A system for computationally generating a protocol for treatment of at least one target BBB, blood-brain barrier, region including multiple tissue types within a tissue region of interest using a source of focused ultrasound, the system comprising: an imaging device for obtaining a digital image of at least a portion of the target BBB region; a processor configured to identify multiple tissue types in the target BBB region; and memory storing the treatment protocol specifying (i) a setting of at least one sonication parameter for applying multiple sequences of sonications to the target BBB region using the source of focused ultrasound, each of the sonication sequences corresponding to one of the multiple tissue types, (ii) a characteristic of microbubbles selected to be administered into the target BBB region, and (iii) instructions which, when executed by the processor, cause the processor to: (a) electronically simulate treatment in accordance with the specified sonication parameter setting and microbubble characteristic at least in part by computationally executing the multiple sequences of sonications and computationally administer the microbubbles having the characteristic; (b) computationally predict a degree of tissue disruption of the target BBB region resulting from the treatment based on the simulation thereof; and (c) computationally generate the protocol based at least in part on the predicted degree of tissue disruption. an imaging device for obtaining a digital image of at least a portion of the target BBB region; a processor configured to identify multiple tissue types in the target BBB region; and memory storing the treatment protocol specifying (i) a setting of at least one sonication parameter for applying multiple sequences of sonications to the target BBB region using the source of focused ultrasound, each of the sonication sequences corresponding to one of the multiple tissue types, (ii) a characteristic of microbubbles selected to be administered into the target BBB region, and (iii) instructions which, when executed by the processor, cause the processor to: (a) electronically simulate treatment in accordance with the specified sonication parameter setting and microbubble characteristic at least in part by computationally executing the multiple sequences of sonications and computationally administer the microbubbles having the characteristic; (b) computationally predict a degree of tissue disruption of the target BBB region resulting from the treatment based on the simulation thereof; and (c) computationally generate the protocol based at least in part on the predicted degree of tissue disruption. (a) electronically simulate treatment in accordance with the specified sonication parameter setting and microbubble characteristic at least in part by computationally executing the multiple sequences of sonications and computationally administer the microbubbles having the characteristic; (b) computationally predict a degree of tissue disruption of the target BBB region resulting from the treatment based on the simulation thereof; and (c) computationally generate the protocol based at least in part on the predicted degree of tissue disruption.