import scipy.ndimage as ndim
from skimage.filters import gaussian
from skimage.morphology import convex_hull_image

def patch_up_roi(roi, sigma=0.5, truncate=2):
    """
    After being non-linearly transformed, ROIs tend to have holes in them.
    We perform a couple of computational geometry operations on the ROI to
    fix that up.

    Parameters
    ----------
    roi : 3D binary array
        The ROI after it has been transformed.

    sigma : float
        The sigma for initial Gaussian smoothing.

    truncate : float
        The truncation for the Gaussian

    Returns
    -------
    ROI after dilation and hole-filling
    """

    return convex_hull_image(gaussian(ndim.binary_fill_holes(roi),
                                      sigma=sigma, truncate=truncate) > 0.1)

import scipy.ndimage as ndim
from skimage.filters import gaussian
from skimage.morphology import convex_hull_image

def patch_up_roi(roi, sigma=0.5, truncate=2):
    """
    After being non-linearly transformed, ROIs tend to have holes in them.
    We perform a couple of computational geometry operations on the ROI to
    fix that up.

    Parameters
    ----------
    roi : 3D binary array
        The ROI after it has been transformed.

    sigma : float
        The sigma for initial Gaussian smoothing.

    truncate : float
        The truncation for the Gaussian

    Returns
    -------
    ROI after dilation and hole-filling
    """

    return convex_hull_image(gaussian(ndim.binary_fill_holes(roi),
                                      sigma=sigma, truncate=truncate) > 0)

Set the Gaussian threshold to 0.