numpynibabelnilearn

Swap axes of a 3D image in nilearn/numpy

I am working with some neuroimaging data and my dimensions for a scan is (100, 150, 100). I am currently working with the nibabel formatted file.

Is there a nice way to swap the axes? For example, I want my image to be (100, 100, 150). I would preferable want this in the nibabel format, but if need be, I can get the image to a numpy ndarray and then do the work there as well. In this case, is there a nice way of doing this in numpy?

Thank you for the help!

Solution

  • If you are using numpy use: 

    import numpy as np

arr = np.swapaxes(arr, 1, 2)

    This will swap axis 1 and 2 (which are 2nd and 3rd dimension with 150 and 100 size respectively).

    Example code: 

    arr = np.zeros((100,150,100))
arr = np.swapaxes(arr, 1, 2)
print(arr.shape)

    output: 

    (100, 100, 150)