3D whole heart phase sensitive late gadolinium enhanced (LGE) imaging can improve myocardial scar detection. Phase sensitive inversion recovery (PSIR) LGE is sub-optimal for clinical 3D application as it doubles the scan time with a fully sampled reference image. To address this, we develop 3D True Polarity Recovery with Independent Phase Estimation Using Multi-layer Stacks Based Region-Growing (3D-TRIPS) for direct reconstruction of 3D phase sensitive images without need for a separate reference scan. We demonstrate that 3D-TRIPS images shows good agreement and less artifacts compared with PSIR images. 3D-TRIPS will allow 3D-LGE imaging with half the scan time of PSIR.