get_tumor_volume.py

"""Example of how to get volume of tumor from mask NIfTI."""

import nibabel as nb

# The mask nifti image has contains a 1 in voxels that contain
# tumor and a 0 in voxels that do not contain tumor.
mask_filepath = "/path/to/tumor_mask.nii.gz"
img = nb.load(mask_filepath)
data = img.get_fdata()

# The tumor volume is the sum of all values in the mask array,
# because tumor voxels have a value 1 and non-tumor voxels have
# value 0.
tumor_volume = data.sum()

# Tumor volume can also be found by calculating the number of
# voxels that contain the label value.
# If the tumor label is 1:
tumor_volume = (data == 1).sum()

# If the tumor label is 20:
tumor_volume = (data == 20).sum()