But what if the guy who paints the connectors at the previous step get it wrong ;-)

The program displays fiber tracks computed from the diffusion tensor images. This involves more than just fusioning images from different modalities (fiber tracking is far from obvious). Also, some images are 3D surfaces reconstructed from 2D slices. This being said, it has been possible to make and manipulate this kind of images for a while with the (freely available) program "anatomist/brainvisa" (cf. www.brainvisa.info).