You can also use MRIcroGL to resolve this graphically. Choose Import/Tools/Rotation. It will guide you to sequentially select the axis that best represents Left/Right, Anterior/Posterior, Inferior/Superior. It re-slices the data to canonical NIfTI space, so it is probably not a good choice for EPI data where you want to apply slice time corrections (though human EPI sequences are typically axially acquired, in which case this method works).
