The present invention involves methods and systems for treatment of brain disorders using neuromodulation of brain networks. Implantation occurs by selecting sites which modulate the network in selected manners, or are modulated by a stimulus in a particular manner that is relevant to treatment of the network. The candidate locations within a brain region are evaluated in relation to how these are indirectly modulated by stimulation at a different brain region. Treatment of one or more brain networks associated with a brain disorder is realized with a consideration of network dynamics and coupling effects such as indirect stimulation of non-target regions. A brain modulation system (BMS) increases, decreases, or otherwise modulates network regional activity in a differential manner. Therapy and electrode locations are adjusted using sensed data and target implantation criteria related to the brain network model. Linking rules be derived during the implantation procedure and used in the subsequent adjusting of the therapy of regions of a brain network.
