--- a
+++ b/CLI/MusculoskeletalAnalysisCLITools/fill.py
@@ -0,0 +1,28 @@
+
+
+def fill(mask, radius):
+    """Performs morphological close with the given radius, then fills any holes not connected to the outer edge.
+
+    Takes a 2D binary numpy array and an integer radius.
+
+    Returns the transformed array.
+    """
+    import numpy as np
+    import skimage.morphology
+    # Performs morphological close, filling small gaps
+    strel = skimage.morphology.disk(radius, dtype='bool')
+    # Pad image to remove edge related problems
+    mask=np.pad(mask, radius, mode='constant', constant_values=0)
+    skimage.morphology.binary_closing(mask, footprint=strel, out=mask)
+    mask=mask[radius:-radius, radius:-radius]
+    # Fills in all holes not connected to the edges
+    seed = np.ones_like(mask, dtype='bool')
+
+    # seed is a mask of all ones, except zero where mask has zeros on the edges
+    seed[0,:] = mask[0,:]
+    seed[-1,:] = mask[-1,:]
+    seed[:,-1] = mask[:,-1]
+    seed[:,0] = mask[:,0]
+    # seed's zero areas are expanded to match mask's zeros
+    mask = skimage.morphology.reconstruction(seed, mask, method='erosion')
+    return mask