Summary: We study the occurrence and dynamics of rogue waves in three-dimensional deep water using phase-resolved numerical simulations based on a high-order spectral (HOS) method. We obtain a large ensemble of nonlinear wave-field simulations (\(M=3\) in HOS method), initialized by spectral parameters over a broad range, from which nonlinear wave statistics and rogue wave occurrence are investigated. The HOS results are compared to those from the broad-band modified nonlinear Schrödinger (BMNLS) equations. Our results show that for (initially) narrow-band and narrow directional spreading wave fields, modulational instability develops, resulting in non-Gaussian statistics and a probability of rogue wave occurrence that is an order of magnitude higher than linear theory prediction. For longer times, the evolution becomes quasi-stationary with non-Gaussian statistics, a result not predicted by the BMNLS equations (without consideration of dissipation). When waves spread broadly in frequency and direction, the modulational instability effect is reduced, and the statistics and rogue wave probability are qualitatively similar to those from linear theory. To account for the effects of directional spreading on modulational instability, we propose a new modified Benjamin-Feir index for effectively predicting rogue wave occurrence in directional seas. For short-crested seas, the probability of rogue waves based on number frequency is imprecise and problematic. We introduce an area-based probability, which is well defined and convergent for all directional spreading. Based on a large catalogue of simulated rogue wave events, we analyse their geometry using proper orthogonal decomposition (POD). We find that rogue wave profiles containing a single wave can generally be described by a small number of POD modes.