/usr/share/doc/mia-2.4/userref/Secmia3dprealignnonrigid.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 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3dprealign-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="SecRegistrationofseriesof3Dimages.html" title="Registration of series of 3D images"><link rel="prev" href="Secmia3dmotioncompicanonrigid.html" title="mia-3dmotioncompica-nonrigid"><link rel="next" href="Secmia3dserialnonrigid.html" title="mia-3dserial-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-3dprealign-nonrigid</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><th width="60%" align="center">Registration of series of 3D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia3dserialnonrigid.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3dprealignnonrigid"></a>mia-3dprealign-nonrigid</h3></div></div></div><h4><a name="idp12647"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3dprealign-nonrigid</code> {-i <em class="replaceable"><code>io</code></em>} {-o <em class="replaceable"><code>io</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp12656"></a>Description:</h4><p>This program runs the non-rigid registration of an image series by first registering an already aligned subset of the images to one reference, and then by registering the remaining images by using synthetic references. The is a 3D version of G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.</p><h4><a name="idp12658"></a>Options:</h4><h4><a name="idp12659"></a>
File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); io</span></dt><dd><p>input images following the naming pattern nameXXXX.ext. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">-o, --out-file=(output, required); io</span></dt><dd><p>file name base for registered files given as C-format string. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">--save-references</span></dt><dd><p>Save synthetic references to files refXXXX.v</p></dd></dl></div><h4><a name="idp12675"></a>
Preconditions & Preprocessing</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-k, --skip=0; ulong</span></dt><dd><p>Skip images at the begin of the seriesSkip images at the begin of the series</p></dd><dt><span class="term">--preskip=20; ulong</span></dt><dd><p>Skip images at the beginning+skip of the series when searching for high contrats imageSkip images at the beginning+skip of the series when searching for high contrats image</p></dd><dt><span class="term">--postskip=2; ulong</span></dt><dd><p>Skip images at the end of the series when searching for high contrats imageSkip images at the end of the series when searching for high contrats image</p></dd><dt><span class="term">--max-candidates=20; ulong</span></dt><dd><p>maximum number of candidates for global reference imagemaximum number of candidates for global reference image</p></dd><dt><span class="term">-S, --cost-series=image:cost=[ngf:eval=ds]; factory</span></dt><dd><p>Const function to use for the analysis of the seriesConst function to use for the analysis of the series. For supported plug-ins see <a class="xref" href="SecPlugintype3dimagefullcost.html" title="Plugin type: 3dimage/fullcost">Plugin type: 3dimage/fullcost</a></p></dd><dt><span class="term">--ref-idx=STRING</span></dt><dd><p>save reference index number to this file</p></dd><dt><span class="term">-R, --global-reference=-1; int</span></dt><dd><p>save reference index number to this filesave reference index number to this file</p></dd><dt><span class="term">-D, --max-subset-delta=0; ulong</span></dt><dd><p>Maximum delta between two elements of the prealigned subsetMaximum delta between two elements of the prealigned subset</p></dd></dl></div><h4><a name="idp12710"></a>
Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-O, --optimizer=gsl:opt=gd,step=0.01; 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, --mr-levels=3; ulong</span></dt><dd><p>multi-resolution levelsmulti-resolution levels</p></dd><dt><span class="term">-f, --transForm=spline; factory</span></dt><dd><p>transformation typetransformation type. For supported plug-ins see <a class="xref" href="SecPlugintype3dimagetransform.html" title="Plugin type: 3dimage/transform">Plugin type: 3dimage/transform</a></p></dd><dt><span class="term">-1, --cost-subset=image:cost=[ngf:eval=ds]; factory</span></dt><dd><p>Cost function for registration during the subset registrationCost function for registration during the subset registration. For supported plug-ins see <a class="xref" href="SecPlugintype3dimagefullcost.html" title="Plugin type: 3dimage/fullcost">Plugin type: 3dimage/fullcost</a></p></dd><dt><span class="term">-2, --cost-final=image:cost=ssd; factory</span></dt><dd><p>Cost function for registration during the final registrationCost function for registration during the final registration. For supported plug-ins see <a class="xref" href="SecPlugintype3dimagefullcost.html" title="Plugin type: 3dimage/fullcost">Plugin type: 3dimage/fullcost</a></p></dd></dl></div><h4><a name="idp12736"></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="idp12787"></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="idp12793"></a>Example:</h4><p>Register the image series given by images imageXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel, skipping two images at the beginning and using normalized gradient fields as initial cost measure and SSD as final measure. Penalize the transformation by using divcurl with aweight of 2.0. As optimizer an nlopt based newton method is used.</p><pre class="screen">mia-3dprealign-nonrigid mia-3dprealign-nonrigid -i imageXXXX.v -o registered -t vista -k 2-F spline:rate=16,penalty=[divcurl:weight=2] -1 image:cost=[ngf:eval=ds] -2 image:cost=ssd -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a name="idp12796"></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="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia3dserialnonrigid.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dmotioncompica-nonrigid </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dserial-nonrigid</td></tr></table></div></body></html>
|