<strong>registration</strong>, using <em>elastix</em> [1].
In registration there are a <strong>reference</strong> (or target) image and a <strong>moving</strong> (or floating) image, which is warped to the reference image.
The reference image is already segmented, whereas the moving image has to be segmented.</p>
<p>In <em>pyKNEEr</em>, atlas-based segmentation has three steps:</p>
<ol class="arabic simple">
<li><p>The moving image is registered to the reference image though transformations</p></li>
<li><p>