Simple morphological operations on MRI data (nifti).

dilate_erode_MRI_data.py

"""Dilation, erosion, opening, closing operations on binary nifti files."""

import os
import numpy as np
from scipy.ndimage import morphology
from nibabel import load, save, Nifti1Image

# Load data
nii = load('/path/to/your/file.nii.gz')
basename = nii.get_filename().split(os.extsep, 1)[0]
dirname = os.path.dirname(nii.get_filename())
data = np.asarray(nii.dataobj)

# Perform closing
data = morphology.binary_dilation(data, iterations=1)
data = morphology.binary_erosion(data, iterations=1)

# Perform opening
data = morphology.binary_erosion(data, iterations=1)
data = morphology.binary_dilation(data, iterations=1)

# Save as nifti
out = Nifti1Image(data, header=nii.header, affine=nii.affine)
save(out, basename + "_opening_closing.nii.gz")

print 'Finished.'