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<html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoset-all2one-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="Secmia2dmyoserialnonrigid.html" title="mia-2dmyoserial-nonrigid"><link rel="next" href="SecToolsfortheAnalysisof2Dimageseries.html" title="Tools for the Analysis of 2D image series"></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-2dmyoset-all2one-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyoserialnonrigid.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="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyosetall2onenonrigid"></a>mia-2dmyoset-all2one-nonrigid</h3></div></div></div><h4><a name="idp5839"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoset-all2one-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>
        ...] [
          <em class="replaceable"><code>
            <a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a>
          </code></em>
        ...]</p></div><h4><a name="idp5851"></a>Description:</h4><p>This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.</p><h4><a name="idp5853"></a>Options:</h4><h4><a name="idp5854"></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">--out-filebase=reg; stringSTRING</span></dt><dd><p>file name basae for registered files, file type is deducted from the image file type in the input data set.</p></dd></dl></div><h4><a name="idp5868"></a>
Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-k, --skip=0; int</span></dt><dd><p>Skip images at the beginning of the seriesSkip images at the beginning of the series</p></dd><dt><span class="term">-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING</span></dt><dd><p>Optimizer used for minimization</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">-f, --transForm=spline; factory</span></dt><dd><p>transformation typetransformation type. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagetransform.html" title="Plugin type: 2dimage/transform">Plugin type: 2dimage/transform</a></p></dd><dt><span class="term">-r, --ref=-1; int</span></dt><dd><p>reference frame (-1 == use image in the middle)reference frame (-1 == use image in the middle)</p></dd></dl></div><h4><a name="idp5891"></a>Help &amp; 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="idp5942"></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="idp5948"></a>Example:</h4><p>Register the perfusion series given in segment.set by optimizing a spline based transformation with a coefficient rate of 16 pixel using Mutual Information and penalize the transformation by using divcurl with aweight of 2.0.</p><pre class="screen">mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set 
    -f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0</pre><h4><a name="idp5951"></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="Secmia2dmyoserialnonrigid.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="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyoserial-nonrigid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> Tools for the Analysis of 2D image series</td></tr></table></div></body></html>
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