/usr/share/doc/mia-2.4/userref/Secmia2dmyoserialnonrigid.html is in mia-tools-doc 2.4.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoserial-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="Secmia2dmyopgtnonrigid.html" title="mia-2dmyopgt-nonrigid"><link rel="next" href="Secmia2dmyosetall2onenonrigid.html" title="mia-2dmyoset-all2one-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-2dmyoserial-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyopgtnonrigid.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="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyoserialnonrigid"></a>mia-2dmyoserial-nonrigid</h3></div></div></div><h4><a name="idp5722"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoserial-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>
...] [
<em class="replaceable"><code>
<a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a>
</code></em>
...]</p></div><h4><a name="idp5734"></a>Description:</h4><p>This program runs the non-rigid motion compensation registration of an perfusion image series. The registration is run in a serial manner, this is, only images in temporal succession are registered, and the obtained transformations are applied accumulated to reach full registration. See e.g. Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI ". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008, doi:10.1109/IEMBS.2008.4649933,</p><h4><a name="idp5736"></a>Options:</h4><h4><a name="idp5737"></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></dl></div><h4><a name="idp5751"></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">-l, --mg-levels=3; ulong</span></dt><dd><p>multi-resolution levelsmulti-resolution levels</p></dd><dt><span class="term">-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory</span></dt><dd><p>transformation typetransformation type. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagetransform.html" title="Plugin type: 2dimage/transform">Plugin type: 2dimage/transform</a></p></dd><dt><span class="term">-r, --ref=-1; int</span></dt><dd><p>reference frame (-1 == use image in the middle)reference frame (-1 == use image in the middle)</p></dd><dt><span class="term">-k, --skip=0; int</span></dt><dd><p>skip registration of these images at the beginning of the seriesskip registration of these images at the beginning of the series</p></dd></dl></div><h4><a name="idp5775"></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="idp5826"></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="idp5832"></a>Example:</h4><p>Register the perfusion series given in 'segment.set' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'.
</p><pre class="screen">mia-2dmyoserial-nonrigid -i segment.set -o registered.set -k 2 -r 30 image:cost=mi -f spline:rate=5,penalty=[divcurl:weight=5]</pre><h4><a name="idp5835"></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="Secmia2dmyopgtnonrigid.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="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyopgt-nonrigid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyoset-all2one-nonrigid</td></tr></table></div></body></html>
|