteAxes function that can saw the Y and Z axes. And it will properly preserve the transformation of the image.

Here's an example of how to do it:

import SimpleITK as sitk

img = sitk.ReadImage("tetra.nii.gz")
print (img.GetDirection())

img2 = sitk.PermuteAxes(img, [0,2,1])
print (img2.GetDirection())

sitk.WriteImage(img2, "permuted.nii.gz")

And here's the 3x3 direction matrix output:

(1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
(1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0)

The input image has the identity matrix for the direction, and for the permuted matrix the Y and Z rows are swapped.

Here is the documentation for the PermuteAxesImageFilter and the PermuteAxes function:

https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1PermuteAxesImageFilter.html https://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#a892cc754413ba3b60c731aac05dddc65

Reorder Nifti file axes

1 Answers