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1 2 3 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoica-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="Secmia2dmyoicafull.html" title="mia-2dmyoica-full"><link rel="next" href="Secmia2dmyoicanonrigidparallel.html" title="mia-2dmyoica-nonrigid-parallel"></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-2dmyoica-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyoicafull.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="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyoicanonrigid"></a>mia-2dmyoica-nonrigid</h3></div></div></div><h4><a name="idp4606"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoica-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="idp4615"></a>Description:</h4><p>This program implements 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="idp4617"></a>Options:</h4><h4><a name="idp4618"></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-cropped=STRING</span></dt><dd><p>save cropped set to this file</p></dd><dt><span class="term">--save-feature=STRING</span></dt><dd><p>save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.</p></dd><dt><span class="term">--save-refs=STRING</span></dt><dd><p>save synthetic reference images</p></dd><dt><span class="term">--save-regs=STRING</span></dt><dd><p>save intermediate registered images</p></dd></dl></div><h4><a name="idp4648"></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="idp4699"></a>ICA</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">--fastica=internal; factory</span></dt><dd><p>FastICA implementationto be used. For supported plug-ins see <a class="xref" href="SecPlugintypefasticaimplementation.html" title="Plugin type: fastica/implementation">Plugin type: fastica/implementation</a></p></dd><dt><span class="term">-C, --components=0; ulong</span></dt><dd><p>ICA components 0 = automatic estimation</p></dd><dt><span class="term">--normalize</span></dt><dd><p>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">-s, --segscale=0; float</span></dt><dd><p>segment and scale the crop box around the LV (0=no segmentation)</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 modalities</p></dd><dt><span class="term">-m, --max-ica-iter=400; ulong</span></dt><dd><p>maximum number of iterations in ICA</p></dd><dt><span class="term">-E, --segmethod=features; dict</span></dt><dd><p>Segmentation method</p><div class="informaltable"><table class="informaltable" border="0"><colgroup><col class="c1"><col class="c2"></colgroup><tbody><tr><td align="left" valign="top">delta-peak:</td><td align="left" valign="top">difference of the peak enhancement images</td></tr><tr><td align="left" valign="top">features:</td><td align="left" valign="top">feature images</td></tr><tr><td align="left" valign="top">delta-feature:</td><td align="left" valign="top">difference of the feature images</td></tr></tbody></table></div></dd><dt><span class="term">-b, --min-breathing-frequency=-1; float</span></dt><dd><p>minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.</p></dd></dl></div><h4><a name="idp4752"></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="idp4758"></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 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">-R, --refiner=</span></dt><dd><p>optimizer used for refinement after the main optimizer was called. 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=16; double</span></dt><dd><p>start coefficinet rate in spines, gets divided by --c-rate-divider with every pass</p></dd><dt><span class="term">--c-rate-divider=2; double</span></dt><dd><p>cofficient rate divider for each pass</p></dd><dt><span class="term">-d, --start-divcurl=10; double</span></dt><dd><p>start divcurl weight, gets divided by --divcurl-divider with every pass</p></dd><dt><span class="term">--divcurl-divider=2; double</span></dt><dd><p>divcurl weight scaling with each new pass</p></dd><dt><span class="term">-w, --imagecost=image:weight=1,cost=ssd; factory</span></dt><dd><p>image cost. 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">-l, --mg-levels=3; ulong</span></dt><dd><p>multi-resolution levels</p></dd><dt><span class="term">-P, --passes=5; ulong</span></dt><dd><p>registration passes</p></dd></dl></div><h4><a name="idp4799"></a>Example:</h4><p>Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.</p><pre class="screen">mia-2dmyoica-nonrigid -i segment.set -o registered.set -k 2</pre><h4><a name="idp4802"></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="Secmia2dmyoicafull.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="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyoica-full </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyoica-nonrigid-parallel</td></tr></table></div></body></html>
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