Motion artefacts are damaging to fMRI studies, masking real effects or forcing data to be discarded. Standard processing pipelines include linear registration steps between frames, though some groups proposed prospectively exploiting the slice-based nature of acquisition. The improvement this offers is rarely quantified as no “baseline” is available. Here, we simulated MRI acquisitions with a general slice-based navigation method to quantify the accuracy of prospective correction over retrospective registration. Compared to retrospective linear and non-linear techniques, registration of individual slices most accurately matched trial motion trajectories with better image quality than linear methods.