How to convert Nifti file to Numpy array?

Question

I have 3D array in Nifti file (.ii.gz) and I want to save it as a 3D numpy array. I used Nibabel to convert Numpy to Nifti1. Can I do the opposite?

piRSquared · Accepted Answer · 2017-06-07T21:26:18.383

22

import numpy as np
import nibabel as nib

img = nib.load(example_filename)

a = np.array(img.dataobj)

edited Jun 07 '17 at 21:26

answered Jun 07 '17 at 20:51

piRSquared

How do I convert img to numpy array? np.array(img)? – Char Jun 07 '17 at 21:06
4

How to convert back the numpy array to .nii? – Soyol May 20 '18 at 03:18
@Soyol you can post a new question about this. There is a way to do it – seralouk Jun 17 '19 at 17:10

score 8 · Answer 2 · answered Jun 05 '20 at 10:22

8

You can also do this:

import numpy as np
import nibabel as nib

img_nifti = nib.load(filepath)
img = img_nifti.get_data()

answered Jun 05 '20 at 10:22

schrodingercat

4

`get_data()` is now deprecated, now you can use `get_fdata()` instead – Aelius Jun 17 '21 at 13:23

2 Answers2