This function is quite likely not respecting center-based World coordinates.
//##Documentation
//## @brief Convert world coordinates (in mm) of a \em point to index coordinates (in units).
//## This method rounds to integer indices!
template <unsigned int VIndexDimension>
void WorldToIndex(const mitk::Point3D &pt_mm, itk::Index<VIndexDimension> &index) const
{
typedef itk::Index<VIndexDimension> IndexType;
mitk::Point3D pt_units;
WorldToIndex(pt_mm, pt_units);
int i, dim=index.GetIndexDimension();
if(dim>3)
{
index.Fill(0);
dim=3;
}
for(i=0;i<dim;++i){
if(pt_units[i]<0)
pt_units[i]-=0.5;
else
pt_units[i]+=0.5;
index[i]=(typename IndexType::IndexValueType)pt_units[i];
}
}