Correction of EPI geometric distortion in slice direction using reversed slice-select gradients and topup

Conventional single-shot Echo Planar Imaging (EPI) protocols used by fMRI studies suffer from geometric distortion occurring in the phase-encoding direction. Ultrahigh field (>3T), high-resolution fMRI using thin slices requires decrease of the slice-encoding bandwidth, which may lead to the additional geometric distortions and “slice bending” in the slice-encoding direction. Here we use gradient-echo (GRE) EPI sequence that allows the polarity of the slice-select gradient to be flipped between positive and negative values to demonstrate this effect and to enable the application of FSL’s topup to perform distortion correction. This correction will further improve geometric alignment of the EPI data with anatomical reference data used in fMRI studies.