A method and system for setting the direction of pinned layers in a magnetic junction are described. In one aspect, a magnetic field greater than the coercivity of the layers in a pinned layer but less than the coupling field between the layers is applied. In another aspect the pinned layers are switched from an anti-dual state to a dual state using a spin transfer torque current. In another aspect, a magnetic junction having a partial perpendicular anisotropy (PPMA) layer in the pinned layer is provided. In some aspects, the PPMA layer is part of a synthetic antiferromagnetic structure. In some embodiments, a decoupling layer is provided between the PPMA layer and another ferromagnetic layer in the pinned layer.