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1 2 3 4 5 6 7 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid2</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="Secmia2dmyoicanonrigidparallel.html" title="mia-2dmyoica-nonrigid-parallel"><link rel="next" href="Secmia2dmyoicapgt.html" title="mia-2dmyoicapgt"></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-nonrigid2</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyoicanonrigidparallel.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="Secmia2dmyoicapgt.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyoicanonrigid2"></a>mia-2dmyoica-nonrigid2</h3></div></div></div><h4><a name="idp4845"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoica-nonrigid2</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="idp4854"></a>Description:</h4><p>This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation
Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.</p><h4><a name="idp4856"></a>Options:</h4><h4><a name="idp4857"></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 segmentation feature images and initial ICA mixing matrix</p></dd></dl></div><h4><a name="idp4879"></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>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">-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></dl></div><h4><a name="idp4923"></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">-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, --imageweight=1; double</span></dt><dd><p>image cost weightimage cost weight</p></dd><dt><span class="term">-p, --interpolator=bspline:d=3; factory</span></dt><dd><p>image interpolator kernelimage interpolator kernel. For supported plug-ins see <a class="xref" href="SecPlugintype1dsplinekernel.html" title="Plugin type: 1d/splinekernel">Plugin type: 1d/splinekernel</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=3; ulong</span></dt><dd><p>registration passesregistration passes</p></dd></dl></div><h4><a name="idp4963"></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="idp5014"></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="idp5020"></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-nonrigid2 -i segment.set -o registered.set -k 2</pre><h4><a name="idp5023"></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="Secmia2dmyoicanonrigidparallel.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="Secmia2dmyoicapgt.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyoica-nonrigid-parallel </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyoicapgt</td></tr></table></div></body></html>
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