Permutation testing made practical for functional magnetic resonance image analysis

We describe an efficient algorithm for the step-down permutation test, applied to the analysis of functional magnetic resonance images. The algorithm's time bound is nearly linear, making it feasible as an interactive tool. Results of the permutation test algorithm applied to data from a cognitive activation paradigm are compared with those of a standard parametric test corrected for multiple comparisons. The permutation test identifies more weakly activated voxels than the parametric test, always activates a superset of the voxels activated by this parametric method, almost always yields significance levels greater than or equal to those produced by the parametric method, and tends to enlarge activated clusters rather than adding isolated voxels. Our implementation of the permutation test is freely available as part of a widely distributed software package for analysis of functional brain images.