How to close a surface with holes?

Question

I have a binary volume that I have read into itk::Image . After creating the surface and the mesh, there are some wholes that need to be closed. I need to create a closed surface, however, the object values are reaching to the first row (horizontal or axial view of the volume) and also there are wholes in the starting and ending slice (z-direction), that is not letting the surface to be closed. There are some wholes on the surface as well. What solution do you suggest?

Answer 1

To fix the holes at the edges of the volume, simply pad out the volume with blank space so that the object does not reach the edge of the volume.

For other holes you could try VTK's FillHolesFilter:

https://vtk.org/doc/nightly/html/classvtkFillHolesFilter.html

You might have to play with the HoleSize parameter to get good results.