Function fill_holes 

pub fn fill_holes(
    mask: &[u8],
    nx: usize,
    ny: usize,
    nz: usize,
    max_hole_size: usize,
) -> Vec<u8> 

Fill holes in a binary mask

Matches MriResearchTools.jl’s fill_holes function. Fills connected components of zeros (holes) up to max_hole_size. Uses 6-connectivity for 3D.