Sort 4D nifti files to get minimum/maximum intensity volume projections.

sort_4D_nifti.py

"""Example for sorting 4D nifti data."""

import numpy as np
import os
from nibabel import load, save, Nifti1Image
from __future__ import division

nii = load('/path/to/your/4D_nifti_file.nii.gz')
basename = nii.get_filename().split(os.extsep, 1)[0]
niiHeader = nii.header
niiAffine = nii.affine

data = nii.get_data()
data = np.sort(data, axis=3)

# for only saving min and max
data_min = data[:, :, :, 0]
data_max = data[:, :, :, 3]

# save
out = Nifti1Image(data, header=niiHeader, affine=niiAffine)
save(out, basename + '_sorted.nii.gz')

out = Nifti1Image(data_min, header=niiHeader, affine=niiAffine)
save(out, basename + '_min.nii.gz')

out = Nifti1Image(data_max, header=niiHeader, affine=niiAffine)
save(out, basename + '_max.nii.gz')