Module mask 

Brain-mask thresholding and morphology.

Mask generation (otsu_threshold) plus morphological operations (erode/dilate/close/fill-holes) and sphere masks.

Functions

apply_mask_zero

Zero out elements where mask is 0.

create_sphere_mask

Create a binary sphere mask on a 3D volume

dilate_mask

Dilate a binary mask by expanding into neighboring voxels (6-connectivity).

erode_mask

Erode a binary mask by removing boundary voxels (6-connectivity).

fill_holes

Fill holes in a binary mask

morphological_close

Morphological closing (dilation followed by erosion)

otsu_threshold

Otsu’s method for automatic threshold selection