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1 2 3 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3dmotioncompica-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="SecRegistrationofseriesof3Dimages.html" title="Registration of series of 3D images"><link rel="prev" href="Secmia3dmany2onenonrigid.html" title="mia-3dmany2one-nonrigid"><link rel="next" href="Secmia3dprealignnonrigid.html" title="mia-3dprealign-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-3dmotioncompica-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dmany2onenonrigid.html">Prev</a> </td><th width="60%" align="center">Registration of series of 3D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia3dprealignnonrigid.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3dmotioncompicanonrigid"></a>mia-3dmotioncompica-nonrigid</h3></div></div></div><h4><a name="idp12487"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3dmotioncompica-nonrigid</code> {-i <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="idp12496"></a>Description:</h4><p>This program implements a 3D version of the motion compensation algorithm described in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004.</p><h4><a name="idp12498"></a>Options:</h4><h4><a name="idp12499"></a>File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); io</span></dt><dd><p>input images of consecutively numbered filed (nameXXXX.ext). 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, --out-file=(output, required); io</span></dt><dd><p>output image name (as C format string including a %04d in order to define the file numbering). 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">--save-refs=STRING</span></dt><dd><p>save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'</p></dd><dt><span class="term">--save-regs=STRING</span></dt><dd><p>save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'</p></dd><dt><span class="term">--save-coeffs=STRING</span></dt><dd><p>save mixing matrix to a text file</p></dd><dt><span class="term">--save-features=STRING</span></dt><dd><p>save feature images as PNG</p></dd></dl></div><h4><a name="idp12527"></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="idp12578"></a>ICA</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-C, --components=0; ulong</span></dt><dd><p>ICA components 0 = automatic estimationICA components 0 = automatic estimation</p></dd><dt><span class="term">--no-normalize</span></dt><dd><p>don't normalized ICs</p></dd><dt><span class="term">--no-meanstrip</span></dt><dd><p>don't strip the mean from the mixing curves</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><dt><span class="term">-m, --max-ica-iter=400; ulong</span></dt><dd><p>maximum number of iterations in ICAmaximum number of iterations in ICA</p></dd></dl></div><h4><a name="idp12600"></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="idp12606"></a>Registration</h4><div class="variablelist"><dl class="variablelist compact"><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">-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, --imagecost=image:weight=1,cost=ssd,; stringSTRING</span></dt><dd><p>image cost</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=3; ulong</span></dt><dd><p>registration passesregistration passes</p></dd></dl></div><h4><a name="idp12640"></a>Example:</h4><p>Register the perfusion series given in images imagesXXXX.v by using 4-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v </p><pre class="screen">mia-3dmotioncompica-nonrigid -i images0000.v -o registered%04d.v -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a name="idp12643"></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="Secmia3dmany2onenonrigid.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia3dprealignnonrigid.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dmany2one-nonrigid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dprealign-nonrigid</td></tr></table></div></body></html>
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