pythonimageniftinibabel

How can I obtain 2D slices from a 3D NIfti volume?

I'm currently using the following code to convert DCM slices into NIfti images:

import dicom2nifti
import os

dicom2nifti.convert_directory("input_path", "output_path", compression=True, reorient=True)

This code will generate a 3D NIfti volume.

How can I obtain all the slices from this 3D NIfti volume?

Solution

  • Use the package nibabel. A simple working example opens your NIfTI file as a numpy 3D matrix, which can use for your processing needs:

    import nibabel as nib
import numpy as np
import matplotlib.plot as plt


my_nifti = nib.load('YOURNIFTIFILE.nii').get_fdata()

# get the shape of your NIfTI
my_nifti.shape

# access it as 3D numpy array
nifti_slice = my_nifti[:,:,59]

# display the slice
plt.imshow(nifti_slice)
plt.show()