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<html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoperiodic-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="Secmia2dmyomilles.html" title="mia-2dmyomilles"><link rel="next" href="Secmia2dmyopgtnonrigid.html" title="mia-2dmyopgt-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-2dmyoperiodic-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyomilles.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="Secmia2dmyopgtnonrigid.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyoperiodicnonrigid"></a>mia-2dmyoperiodic-nonrigid</h3></div></div></div><h4><a name="idp5427"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoperiodic-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="idp5436"></a>Description:</h4><p>This program runs the non-rigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010
</p><h4><a name="idp5438"></a>Options:</h4><h4><a name="idp5439"></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 fiels</p></dd><dt><span class="term">--save-references</span></dt><dd><p>Save synthetic references to files refXXXX.v</p></dd></dl></div><h4><a name="idp5457"></a>
Preconditions</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-k, --skip=0; ulong</span></dt><dd><p>Skip images at the begin of the seriesSkip images at the begin of the series</p></dd><dt><span class="term">--max-candidates=20; ulong</span></dt><dd><p>maximum number of candidates for global reference imagemaximum number of candidates for global reference image</p></dd><dt><span class="term">-S, --cost-series=image:cost=[ngf:eval=ds]; factory</span></dt><dd><p>Const function to use for the analysis of the seriesConst function to use for the analysis of the series. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a></p></dd><dt><span class="term">--ref-idx=STRING</span></dt><dd><p>save reference index number to this file</p></dd><dt><span class="term">-R, --global-reference=-1; int</span></dt><dd><p>save reference index number to this filesave reference index number to this file</p></dd><dt><span class="term">-D, --max-subset-delta=0; ulong</span></dt><dd><p>Maximum delta between two elements of the prealigned subsetMaximum delta between two elements of the prealigned subset</p></dd></dl></div><h4><a name="idp5484"></a>
Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-O, --optimizer=gsl:opt=gd,step=0.01; 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">--refiner=</span></dt><dd><p>optimizer used for additional minimizationoptimizer used for additional 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">-l, --mr-levels=3; ulong</span></dt><dd><p>multi-resolution levelsmulti-resolution levels</p></dd><dt><span class="term">-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; 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">-1, --cost-subset=image:cost=[ngf:eval=ds]; factory</span></dt><dd><p>Cost function for registration during the subset registrationCost function for registration during the subset registration. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a></p></dd><dt><span class="term">-2, --cost-final=image:cost=ssd; factory</span></dt><dd><p>Cost function for registration during the final registrationCost function for registration during the final registration. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a></p></dd></dl></div><h4><a name="idp5515"></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="idp5566"></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="idp5572"></a>Example:</h4><p>Register the perfusion series given in 'segment.set'. Skip two images at the beginning, usa spline transformation of a knot rate 16 pixels, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'.
</p><pre class="screen">mia-2dmyoperiodic-nonrigid   -i segment.set -o registered.set -k 2 -d 5 -f spline:rate=16,penalty=[divcurl:weight=5]</pre><h4><a name="idp5575"></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="Secmia2dmyomilles.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="Secmia2dmyopgtnonrigid.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyomilles </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyopgt-nonrigid</td></tr></table></div></body></html>
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