Viscous flow, effusion, and thermal transpiration are the main gas transport modalities for a rarefied gas in a macro-porous medium. They have been well quantified only in the case of simple geometries. This paper presents a numerical method based on the homogenization of kinetic equations producing effective transport properties ( permeability, Knudsen diffusivity, thermal transpiration ratio) in any porous medium sample, as described, e. g. by a digitized 3D image. The homogenization procedure-neglecting the effect of gas density gradients on heat transfer through the solid - leads to closure problems in R-6 for the obtention of effective properties; they are then simplified using a Galerkin method based on a 21-element basis set. The kinetic equations are then discretized in R-3 space with a finite-volume scheme. The method is validated against experimental data in the case of a closed test tube. It shows to be coherent with past approaches of thermal transpiration. Then, it is applied to several 3D images of increasing complexity. Another validation is brought by comparison with other distinct numerical approaches for the evaluation of the Darcian permeability