Susceptibility-weighted imaging (SWI) venography can produce detailed venous contrast and complement arterial dominated MR angiography (MRA) techniques. However, these dense reversed-contrast SWI venograms pose new segmentation challenges. We present an automatic method for whole-brain venous blood segmentation in SWI using Conditional Random Fields (CRF). The CRF model combines different first and second order potentials. First-order association potentials are modeled as the composite of an appearance potential, a Hessian-based shape potential and a non-linear location potential. Second-order interaction potentials are modeled using an auto-logistic (smoothing) potential and a data-dependent (edge) potential. Minimal post-processing is used for excluding voxels outside the brain parenchyma and visualizing the surface vessels. The CRF model is trained and validated using 30 SWI venograms acquired within a population of deep brain stimulation (DBS) patients (age range [Formula: see text] years). Results demonstrate robust and consistent segmentation in deep and sub-cortical regions (median kappa = 0.84 and 0.82), as well as in challenging mid-sagittal and surface regions (median kappa = 0.81 and 0.83) regions. Overall, this CRF model produces high-quality segmentation of SWI venous vasculature that finds applications in DBS for minimizing hemorrhagic risks and other surgical and non-surgical applications.