An automated system and method for assisting in decision making for the treatment of stroke patients is provided, and specifically for assisting a physician whether the patient should be administered a drug or transferred to another hospital to undergo an endovascular thrombectomy procedure. A variety of factors are input into the system with limited human intervention and a tool automatically determines the probability of whether the patient will have a better outcome if transferred or not. The factors include clinical factors, imaging factors and time to transfer factors. The tool includes processes for automatically determining several imaging factors, including the determination of clot length, collateral blood flow, the presence of forward blood flow within and around the clot, and the clot permeability. The tool has capability to continuously update the treatment protocol and other output results using current clinical, health system or other relevant information or feedback.