Eddy Current Correction

Eddy currents in the gradient coils induce (approximate) stretches and shears in the diffusion weighted images. These distortions are different for different gradient directions. Eddy Current Correction corrects for these distortions, and for simple head motion, using affine registration to a reference volume.

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 diffusion weighted dataset (a 4D image).
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>