Calculate brain parenchymal fraction from a GIFv2 segmentation

bpf.py

#!/usr/bin/env python3.7

"""Calculate brain parenchymal fraction from a GIFv2 segmentation.

Intracranial volume (ICV) is grey-matter + CSF + white-matter.
Brain parenchymal fraction is (grey-matter + white-matter) / ICV.
"""

import os
import subprocess
import sys
import tempfile


def read_next_volume(lines):
    return float(lines.pop(0).split("=")[1].strip())


segmentation = sys.argv[1]
tfh, tf = tempfile.mkstemp(suffix=".nii.gz")

# flatten the segmentation to a single volume
flatten_command = [
    "seg_maths",
    segmentation,
    "-tpmax",
    tf
]
subprocess.run(flatten_command)

# read volume of each label
volumes_command = [
    "seg_stats",
    tf,
    "-vl"
]
output = subprocess.run(volumes_command, capture_output=True, text=True)

# parse output
output_lines = output.stdout.split("\n")
output_lines = output_lines[2:]  # discard header and background
csf = read_next_volume(output_lines)
cgm = read_next_volume(output_lines)
wm = read_next_volume(output_lines)
dgm = read_next_volume(output_lines)
brain_stem = read_next_volume(output_lines)

# do calculations
icv = cgm + dgm + wm + brain_stem + csf
bpf = (cgm + dgm + wm + brain_stem) / icv
print("Brain parenchymal fraction:", bpf)

# clean up
os.unlink(tf)