To call the FDT GUI, either run Fdt, or run fsl and press the FDT button. Use the top left drop down menu to select Eddy Current Correction.
Diffusion Weighted data: Use the browse button to select your 4D
analyze format series of diffusion weighted data.
Corrected output data: Use the browse button to specify a filename for
the corrected 4D dataset.
Reference Volume: (default 0). Set the volume number for the reference volume
that will be used as a target to register all other volumes to.
command line utility
eddy_correct <4dinput> <4doutput> <reference_no>