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<!doctype html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta content="Overview over the Medical Image Registration ToolKit (MIRTK)" name="description" />
<meta content="image processing, image registration, IRTK, MIRTK" name="keywords" />
<title>Home — MIRTK</title>
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<li class="nav-item nav-item-0"><a href="sidebar.html">MIRTK</a> »</li>
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<h3><a href="sidebar.html">Table Of Contents</a></h3>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Overview</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#modules">Modules</a></li>
<li class="toctree-l2"><a class="reference internal" href="#commands">Commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#background">Background</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="getstarted.html">Get Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Applications</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="apidoc.html">Reference</a></li>
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<li class="toctree-l1"><a class="reference internal" href="changelog.html">News</a></li>
<li class="toctree-l1"><a class="reference internal" href="download.html">Download</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="publications.html">Publications</a></li>
<li class="toctree-l1"><a class="reference internal" href="people.html">People</a></li>
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<div class="section" id="medical-image-registration-toolkit-mirtk">
<h1>Medical Image Registration ToolKit (MIRTK)<a class="headerlink" href="#medical-image-registration-toolkit-mirtk" title="Permalink to this headline">¶</a></h1>
<p>The MIRTK is a research-focused image processing toolkit, developed at the
<a class="reference external" href="https://biomedia.doc.ic.ac.uk/">BioMedIA</a> research group. It provides a collection of libraries and command-line
tools to assist in processing and analyzing imaging data.
The main application of the MIRTK is in adult and neonatal brain MR image registration
as well as the reconstruction of cortical surface meshes. The modular project
organization of the MIRTK enables the installation of selected modules.</p>
<p>In the event you found the MIRTK useful, please consider giving appropriate credit
to the software with a citation of the research article(s) describing the implemented
algorithm(s). See the <a class="reference internal" href="publications.html"><span class="doc">list of publications</span></a> for suitable references.</p>
<div class="section" id="modules">
<h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h2>
<table border="1" class="docutils">
<colgroup>
<col width="20%" />
<col width="80%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Module</th>
<th class="head">Brief Description</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td><a class="reference internal" href="modules/common.html"><span class="doc">Common</span></a></td>
<td>Base classes and common functions. (required)</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="modules/numerics.html"><span class="doc">Numerics</span></a></td>
<td>Utility types such as matrices and functions for numerical optimization.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="modules/image.html"><span class="doc">Image</span></a></td>
<td>Image containers, interpolators, and basic image processing filters.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="modules/io.html"><span class="doc">I/O</span></a></td>
<td>I/O functions such as image and point set file readers and writers.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="modules/pointset.html"><span class="doc">Point Set</span></a></td>
<td>VTK point set/surface filters. Required for point set/surface registration.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="modules/transformation.html"><span class="doc">Transformation</span></a></td>
<td>Image and point set transformation types and regularization terms.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="modules/registration.html"><span class="doc">Registration</span></a></td>
<td>Image and point set registration library.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="modules/deformable.html"><span class="doc">Deformable</span></a></td>
<td>Library for Euler integration of deformable meshes such as cortical surfaces.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="modules/mapping.html"><span class="doc">Mapping</span></a></td>
<td>Filters for the mapping of brain surfaces and volumes.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="modules/scripting.html"><span class="doc">Scripting</span></a></td>
<td>Collection of auxiliary modules for scripting languages such as Python.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="modules/drawem.html"><span class="doc">Draw-EM</span></a></td>
<td>Structural and tissue segmentation of neonatal brain MR images.</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="commands">
<h2>Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h2>
<table border="1" class="docutils">
<colgroup>
<col width="25%" />
<col width="25%" />
<col width="25%" />
<col width="25%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="commands/aggregate-images.html"><span class="doc">aggregate-images</span></a></td>
<td><a class="reference internal" href="commands/average-dofs.html"><span class="doc">average-dofs</span></a></td>
<td><a class="reference internal" href="commands/average-images.html"><span class="doc">average-images</span></a></td>
<td><a class="reference internal" href="commands/average-measure.html"><span class="doc">average-measure</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/average-overlap.html"><span class="doc">average-overlap</span></a></td>
<td><a class="reference internal" href="commands/bisect-dof.html"><span class="doc">bisect-dof</span></a></td>
<td><a class="reference internal" href="commands/blend-surface.html"><span class="doc">blend-surface</span></a></td>
<td><a class="reference internal" href="commands/calculate-boundary-map.html"><span class="doc">calculate-boundary-map</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-distance-map.html"><span class="doc">calculate-distance-map</span></a></td>
<td><a class="reference internal" href="commands/calculate-element-wise.html"><span class="doc">calculate-element-wise</span></a></td>
<td><a class="reference internal" href="commands/calculate-exponential-map.html"><span class="doc">calculate-exponential-map</span></a></td>
<td><a class="reference internal" href="commands/calculate-filtering.html"><span class="doc">calculate-filtering</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-gradients.html"><span class="doc">calculate-gradients</span></a></td>
<td><a class="reference internal" href="commands/calculate-lie-bracket.html"><span class="doc">calculate-lie-bracket</span></a></td>
<td><a class="reference internal" href="commands/calculate-logarithmic-map.html"><span class="doc">calculate-logarithmic-map</span></a></td>
<td><a class="reference internal" href="commands/calculate-surface-attributes.html"><span class="doc">calculate-surface-attributes</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-surface-map.html"><span class="doc">calculate-surface-map</span></a></td>
<td><a class="reference internal" href="commands/calculate-surface-spectrum.html"><span class="doc">calculate-surface-spectrum</span></a></td>
<td><a class="reference internal" href="commands/calculate-volume-map.html"><span class="doc">calculate-volume-map</span></a></td>
<td><a class="reference internal" href="commands/change-label.html"><span class="doc">change-label</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/close-image.html"><span class="doc">close-image</span></a></td>
<td><a class="reference internal" href="commands/close-scalars.html"><span class="doc">close-scalars</span></a></td>
<td><a class="reference internal" href="commands/combine-images.html"><span class="doc">combine-images</span></a></td>
<td><a class="reference internal" href="commands/compose-dofs.html"><span class="doc">compose-dofs</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/compose-maps.html"><span class="doc">compose-maps</span></a></td>
<td><a class="reference internal" href="commands/construct-atlas.html"><span class="doc">construct-atlas</span></a></td>
<td><a class="reference internal" href="commands/convert-dof.html"><span class="doc">convert-dof</span></a></td>
<td><a class="reference internal" href="commands/convert-image.html"><span class="doc">convert-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/convert-pointset.html"><span class="doc">convert-pointset</span></a></td>
<td><a class="reference internal" href="commands/copy-pointset-attributes.html"><span class="doc">copy-pointset-attributes</span></a></td>
<td><a class="reference internal" href="commands/cut-brain.html"><span class="doc">cut-brain</span></a></td>
<td><a class="reference internal" href="commands/decimate-surface.html"><span class="doc">decimate-surface</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/deform-mesh.html"><span class="doc">deform-mesh</span></a></td>
<td><a class="reference internal" href="commands/delete-pointset-attributes.html"><span class="doc">delete-pointset-attributes</span></a></td>
<td><a class="reference internal" href="commands/detect-edges.html"><span class="doc">detect-edges</span></a></td>
<td><a class="reference internal" href="commands/dilate-image.html"><span class="doc">dilate-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/dilate-scalars.html"><span class="doc">dilate-scalars</span></a></td>
<td><a class="reference internal" href="commands/downsample-image.html"><span class="doc">downsample-image</span></a></td>
<td><a class="reference internal" href="commands/draw-em.html"><span class="doc">draw-em</span></a></td>
<td><a class="reference internal" href="commands/edit-dof.html"><span class="doc">edit-dof</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/edit-image.html"><span class="doc">edit-image</span></a></td>
<td><a class="reference internal" href="commands/em.html"><span class="doc">em</span></a></td>
<td><a class="reference internal" href="commands/em-hard-segmentation.html"><span class="doc">em-hard-segmentation</span></a></td>
<td><a class="reference internal" href="commands/erode-image.html"><span class="doc">erode-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/erode-scalars.html"><span class="doc">erode-scalars</span></a></td>
<td><a class="reference internal" href="commands/evaluate-atlas.html"><span class="doc">evaluate-atlas</span></a></td>
<td><a class="reference internal" href="commands/evaluate-cardiac-motion.html"><span class="doc">evaluate-cardiac-motion</span></a></td>
<td><a class="reference internal" href="commands/evaluate-distance.html"><span class="doc">evaluate-distance</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-distortion.html"><span class="doc">evaluate-distortion</span></a></td>
<td><a class="reference internal" href="commands/evaluate-dof.html"><span class="doc">evaluate-dof</span></a></td>
<td><a class="reference internal" href="commands/evaluate-jacobian.html"><span class="doc">evaluate-jacobian</span></a></td>
<td><a class="reference internal" href="commands/evaluate-overlap.html"><span class="doc">evaluate-overlap</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-similarity.html"><span class="doc">evaluate-similarity</span></a></td>
<td><a class="reference internal" href="commands/evaluate-surface-map.html"><span class="doc">evaluate-surface-map</span></a></td>
<td><a class="reference internal" href="commands/evaluate-surface-mesh.html"><span class="doc">evaluate-surface-mesh</span></a></td>
<td><a class="reference internal" href="commands/evaluate-surface-overlap.html"><span class="doc">evaluate-surface-overlap</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-volume-map.html"><span class="doc">evaluate-volume-map</span></a></td>
<td><a class="reference internal" href="commands/extract-connected-components.html"><span class="doc">extract-connected-components</span></a></td>
<td><a class="reference internal" href="commands/extract-connected-points.html"><span class="doc">extract-connected-points</span></a></td>
<td><a class="reference internal" href="commands/extract-image-region.html"><span class="doc">extract-image-region</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/extract-image-slice.html"><span class="doc">extract-image-slice</span></a></td>
<td><a class="reference internal" href="commands/extract-image-volume.html"><span class="doc">extract-image-volume</span></a></td>
<td><a class="reference internal" href="commands/extract-pointset-cells.html"><span class="doc">extract-pointset-cells</span></a></td>
<td><a class="reference internal" href="commands/extract-pointset-surface.html"><span class="doc">extract-pointset-surface</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/extract-surface.html"><span class="doc">extract-surface</span></a></td>
<td><a class="reference internal" href="commands/fill-holes.html"><span class="doc">fill-holes</span></a></td>
<td><a class="reference internal" href="commands/fill-holes-nn-based.html"><span class="doc">fill-holes-nn-based</span></a></td>
<td><a class="reference internal" href="commands/flip-image.html"><span class="doc">flip-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/help-rst.html"><span class="doc">help-rst</span></a></td>
<td><a class="reference internal" href="commands/info.html"><span class="doc">info</span></a></td>
<td><a class="reference internal" href="commands/init-dof.html"><span class="doc">init-dof</span></a></td>
<td><a class="reference internal" href="commands/invert-dof.html"><span class="doc">invert-dof</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/kmeans.html"><span class="doc">kmeans</span></a></td>
<td><a class="reference internal" href="commands/match-histogram.html"><span class="doc">match-histogram</span></a></td>
<td><a class="reference internal" href="commands/match-points.html"><span class="doc">match-points</span></a></td>
<td><a class="reference internal" href="commands/measure-volume.html"><span class="doc">measure-volume</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/merge-surfaces.html"><span class="doc">merge-surfaces</span></a></td>
<td><a class="reference internal" href="commands/normalize.html"><span class="doc">normalize</span></a></td>
<td><a class="reference internal" href="commands/offset-surface.html"><span class="doc">offset-surface</span></a></td>
<td><a class="reference internal" href="commands/open-image.html"><span class="doc">open-image</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/open-scalars.html"><span class="doc">open-scalars</span></a></td>
<td><a class="reference internal" href="commands/project-onto-surface.html"><span class="doc">project-onto-surface</span></a></td>
<td><a class="reference internal" href="commands/recon-neonatal-cortex.html"><span class="doc">recon-neonatal-cortex</span></a></td>
<td><a class="reference internal" href="commands/reflect-image.html"><span class="doc">reflect-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/register.html"><span class="doc">register</span></a></td>
<td><a class="reference internal" href="commands/remesh-surface.html"><span class="doc">remesh-surface</span></a></td>
<td><a class="reference internal" href="commands/resample-image.html"><span class="doc">resample-image</span></a></td>
<td><a class="reference internal" href="commands/smooth-image.html"><span class="doc">smooth-image</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/smooth-surface.html"><span class="doc">smooth-surface</span></a></td>
<td><a class="reference internal" href="commands/split-labels.html"><span class="doc">split-labels</span></a></td>
<td><a class="reference internal" href="commands/subdivide-brain-image.html"><span class="doc">subdivide-brain-image</span></a></td>
<td><a class="reference internal" href="commands/transform-image.html"><span class="doc">transform-image</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/transform-points.html"><span class="doc">transform-points</span></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="background">
<h2>Background<a class="headerlink" href="#background" title="Permalink to this headline">¶</a></h2>
<p>Parts of the Common, Numerics, Image, Transformation, and Registration modules and
command-line tools of the MIRTK originated from the <a class="reference external" href="https://github.com/BioMedIA/IRTK">IRTK</a> written by <a class="reference external" href="http://www.imperial.ac.uk/people/d.rueckert">Daniel Rueckert</a>
and <a class="reference external" href="http://www.imagingcdt.com/about/cdt-management/professor-julia-schnabel">Julia Schnabel</a>. All of the transformation and registration code of the IRTK was
rewritten from scratch by <a class="reference external" href="http://www.andreasschuh.com/">Andreas Schuh</a> during his PhD studies, with a new modular and
extended registration framework. Additional modules and commands for the reconstruction
and inflation of cortical surface meshes, the registration of surface meshes, and the
harmonic mapping of brain volumes were subsequently added to the MIRTK.</p>
</div>
</div>
</div>
</div>
</div>
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>previous</a> |</li>
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