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1 2 3 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3dbrainextractT1</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="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html" title="Analysis, filtering, combining, and segmentation of 3D images"><link rel="prev" href="Secmia3dbinarycombine.html" title="mia-3dbinarycombine"><link rel="next" href="Secmia3dcombineimageseries.html" title="mia-3dcombine-imageseries"></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-3dbrainextractT1</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dbinarycombine.html">Prev</a> </td><th width="60%" align="center">Analysis, filtering, combining, and segmentation of 3D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia3dcombineimageseries.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3dbrainextractT1"></a>mia-3dbrainextractT1</h3></div></div></div><h4><a name="idp9024"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3dbrainextractT1</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="idp9033"></a>Description:</h4><p>This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images.</p><h4><a name="idp9035"></a>Options:</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); io</span></dt><dd><p>input image(s) to be segmented. 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>brain mask. 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">-n, --no-of-classes=3; int</span></dt><dd><p>number of classesnumber of classes</p></dd><dt><span class="term">-w, --wm-class=2; int</span></dt><dd><p>index of white matterindex of white matter</p></dd><dt><span class="term">-p, --wm-prob=0.7; float</span></dt><dd><p>white matter class probability for initial mask creationwhite matter class probability for initial mask creation</p></dd><dt><span class="term">-t, --grow-threshold=20; int</span></dt><dd><p>intensity threshold for region growingintensity threshold for region growing</p></dd><dt><span class="term">--grow-shape=18n; stringSTRING</span></dt><dd><p>neighbourhood mask region growing</p></dd></dl></div><h4><a name="idp9067"></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="idp9118"></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="idp9124"></a>Example:</h4><p>Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v</p><pre class="screen">mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v</pre><h4><a name="idp9127"></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="Secmia3dbinarycombine.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia3dcombineimageseries.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dbinarycombine </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dcombine-imageseries</td></tr></table></div></body></html>
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