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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<HTML><HEAD><meta http-equiv="Content-Type"
content="text/html;charset=utf-8">
<link REL="stylesheet" TYPE="text/css"
href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><IFRAME width="100%" scrolling="no" frameborder="0" src="fdt_top.html">Broken</IFRAME>
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<h3>Eddy Current Correction</h3>
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Eddy currents in the gradient coils induce (approximate) stretches and shears
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in the diffusion weighted images. These distortions are different for
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different gradient directions. Eddy Current Correction corrects for these
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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
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<b>FDT</b> button.  Use the top left drop down menu to select <b>Eddy current correction</b>.  
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<p><b>Diffusion weighted data:</b> Use the browse button to select
your diffusion weighted dataset (a 4D image).
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<br><b>Corrected output data:</b> Use the browse button to specify a filename for
the corrected 4D dataset.
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<br><b>Reference volume:</b> (default 0). Set the volume number for the reference volume
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that will be used as a target to register all other volumes to. <br><br>
<b>command line utility</b><br>
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<code>eddy_correct &#60;4dinput&#62; &#60;4doutput&#62; &#60;reference_no&#62;</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 &lt;4doutput&gt;.ecclog &lt;bvecs&gt;</code> -->