After creating a mask with Segmentator, morphological operations can be used to improve the mask.

Here is an [example python script](https://gist.github.com/ofgulban/21f9b257de849c546f34863aa26f3dd3) to perform [opening](https://en.wikipedia.org/wiki/Opening_(morphology)) and [closing](https://en.wikipedia.org/wiki/Closing_(morphology)) operations:

``` python
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 = nii.get_data()

# 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('Morphology operations are done.')
```

For further information, see [scipy.ndimage.morphology](https://docs.scipy.org/doc/scipy-0.16.1/reference/ndimage.html#module-scipy.ndimage.morphology).

TODO: Images to demonstrate before/after morphological operations.