A method for 3D magnetic resonance imaging (MRI) with slice-direction distortion correction is provided. One or more selective cross-sections with a thickness along a first axis is excited using a RF pulse with a bandwidth, wherein a selective cross-section is either a selective slice or selective slab. A refocusing pulse is applied to form a spin echo. One or more 2D encoded image signals are acquired with readout along a second axis and phase encoding along a third axis. Slice-direction distortion is corrected by resolving the position by resolving the frequency offset.