have a look at the function
mitkBoundingObject::FitGeometry(Geometry3D* a)
This function is for example used by the image cropper
One would think that writing "setGeometry(aGeometry3D)" is enough to make the bounding object fit the underlying image/geometry. But apparently the boundingObject can only be handled correctly, when it's indexBounds are from -1 to 1 in all axis (so it is only 2x2x2 Pixels big) and the spacing specifies it's actual bounds. This behavior needs to be analyzed and maybe changed.