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1 2 3 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3dfluid-syn-registration</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="SecRegistrationComparisonandTransformationof3Dimages.html" title="Registration, Comparison, and Transformation of 3D images"><link rel="prev" href="Secmia3dfluid.html" title="mia-3dfluid"><link rel="next" href="Secmia3dforce.html" title="mia-3dforce"></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-3dfluid-syn-registration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dfluid.html">Prev</a> </td><th width="60%" align="center">Registration, Comparison, and Transformation of 3D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia3dforce.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3dfluidsynregistration"></a>mia-3dfluid-syn-registration</h3></div></div></div><h4><a name="idp11680"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3dfluid-syn-registration</code> {-i <em class="replaceable"><code>io</code></em>} {-r <em class="replaceable"><code>io</code></em>} {-o <em class="replaceable"><code>io</code></em>} {-O <em class="replaceable"><code>io</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp11693"></a>Description:</h4><p>This program implements the registration of two gray scale 3D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.</p><h4><a name="idp11695"></a>Options:</h4><h4><a name="idp11696"></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="idp11747"></a>IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-image=(input, required); io</span></dt><dd><p>test image. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">-r, --ref-image=(input, required); io</span></dt><dd><p>reference image. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">-o, --transform=(output, required); io</span></dt><dd><p>output transformation. For supported file types see <a class="xref" href="SecPlugintype3dtransformio.html" title="Plugin type: 3dtransform/io">Plugin type: 3dtransform/io</a></p></dd><dt><span class="term">-O, --inverse-transform=(output, required); io</span></dt><dd><p>inverse output transformation. For supported file types see <a class="xref" href="SecPlugintype3dtransformio.html" title="Plugin type: 3dtransform/io">Plugin type: 3dtransform/io</a></p></dd></dl></div><h4><a name="idp11769"></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).</p></dd></dl></div><h4><a name="idp11775"></a>Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-l, --mg-levels=3; uint</span></dt><dd><p>Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.</p></dd><dt><span class="term">-S, --step=0.25; float in (0, 0.5]</span></dt><dd><p>Initial step size for all levels</p></dd><dt><span class="term">-c, --cost=ssd; factory</span></dt><dd><p>Image similarity function to be minimized. For supported plug-ins see <a class="xref" href="SecPlugintype3dimagecost.html" title="Plugin type: 3dimage/cost">Plugin type: 3dimage/cost</a></p></dd><dt><span class="term">-R, --regularizer=sor:kernel=fluid,maxiter=50; factory</span></dt><dd><p>Regularization for the force to transformation update. For supported plug-ins see <a class="xref" href="SecPlugintype3dvfregularizer.html" title="Plugin type: 3dvf/regularizer">Plugin type: 3dvf/regularizer</a></p></dd><dt><span class="term">-T, --conv-test-interval= in [4, 40]</span></dt><dd><p>Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.</p></dd><dt><span class="term">-D, --stop-decline-rate= in [0, inf)</span></dt><dd><p>Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.</p></dd><dt><span class="term">-C, --stop-cost=</span></dt><dd><p>Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.</p></dd><dt><span class="term">-I, --iter= in [4, inf)</span></dt><dd><p>Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.</p></dd></dl></div><h4><a name="idp11811"></a>Example:</h4><p>Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.</p><pre class="screen">mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v -l 3 ssd</pre><h4><a name="idp11814"></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="Secmia3dfluid.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia3dforce.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dfluid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dforce</td></tr></table></div></body></html>
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