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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.
<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the
<b>FDT</b> button. Use the top left drop down menu to select <b>Eddy current correction</b>.
<p><b>Diffusion weighted data:</b> Use the browse button to select
your diffusion weighted dataset (a 4D image).
<br><b>Corrected output data:</b> Use the browse button to specify a filename for
the corrected 4D dataset.
<br><b>Reference volume:</b> (default 0). Set the volume number for the reference volume
that will be used as a target to register all other volumes to. <br><br>
<b>command line utility</b><br>
<code>eddy_correct <4dinput> <4doutput> <reference_no></code>
<!-- <h3>Rotating the bvecs after eddy current correction</h3> -->
<!-- Applying eddy current correction to diffusion data implies rotating (slightly) the data. In order to fit -->
<!-- a directional model to this data (e.g. DTIFIT or BEDPOSTX), you need to rotate the gradient orientations (bvecs) -->
<!-- using the rotations estimated by the eddy current correction. <br><br> -->
<!-- The following command line utility allow you to do that (modified from a script written by Martin Kavec): -->
<!-- <br><br> -->
<!-- <code>rotate_bvecs <4doutput>.ecclog <bvecs></code> -->