I want to use morphology operator for filling holes of a 3d image. The 3d image consists of 116 2-D image slices of the same size (512*512 pixels). I tried using imfill in Matlab for the 3d image but the result is not I want. One of the slices of the 3d input image(a) and the corresponding slice from the 3d output image(b) result of using imfill is shown here . The small holes are filled and other holes are not filled.
When I tried using imfill slice by slice the result is correct. Is there any way for filling holes in 3d images? How can I do this?