If you call the method mitk::Image::SetClonedGeometry(), it can happen, that the cloned geometry is slightly different from the original one.
The transfomation matrices of the two geometries are then different from each other.
This may result in a wrong transformation of (e.g. from index coordinates to world coordinates)
The reason for this lies in the method mitk::SlicedGeometry3D::InitializeEvenlySpaced() which is called in SetClonedGeometry.