If you are simply interested in permeability, Nicos Martys and I have developed a 3-D Stokes solver that works on a 3-D digital image. See: Article A Stokes Permeability Solver for Three Dimensional Porous Media
Unfortunately, the ftp server that used to supply the codes has been taken offline, but if you provide me with your e-mail address ([email protected]), I can send you a zip file with the codes, documentation, etc., if you are interested.
VirtualFluids is a CPU/GPU LBM solver developed at TU Braunschweig. VF uses advanced LBM kernels that are designed to overcome accuracy and stability issues of other counterparts.
Among other applications, VF was used to predict permeability of x-ray ct scans of hydrated cement pastes. Have a look here: https://www.tu-braunschweig.de/irmb/forschung/virtualfluids
Just like D. P. Bentz said, his code Permsolver can be used for your question.
For the implementation of the code, you can read the manual and some of my paper, for example, "Computational investigation of pore permeability and connectivity from transmission X-ray microscope images of a cement paste specimen"