The ensemble of the human brain wiring configuration is known as the connectome. Using diffusion magnetic resonance imaging, we can approximate the connectome and use it to increase our understanding of normal function and of neuro-diseases. However, the complex interactions between each steps from brain images to the final wires give rise to many potential sources of error. Using an array of modern simulations of these steps, we will study and disentangle the effect of their interactions to increase the accuracy of the connectome estimation in humans.