Given the recent trend towards validating the neuroimaging methods, we compared the most popular fMRI analysis softwares: AFNI, FSL and SPM, with regard to autocorrelation modelling. We used both resting-state and task-based fMRI data, for which we assumed different experimental designs. For FSL and SPM we observed a strong relationship that the lower the assumed experimental design frequency, the more likely it was to observe significant activation. It indicates that pre-whitening in FSL and SPM does not remove a substantial part of the temporal autocorrelation in the noise. Our study points to superior autocorrelation modelling in AFNI.