We present algorithms for the automated transition from scanned MRI images to finite element simulations. The algorithms are designed for the reconstruction of fine scale blood vessels as possibly important to defibrillation studies in electrocardiac physiology. The automated nature of the transition is essential for practical usage, as the otherwise necessary human intervention is prohibitive. The automated software relies on a mixture of public domain algorithms and new algorithms developed specifically for the current purpose. The problem of transitions from MRI images to accurate physiology is important in many medical applications, and much of our work will be helpful in more general cases. The definitive nature of the blood vessel problem which makes the entire analysis feasible is a conceptual model of the final geometry, as the connected branches of veins and arteries together with the inner and outer cardiac surface.