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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" />
<title>Modules — MIRTK</title>
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<h3><a href="sidebar.html">Table Of Contents</a></h3>
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<li class="toctree-l1"><a class="reference internal" href="index.html">Overview</a></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 current"><a class="current reference internal" href="#">Modules</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#core-modules">Core Modules</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#common">Common</a></li>
<li class="toctree-l3"><a class="reference internal" href="#numerics">Numerics</a></li>
<li class="toctree-l3"><a class="reference internal" href="#image">Image</a></li>
<li class="toctree-l3"><a class="reference internal" href="#i-o">I/O</a></li>
<li class="toctree-l3"><a class="reference internal" href="#point-set">Point Set</a></li>
<li class="toctree-l3"><a class="reference internal" href="#transformation">Transformation</a></li>
<li class="toctree-l3"><a class="reference internal" href="#registration">Registration</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#external-packages">External Packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#deformable">Deformable</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mapping">Mapping</a></li>
<li class="toctree-l3"><a class="reference internal" href="#scripting">Scripting</a></li>
<li class="toctree-l3"><a class="reference internal" href="#draw-em">Draw-EM</a></li>
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<div class="section" id="modules">
<span id="id1"></span><h1>Modules<a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<div class="section" id="core-modules">
<span id="coremodules"></span><h2>Core Modules<a class="headerlink" href="#core-modules" title="Permalink to this headline">¶</a></h2>
<p>The core modules are always included in the MIRTK source tree.</p>
<div class="section" id="common">
<h3>Common<a class="headerlink" href="#common" title="Permalink to this headline">¶</a></h3>
<p>The Common module of the Medical Image Registration ToolKit (MIRTK) defines the base
classes from which other MIRTK classes are derived. It further contains common
auxiliary functions and a simple command-line parsing library.</p>
<p><a class="reference internal" href="modules/common.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="numerics">
<h3>Numerics<a class="headerlink" href="#numerics" title="Permalink to this headline">¶</a></h3>
<p>The Numerics module of the Medical Image Registration ToolKit (MIRTK) provides basic
support for linear algebra computations. It further defines an abstract interface
for objective functions to be minimized by one of the available iterative optimizers.</p>
<p><a class="reference internal" href="modules/numerics.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="image">
<h3>Image<a class="headerlink" href="#image" title="Permalink to this headline">¶</a></h3>
<p>The Image module of the Medical Image Registration ToolKit (MIRTK) provides containers
and basic filters for imaging data sampled on a uniform grid. It contains image
interpolation functions which enable the evaluation of these finite discrete images
in an infinite continuous domain. This is in particular needed for the deformation of
an image during and after registration.</p>
<p><a class="reference internal" href="modules/image.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="i-o">
<h3>I/O<a class="headerlink" href="#i-o" title="Permalink to this headline">¶</a></h3>
<p>The I/O module of the Medical Image Registration ToolKit (MIRTK) enables the
reading and writing of image and point set files. Supported file formats are
GIPL, PGM, and the <a class="reference external" href="http://nifti.nimh.nih.gov">NIfTI file format</a>.
Image slices can further be written to PNG image files when the MIRTK was built WITH_PNG.</p>
<p><a class="reference internal" href="modules/io.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="point-set">
<h3>Point Set<a class="headerlink" href="#point-set" title="Permalink to this headline">¶</a></h3>
<p>The Point Set module of the Medical Image Registration ToolKit (MIRTK) adds
support for general point sets such as fidicual markers, surface meshes, and
volumetric tetrahedral meshes. It defines different auxiliary types used to
establish point correspondences between two given point sets/surface meshes.
These correpondences can be utilized by the <a class="reference internal" href="modules/registration.html"><span class="doc">Registration</span></a> module to find a
transformation that aligns two given point sets.</p>
<p><a class="reference internal" href="modules/pointset.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="transformation">
<h3>Transformation<a class="headerlink" href="#transformation" title="Permalink to this headline">¶</a></h3>
<p>The Transformation module of the Medical Image Registration ToolKit (MIRTK)
defines the different transformation models supported by the <a class="reference internal" href="modules/registration.html"><span class="doc">Registration</span></a>
module. These include linear homogeneous transformation types and non-rigid
free-form deformations. The Transformation module further includes a number
of transformation constraint terms which can be used to regularize the
registration problem.</p>
<p><a class="reference internal" href="modules/transformation.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="registration">
<span id="registrationabstract"></span><h3>Registration<a class="headerlink" href="#registration" title="Permalink to this headline">¶</a></h3>
<p>The Registration module of the Medical Image Registration ToolKit (MIRTK)
provides the generic framework used to register images and point sets.
This framework expresses the registration problem as configurable function
minimization problem. The object function, referred to as registration energy
in this context, is put together using the various energy terms. An energy
term can be either an image (dis-)similarity measure, a transformation
constraint, or a point set/surface constraint.</p>
<p><a class="reference internal" href="modules/registration.html"><span class="doc">[more]</span></a></p>
</div>
</div>
<div class="section" id="external-packages">
<span id="externalmodules"></span><h2>External Packages<a class="headerlink" href="#external-packages" title="Permalink to this headline">¶</a></h2>
<p>Additional modules which are developed and maintained separate from the core
modules in their own respective repository are referred to as external packages.
These are either loosely bound optional modules or modules contributed by users.</p>
<div class="section" id="deformable">
<h3>Deformable<a class="headerlink" href="#deformable" title="Permalink to this headline">¶</a></h3>
<p>The Deformable module of the Medical Image Registration ToolKit (MIRTK) is a library
for the Euler integration of deformable meshes such as cortical surfaces.
The <a class="reference internal" href="commands/deform-mesh.html"><span class="doc">deform-mesh</span></a> command can be used to deform an initial mesh such as the convex hull
of an input segmentation or a bounding sphere based on internal and external
point set/surface forces. The integration is stopped when a suitable stopping criterion
is fullfilled such as a fixed number of iterations, target objective function value,
or surface smoothness (e.g., for cortical surface inflation). The internal forces
can further be utilized by the <a class="reference internal" href="modules/registration.html"><span class="doc">Registration</span></a> module to constrain the transformation,
for example, to constrain the cortical surface to remain smooth after transformation.</p>
<p><a class="reference internal" href="modules/deformable.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="mapping">
<h3>Mapping<a class="headerlink" href="#mapping" title="Permalink to this headline">¶</a></h3>
<p>The Mapping module of the Medical Image Registration ToolKit (MIRTK) is a library
for the mapping of brain surfaces and volumes. The <a class="reference internal" href="commands/map-surface.html"><span class="doc">map-surface</span></a>
and <a class="reference internal" href="commands/map-volume.html"><span class="doc">map-volume</span></a> commands can be used to compute such (harmonic)
surface or volumetric maps.</p>
<p><a class="reference internal" href="modules/mapping.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="scripting">
<h3>Scripting<a class="headerlink" href="#scripting" title="Permalink to this headline">¶</a></h3>
<p>The Scripting module is a library of modules written in commonly used scripting
languages which can be used to write custom scripts for medical image analysis.</p>
<p><a class="reference internal" href="modules/scripting.html"><span class="doc">[more]</span></a></p>
</div>
<div class="section" id="draw-em">
<h3>Draw-EM<a class="headerlink" href="#draw-em" title="Permalink to this headline">¶</a></h3>
<p>The Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
module of the Medical Image Registration ToolKit (MIRTK) provides command-line
tools for the automatic segmentation of neonatal brain MR images into the major
tissue classes and a detailed structural segmentation. It is developed by
<a class="reference external" href="http://www.doc.ic.ac.uk/~am411">Antonios Makropoulos</a>. Please cite his
TMI paper when you use the Draw-EM segmentations in your research studies.</p>
<p><a class="reference internal" href="modules/drawem.html"><span class="doc">[more]</span></a></p>
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