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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<title>Advanced Normalization Tools</title>
<style type="text/css">
* { margin: 0; padding: 0; }
body { font: 16px Helvetica, Sans-Serif; line-height: 24px; background: url(forhtml/nazca-1.jpg); }
.clear { clear: both; }
#page-wrap { width: 800px; margin: 40px auto 60px; }
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a { color: #980000 ; text-decoration: none; border-bottom: 1px dotted #00006E; }
a:hover { border-bottom-style: solid; color: black; }
ul { margin: 0 0 32px 17px; }
#objective { width: 500px; float: left; }
#objective p { font-family: Georgia, Serif; font-style: italic; color: #00006E; }
dt { font-style: italic; font-weight: bold; font-size: 18px; text-align: right; padding: 0 26px 0 0; width: 150px; float: left; height: 100px; border-right: 1px solid #999; }
dd { width: 600px; float: right; }
dd.clear { float: none; margin: 0; height: 15px; }
</style>
</head>
<body>
<div id="page-wrap">
<div id="contact-info" class="vcard">
<!-- Microformats! -->
<h1 class="fn">Advanced Normalization Tools</h1>
<p>
Questions: <a
href="http://sourceforge.net/p/advants/discussion/">Discussion
Site</a><br />
dot com</a><br />
Install ANTs via pre-built: <a href="http://sourceforge.net/projects/advants/files/ANTS/">Packages</a><br />
Build <a href="https://github.com/stnava/ANTs">ANTs</a> from: <a href="http://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/">Source-Code</a> (recommended)
</p>
</div>
<div id="objective">
<p>
ANTs extracts information from
complex datasets that include imaging (<a
href="http://brianavants.files.wordpress.com/2013/05/avants_wordcloud.jpg">Word
Cloud</a>). Paired with <a
href="http://stnava.github.com/ANTsR/">ANTsR</a> (answer),
ANTs is useful for managing, interpreting and
visualizing multidimensional data. ANTs is <a href="https://sourceforge.net/projects/advants/files/ANTS/stats/timeline?dates=2010-07-19+to+2099-05-25">popularly</a> considered
a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized
multimodality image analysis. ANTs depends on the Insight
ToolKit <a href="http://www.itk.org">(ITK)</a>, a widely used
medical image processing library to which ANTs developers contribute.
</p>
</div>
<div class="clear"></div>
<dl>
<dd class="clear"></dd>
<dt>Authors</dt>
<dd>
<h2>Brian B. Avants - UPENN</h2>
<p><strong>Role:</strong> Creator, Algorithm Design,
Implementation, <a href="http://stnava.github.io/Resume/">more</a><br /></p>
</dd>
<dd>
<h2>Nicholas J. Tustison - UVA</h2>
<p><strong>Role:</strong> Compeller, Algorithm Design,
Implementation Guru<br /></p>
</dd>
<dd>
<p><strong>Team:</strong> Gang Song (Originator),
Jeffrey T. Duda (DTI), Hans J. Johnson (Large-Scale
Application, Testing)<br /></p>
</dd>
<dd class="clear"></dd>
<dt>Methods References</dt>
<dd>
<h2>Image Registration</h2>
<p>Diffeomorphisms: <a
href="http://www.ncbi.nlm.nih.gov/pubmed/17659998">SyN</a>,
Independent Evaluation: <a
href="http://www.ncbi.nlm.nih.gov/pubmed/19195496">Klein</a>,
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/21632295">Murphy</a>,
Template Construction
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/15501083">(2004)</a><a
href="http://www.ncbi.nlm.nih.gov/pubmed/19818860"> (2010)</a>,
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/20851191">Similarity
Metrics</a>,
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/18995188">Multivariate
registration</a>,
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/23151955">Multiple
modality analysis and statistical bias</a>
</p>
<h2>Image Segmentation</h2>
<p>Atropos Multivar-EM Segmentation <a
href="http://www.ncbi.nlm.nih.gov/pubmed/21373993">(link)</a>,
Multi-atlas methods <a href="http://www.ncbi.nlm.nih.gov/pubmed/21237273N4">(link)</a>, Bias
Correction <a
href="http://www.ncbi.nlm.nih.gov/pubmed/20378467">(link)</a>,
DiReCT cortical thickness <a
href="http://www.ncbi.nlm.nih.gov/pubmed/19150502">(link)</a>,
DiReCT in
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/23516289">chimpanzees</a>
</p>
<h2>Multivariate Analysis <span>Eigenanatomy <a
href="http://www.ncbi.nlm.nih.gov/pubmed/23286132">(1)</a>
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/23475817">(2)</a>
</span></h2>
<p>Prior-Based Eigenanatomy <a
href="http://www.ncbi.nlm.nih.gov/pubmed/?">(in
prep)</a>,
Sparse CCA <a
href="http://www.ncbi.nlm.nih.gov/pubmed/20083207">(1)</a>,
<a
href="http://www.ncbi.nlm.nih.gov/pubmed/20879247">(2)</a>,
Sparse Regression <a
href="http://link.springer.com/chapter/10.1007%2F978-3-642-38868-2_8">(link)</a>
</p>
<h2>ImageMath <span>Useful!</span></h2>
<p>morphology, GetLargestComponent, CCA, FillHoles
... much more!</p>
</dd>
<dd class="clear"></dd>
<dt>Application Domains</dt>
<dd>
<h2>Frontotemporal degeneration <span><a href="http://ftd.med.upenn.edu">PENN
FTD center</a></span>
<h2>Neuroimaging <span>Multimodality</span></h2>
<ul>
<li>Structural MRI</li>
<li>Functional MRI</li>
<li>Network Analysis</li>
</ul>
<h2>Lung imaging <span>Translational</span></h2>
<ul>
<li>Structure</li>
<li>Perfusion MRI</li>
<li>Branching</li>
</ul>
</dd>
<dd class="clear"></dd>
<dt>Background & Theory</dt>
<dd>
<ul>
<li>The <a
href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22SyN%22)+AND+%22Avants+B%22">
SyN</a> and <a
href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22N4%22)+AND+%22Tustison+N4ITK%22">
N4 bias correction</a> papers and other relevant references in <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22Tustison+N%22)+AND+%22Avants+B%22">Pubmed</a></li>
<li>Visualization: e.g. <a href="http://vimeo.com/66781467">a gource of ANTs development</a></li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22DIRECT%22)+AND+%22Avants%22+AND+DAS">DiReCT</a> cortical thickness <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22Cortical+Thickness%22)+AND+%22Avants%22">papers</a></li>
<li>A <a
href="https://sourceforge.net/projects/advants/files/Documentation/">folder</a>
of relevant docs: <a
href="http://sourceforge.net/projects/advants/files/Documentation/atropos.pdf/download">segmentation</a>,
<a
href="http://sourceforge.net/projects/advants/files/Documentation/antstheory.pdf/download">registration</a>,
<a
href="http://sourceforge.net/projects/advants/files/Documentation/ants.pdf/download">usage(old)</a>,
<a
href="http://sourceforge.net/projects/advants/files/Documentation/ANTSMethodologySummary.docx/download">for
clinical apps</a></li>
<li>ANTs redesigned for generality, automation,
multi-core computation with ITKv4</li>
<li>Dev'd ITKv4 with Kitware, GE, Natl. Lib of
Medicine & Academia</li>
</ul>
</dd>
<dd class="clear"></dd>
<dt>Acclaim for Robustness & Other News</dt>
<dd>
<h2>ANTs has won several competitions<span>
Unbiased & international</span></h2>
<ul>
<li>New <i>antsRegistration</i> <a href="https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh">bash example</a></li>
<li>New <i>Eigenanatomy</i> for <a
href="http://www.ncbi</a>.nlm.nih.gov/pubmed/23269595">multivariate
neuroimage analysis</a> via <a
href="http://www.ncbi.nlm.nih.gov/pubmed/23286132">PCA</a> &
<a href="http://www.ncbi.nlm.nih.gov/pubmed/20083207">CCA</a> </a></li>
<li>ANTs finished in 1st rank in <a href="http://www.ncbi.nlm.nih.gov/pubmed/19195496">Klein
2009 intl. brain mapping competition</a></li>
<li>ANTs finished 1st overall in <a href="http://www.ncbi.nlm.nih.gov/pubmed/21632295">
EMPIRE10 intl. lung mapping competition</a></li>
<li>ANTs is the standard registration for
<a href="http://www.miccai2013.org/">MICCAI-2013</a> segmentation competitions</li>
<li>Conducting ANTs-based R tutorial @ MICCAI-2013</li>
<li>ITK-focused Frontiers in
Neuroinformatics research topic <a href="http://www.frontiersin.org/neuroinformatics/researchtopics/neuroinformatics_with_the_insi/1580">here</a></li>
</ul>
</dd>
<dd class="clear"></dd>
<dt>Learning about ANTs</dt>
<dd>
<li>Presentations: e.g. <a
href="http://prezi.com/mwrmcm-h9-w4/ants/?kw=view-mwrmcm-h9-w4&rc=ref-40024395">a
Prezi about ANTs</a> (WIP)</li>
<li>Reproducible science as a teaching tool: e.g. <a
href="https://github.com/stnava/ANTS_MultiModality"> compilable ANTs tutorial</a> (WIP)</li>
<li>Other examples <a
href="http://brianavants.wordpress.com"> slideshow</a> </li>
<li>Landmark-based mapping for e.g. hippocampus <a
href="https://sourceforge.net/p/advants/discussion/840261/thread/1cb7b165/?limit=50">
discussed here</a></li>
<li>Brief ANTs segmentation <a href="http://vimeo.com/67814201"> video</a></li>
</dd>
<dd class="clear"></dd>
<dt>References</dt>
<dd><li><a href="http://scholar.google.com/scholar?q=Advanced+Normalization+Tools+%22ANTs%22+-ant&hl=en&as_sdt=1%2C39&as_ylo=2008&as_yhi=">Google Scholar</a></li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=(%22Avants%20B%22)%20OR%20%22Tustison%20N%22">Pubmed</a></li>
<li>ANTs was supported by: R01-EB006266-01</li>
<dd class="clear"></dd>
</dl>
<div class="clear"></div>
</div>
</body>
</html>