Not all anatomic borders are intensity based borders: 1) dividing left and right white matter regions at the corpus callosum 2) spatial resolution of the image is not sufficient to completely resolve discrete tissue regions defining a border (e.g. caudate and putamen)
Sometimes a boundary is placed at a given location using information that is not in the intensity of the current brain slice-- it is taken from adjacent brain slices.
The definition of a boundary or node can be defined arbitrarily.
These borders were drawn in by hand.