We present a theoretical method to simulate magnetotransport in silicon nanowire (Si-NW) MOSFET including the effect of Surface Roughness (SR). We use a full three dimensional (3D) real-space self-consistent Poisson-Schrodinger solver based on Non Equilibrium Green's function Formalism (NEGF) which can treat the influence of an external magnetic field on the device. By comparing magnetoconductance curves with the classical Drude formula we extract magnetoresistance (MR) mobility for nanowires with and without roughness. From the preliminary results it seems that the MR mobility is not dramatically reduced for the SR parameters considered in this work.