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1 2 3 4 5 6 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyopgt-nonrigid</title><link rel="stylesheet" type="text/css" href="progref.css"><meta name="generator" content="DocBook XSL Stylesheets V1.79.1"><link rel="home" href="index.html" title="Mia Program Reference"><link rel="up" href="SecRegistrationofseriesof2Dimages.html" title="Registration of series of 2D images"><link rel="prev" href="Secmia2dmyoperiodicnonrigid.html" title="mia-2dmyoperiodic-nonrigid"><link rel="next" href="Secmia2dmyoserialnonrigid.html" title="mia-2dmyoserial-nonrigid"></head><body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">mia-2dmyopgt-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><th width="60%" align="center">Registration of series of 2D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyopgtnonrigid"></a>mia-2dmyopgt-nonrigid</h3></div></div></div><h4><a name="idp5579"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyopgt-nonrigid</code> {-i <em class="replaceable"><code>string</code></em>} {-o <em class="replaceable"><code>string</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp5588"></a>Description:</h4><p>This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images given as a data set as described in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required.</p><h4><a name="idp5590"></a>Options:</h4><h4><a name="idp5591"></a>
File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); string</span></dt><dd><p>input perfusion data set</p></dd><dt><span class="term">-o, --out-file=(output, required); string</span></dt><dd><p>output perfusion data set</p></dd><dt><span class="term">-r, --registered=reg; stringSTRING</span></dt><dd><p>file name base for registered files, the image file type is the same as given in the input data set</p></dd></dl></div><h4><a name="idp5605"></a>
Pseudo Ground Thruth estimation</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-A, --alpha=1; double</span></dt><dd><p>spacial neighborhood penalty weightspacial neighborhood penalty weight</p></dd><dt><span class="term">-B, --beta=1; double</span></dt><dd><p>temporal second derivative penalty weighttemporal second derivative penalty weight</p></dd><dt><span class="term">-R, --rho-thresh=0.85; double</span></dt><dd><p>correlation threshold for neighborhood analysiscorrelation threshold for neighborhood analysis</p></dd><dt><span class="term">-k, --skip=0; ulong</span></dt><dd><p>skip images at the beginning of the series e.g. because as they are of other modalitiesskip images at the beginning of the series e.g. because as they are of other modalities</p></dd></dl></div><h4><a name="idp5623"></a>
Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-O, --optimizer=gsl:opt=gd,step=0.1; factory</span></dt><dd><p>Optimizer used for minimizationOptimizer used for minimization. For supported plug-ins see <a class="xref" href="SecPlugintypeminimizersinglecost.html" title="Plugin type: minimizer/singlecost">Plugin type: minimizer/singlecost</a></p></dd><dt><span class="term">-a, --start-c-rate=32; double</span></dt><dd><p>start coefficinet rate in spines, gets divided by --c-rate-divider with every passstart coefficinet rate in spines, gets divided by --c-rate-divider with every pass</p></dd><dt><span class="term">--c-rate-divider=4; double</span></dt><dd><p>cofficient rate divider for each passcofficient rate divider for each pass</p></dd><dt><span class="term">-d, --start-divcurl=20; double</span></dt><dd><p>start divcurl weight, gets divided by --divcurl-divider with every passstart divcurl weight, gets divided by --divcurl-divider with every pass</p></dd><dt><span class="term">--divcurl-divider=4; double</span></dt><dd><p>divcurl weight scaling with each new passdivcurl weight scaling with each new pass</p></dd><dt><span class="term">-w, --imageweight=1; double</span></dt><dd><p>image cost weightimage cost weight</p></dd><dt><span class="term">-l, --mg-levels=3; ulong</span></dt><dd><p>multi-resolution levelsmulti-resolution levels</p></dd><dt><span class="term">-P, --passes=4; ulong</span></dt><dd><p>registration passesregistration passes</p></dd></dl></div><h4><a name="idp5658"></a>Help & Info</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-V, --verbose=warning; dict</span></dt><dd><p>verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:</p><div class="informaltable"><table class="informaltable" border="0"><colgroup><col class="c1"><col class="c2"></colgroup><tbody><tr><td align="left" valign="top">info:</td><td align="left" valign="top">Low level messages</td></tr><tr><td align="left" valign="top">trace:</td><td align="left" valign="top">Function call trace</td></tr><tr><td align="left" valign="top">fail:</td><td align="left" valign="top">Report test failures</td></tr><tr><td align="left" valign="top">warning:</td><td align="left" valign="top">Warnings</td></tr><tr><td align="left" valign="top">error:</td><td align="left" valign="top">Report errors</td></tr><tr><td align="left" valign="top">debug:</td><td align="left" valign="top">Debug output</td></tr><tr><td align="left" valign="top">message:</td><td align="left" valign="top">Normal messages</td></tr><tr><td align="left" valign="top">fatal:</td><td align="left" valign="top">Report only fatal errors</td></tr></tbody></table></div></dd><dt><span class="term">--copyright=(); bool</span></dt><dd><p>print copyright information</p></dd><dt><span class="term">-h, --help=(); bool</span></dt><dd><p>print this help</p></dd><dt><span class="term">-?, --usage=(); bool</span></dt><dd><p>print a short help</p></dd><dt><span class="term">--version=(); bool</span></dt><dd><p>print the version number and exit</p></dd></dl></div><h4><a name="idp5709"></a>Processing</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">--threads=-1; int</span></dt><dd><p>Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).</p></dd></dl></div><h4><a name="idp5715"></a>Example:</h4><p>Register the perfusion series given in 'segment.set' by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.</p><pre class="screen">mia-2dmyopgt-nonrigid -i segment.set -o registered.set -k 2</pre><h4><a name="idp5718"></a>Author(s):</h4><p>Gert Wollny</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyoperiodic-nonrigid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyoserial-nonrigid</td></tr></table></div></body></html>
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