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1 2 3 4 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyocard-ica</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="SecToolsforMyocardialPerfusionAnalysis.html" title="Tools for Myocardial Perfusion Analysis"><link rel="prev" href="SecToolsforMyocardialPerfusionAnalysis.html" title="Tools for Myocardial Perfusion Analysis"><link rel="next" href="Secmia2dmyocardicaseries.html" title="mia-2dmyocard-icaseries"></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-2dmyocard-ica</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><th width="60%" align="center">Tools for Myocardial Perfusion Analysis</th><td width="20%" align="right"> <a accesskey="n" href="Secmia2dmyocardicaseries.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyocardica"></a>mia-2dmyocard-ica</h3></div></div></div><h4><a name="idp6242"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyocard-ica</code> {-i <em class="replaceable"><code>io</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp6249"></a>Description:</h4><p>This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries.
This program is essentially used to test different options on how to run the ICA forreference image creation.</p><h4><a name="idp6251"></a>Options:</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-base=(input, required); io</span></dt><dd><p>input file name ofolloing pattern nameXXXX.ext X=numbers. For supported file types see <a class="xref" href="SecPlugintype2dimageio.html" title="Plugin type: 2dimage/io">Plugin type: 2dimage/io</a></p></dd><dt><span class="term">--coefs=STRING</span></dt><dd><p>output mixing coefficients to this file</p></dd><dt><span class="term">-o, --out-base=(output); string</span></dt><dd><p>output file name base</p></dd><dt><span class="term">-t, --type=exr; set</span></dt><dd><p>output file type<td align="left" valign="top"> Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )</td></p></dd><dt><span class="term">-k, --skip=2; ulong</span></dt><dd><p>skip images at beginning of seriesskip images at beginning of series</p></dd><dt><span class="term">-e, --end=60; ulong</span></dt><dd><p>last image in serieslast image in series</p></dd><dt><span class="term">-C, --components=0; ulong</span></dt><dd><p>nr. of components, 0=estimate automaticallynr. of components, 0=estimate automatically</p></dd><dt><span class="term">-m, --strip-mean</span></dt><dd><p>strip mean image from series</p></dd><dt><span class="term">-f, --save-features=STRING</span></dt><dd><p>save feature image</p></dd><dt><span class="term">-p, --strip-periodic</span></dt><dd><p>strip only periodic component</p></dd><dt><span class="term">-x, --max-ica-iterations=0; int</span></dt><dd><p>max ICA solver iterationsmax ICA solver iterations</p></dd><dt><span class="term">-n, --ica-normalize</span></dt><dd><p>ica_normalize feature images</p></dd><dt><span class="term">--all-features=STRING</span></dt><dd><p>save all feature images to</p></dd><dt><span class="term">-L, --LV-crop-amp=0; float</span></dt><dd><p>LV crop mask amplification, 0.0 = don't cropLV crop mask amplification, 0.0 = don't crop</p></dd></dl></div><h4><a name="idp6311"></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="idp6362"></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="idp6368"></a>Example:</h4><p>Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independend components, mean stripping, normalizing, and skipping 2 images.</p><pre class="screen">mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n</pre><h4><a name="idp6371"></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="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia2dmyocardicaseries.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Tools for Myocardial Perfusion Analysis </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyocard-icaseries</td></tr></table></div></body></html>
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