Compute volume of non-zero voxels in a nifti image.

nifti_nonzero_volume.py

"""Compute volume of non-zero voxels in a nifti image."""

import numpy as np
import nibabel as nb

INPUT = "/path/to/image.nii.gz"

# Load data
nii = nb.load(INPUT)
img = nii.get_fdata()

# Get voxel dimensions
voxel_dims = (nii.header["pixdim"])[1:4]
print("Voxel dimensions:")
print("  x = {} mm".format(voxel_dims[0]))
print("  y = {} mm".format(voxel_dims[1]))
print("  z = {} mm".format(voxel_dims[2]))

# Compute volume
nonzero_voxel_count = np.sum(img != 0)
voxel_volume = np.prod(voxel_dims)
nonzero_voxel_volume = nonzero_voxel_count * voxel_volume

print("Number of non-zero voxels = {}".format(nonzero_voxel_count))
print("Volume of non-zero voxels = {} mm^3".format(nonzero_voxel_volume))