Cortico-striato-thalamo-cortical (CSTC) loops are thought to play critical roles in the pathophysiology of several brain disorders. Despite the widespread evidence of CSTC circuits' crucial roles in brain disorders, a systematic approach to map their fiber pathways is missing. In order to advance our understanding on these critical circuits and how they are related to brain disorders, we propose a fully automatic approach for the in-vivo reconstruction based on diffusion MRI tractography. To demonstrate our approach, we studied MRI data from 19 patients with obsessive-compulsive disorder and 15 controls. Our approach enables in-dept analysis of the individual connections and also the full CSTC networks of the motor and lateral orbitofrontal loops.