How to convert 3D numpy array to nifti image in nibabel?

Question

From this question How to convert Nifti file to Numpy array? , I created a 3D numpy array of nifti image. I made some modifications to this array, like I changed depth of the array by adding padding of zeroes. Now I want to convert this array back to nifti image, how can I do that?

I tried:

imga = Image.fromarray(img, 'RGB')
imga.save("modified/volume-20.nii")

but it doesn't identify nii extension. I also tried:

nib.save(img,'modified/volume-20.nii')

this is also not working, because img must be nibabel.nifti1.Nifti1Image if I want to use nib.save feature. In both of the examples above img is a 3D numpy array.

Answer 1

Assuming that you a numpy array and you want to use nib.save function, you need to first get the affine transformation.

Example:

# define the path to the data
func_filename = os.path.join(data_path, 'task-rest_bold.nii.gz')

# load the data
func = nib.load(func_filename)

# do computations that lead to a 3D numpy array called "output"
# bla bla bla
# output = np.array(....)

# to save this 3D (ndarry) numpy use this
ni_img = nib.Nifti1Image(output, func.affine)

nib.save(ni_img, 'output.nii.gz')

Now you will be able to overlay the output.nii.gz onto the task-rest_bold.nii.gz