We present a Shack-Hartmann (SH) centroid detection algorithm capable to measure in presence of strong noise, background illumination and spot modulating signals, which are typical limiting factors of traditional centroid detection algorithms. The proposed method is based on performing a normalization of the SH pattern using the spiral phase transform method and Fourier filtering. The spot centroids are then obtained using global thresholding and weighted average methods. We have tested the algorithm with simulations and experimental data obtaining satisfactory results. A complete MATLAB package that can reproduce all the results can be downloaded from [http://goo.gl/o2JhD].