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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="idp4460"></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="idp4469"></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="idp4471"></a>Options:</h4><h4><a name="idp4472"></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="idp4502"></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="idp4553"></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">--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)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 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><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.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="idp4601"></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="idp4607"></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 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">-R, --refiner=</span></dt><dd><p>optimizer used for refinement after the main optimizer was calledoptimizer 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 passstart 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 passcofficient 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 passstart 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 passdivcurl 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 costimage 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 levelsmulti-resolution levels</p></dd><dt><span class="term">-P, --passes=5; ulong</span></dt><dd><p>registration passesregistration passes</p></dd></dl></div><h4><a name="idp4648"></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="idp4651"></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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