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‎command_line_example.html

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‎dev.php

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<div class="selected_heading">
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Developer
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</div>
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<div class="part_content">
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<center><img src="img/undconstand.gif"></center>
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</div>
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‎doc.php

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<div class="selected_heading">
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Documentation
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</div>
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<div class="part_content">
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<center><img src="img/undconstand.gif"></center>
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</div>
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<div class="part_title">
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<a href="ftp://ftp-sop.inria.fr/odyssee/Publications/2010/OpenMEEGHandsOnTutorial2010.pdf"> Hands-on Tutorial</a>
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</div>
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<div class="part_content">
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‎doc/OpenMEEG_BiomagSatellite_slides.pdf

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‎doc/OpenMEEG_tutorial_v2.pdf

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‎doc/openmeeg_tutorial.pdf

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‎documentation.php

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<div class="selected_heading">
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Documentation
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</div>
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<div class="part_title">
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OpenMEEG 2.0
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</div>
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<div class="part_content">
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Tutorial <a href="doc/OpenMEEG_tutorial_v2.pdf">[PDF]</a>
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</div>
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<div class="part_title">
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OpenMEEG 1.0
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</div>
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<div class="part_content">
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Tutorial <a href="doc/openmeeg_tutorial.pdf">[PDF]</a>
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</div>
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<div class="part_title">
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More
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</div>
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<div class="part_content">
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The <a href="doc/OpenMEEG_BiomagSatellite_slides.pdf">slides on OpenMEEG</a>
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presented at <a href="http://www.biomag2010.org/" title="News - Biomag 2010">
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Biomag 2010</a> in Dubrovnik.
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</div>
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<div class="part_content">
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<p>The following publication can also be used for an introduction to OpenMEEG (version 2.0):</p>
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A. Gramfort, T. Papadopoulo, E. Olivi, M. Clerc.,
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<strong>
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OpenMEEG: opensource software for quasistatic bioelectromagnetics,
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</strong>
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<a
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href="http://www.biomedical-engineering-online.com/content/9/1/45"
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title="OpenMEEG: opensource software for quasistatic bioelectromagnetics"> BioMedical Engineering OnLine 45:9, 2010</a>
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</div>
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‎download.php

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<div class="selected_heading">
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Downloads
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</div>
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<div class="part_title">
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Description
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</div>
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<div class="part_content">
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OpenMEEG software can be used in command line interface or with a user friendly interface thanks to <a href="http://brainvisa.info/index_f.html" target="_blank">BrainVisa</a>/<a href="http://cogimage.dsi.cnrs.fr/logiciels" target="_blank">BrainStorm</a> integration.<br>
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In any case, it is necessary to download and install the <a href="#OpenMEEG">OpenMEEG C++ package</a>. For the BrainVisa/BrainStorm interface only, it is also necessary to download and install the python package <a href="#OpenMEEGForBV">OpenMEEG for BV</a>. <br/><br/>
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Note that the command line interfaceis intended for advanced users only.
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</div>
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<div class="part_title">
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<a name="OpenMEEG"></a>
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OpenMEEG C++ Package
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</div>
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<div class="part_content">
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RPMs <a href=""><img src="img/down.png" width=2% height=2% ></a> <br/>
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See <a href="">instructions to install RPMs</a><br/><br/>
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Source Code <a href=""><img src="img/down.png" width=2% height=2% ></a> <br/>
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You need the <a href="#CMake">CMake</a> tool to compile the source code. <br/>
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See <a href="">instructions to compile and install source code</a><br/><br/>
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Libraries <a href=""><img src="img/down.png" width=2% height=2% ></a> <br/>
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See <a href="">instructions about libraries</a><br/> <br/>
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</div>
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<div class="part_title">
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<a name="OpenMEEGForBV"></a>
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OpenMEEG BrainVisa Interface
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</div>
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<div class="part_content">
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Available soon...<br/>
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This interface is structured for BrainVisa3.1. <br/><br/>
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RPMs <br/>
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See instructions to install RPMs <br/><br/>
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Source Code <br/>
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See instructions to install from source code <br/><br/>
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</div>
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<div class="part_title">
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<a name="CMake"></a>
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The CMake's tool suite
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</div>
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<div class="part_content">
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<div class="part_subtitle">What is CMake ? </div>
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CMake is a cross-plateform for makefile generation. For more information, see <a href="http://www.cmake.org/HTML/Index.html" target="_blank">the official web site</a> (or its <a href="http://www.cmake.org/Wiki/CMake" target="_blank">wiki section</a>) and <a href="http://en.wikipedia.org/wiki/CMake" target="_blank">the wikipedia page</a>.
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<div class="part_subtitle">Why did we choose it ? </div>
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It creates makefiles for any user system and enables compilation on linux, mac and windows systems. Moreover, the CMake tool suite supplies CTest for automatic test generation that is very useful for developpers, and CPack for distibution via rpm packaging.
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<div class="part_subtitle">Download CMake </div>
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Access to the <a href="http://www.cmake.org/HTML/Download.html" target="_blank">CMake download page</a>
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</div>
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‎examples/bash_script.html

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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN"
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"http://www.w3.org/TR/html4/strict.dtd">
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<html>
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<head>
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<title></title>
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<meta http-equiv="content-type" content="text/html; charset=latin1">
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<style type="text/css">
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td.linenos { background-color: #f0f0f0; padding-right: 10px; }
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span.lineno { background-color: #f0f0f0; padding: 0 5px 0 5px; }
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pre { line-height: 125%; }
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body .hll { background-color: #ffffcc }
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body { background: #f8f8f8; }
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body .c { color: #408080; font-style: italic } /* Comment */
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body .err { border: 1px solid #FF0000 } /* Error */
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body .gt { color: #0040D0 } /* Generic.Traceback */
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body .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
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body .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
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body .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
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body .kp { color: #008000 } /* Keyword.Pseudo */
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body .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
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body .kt { color: #B00040 } /* Keyword.Type */
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body .m { color: #666666 } /* Literal.Number */
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body .s { color: #BA2121 } /* Literal.String */
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body .na { color: #7D9029 } /* Name.Attribute */
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body .nc { color: #0000FF; font-weight: bold } /* Name.Class */
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body .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
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body .nt { color: #008000; font-weight: bold } /* Name.Tag */
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body .nv { color: #19177C } /* Name.Variable */
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body .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
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body .w { color: #bbbbbb } /* Text.Whitespace */
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body .mh { color: #666666 } /* Literal.Number.Hex */
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body .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
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body .s2 { color: #BA2121 } /* Literal.String.Double */
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body .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */
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body .il { color: #666666 } /* Literal.Number.Integer.Long */
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</style>
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</head>
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<body>
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<h2></h2>
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<div class="highlight"><pre><span class="c">#!/usr/bin/env bash</span>
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<span class="nv">GEOMETRY</span><span class="o">=</span>head_model.geom
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<span class="nv">CONDUCTIVITIES</span><span class="o">=</span>head_model.cond
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<span class="nv">DIPOLES</span><span class="o">=</span>cortex_dipoles.txt
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<span class="nv">EEG_ELECTRODES</span><span class="o">=</span>eeg_channels_locations.txt
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<span class="nv">SQUIDS</span><span class="o">=</span>meg_channels_locations.squids
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<span class="nv">INTERNAL_ELECTRODES</span><span class="o">=</span>internal_electrodes_locations.txt
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<span class="c"># Leadfields</span>
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<span class="nv">EEG_LEADFIELD</span><span class="o">=</span>eeg_leadfield.mat
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<span class="nv">MEG_LEADFIELD</span><span class="o">=</span>meg_leadfield.mat
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<span class="nv">EIT_LEADFIELD</span><span class="o">=</span>eit_leadfield.mat
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<span class="nv">IP_LEADFIELD</span><span class="o">=</span>ip_leadfield.mat
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<span class="c"># Name temporary matrices</span>
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<span class="nv">HM</span><span class="o">=</span>tmp/tmp.hm <span class="c"># For EEG and MEG</span>
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<span class="nv">HMINV</span><span class="o">=</span>tmp/tmp.hm_inv <span class="c"># For EEG and MEG</span>
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<span class="nv">DSM</span><span class="o">=</span>tmp/tmp.dsm <span class="c"># For EEG and MEG</span>
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<span class="nv">H2EM</span><span class="o">=</span>tmp/tmp.h2em <span class="c"># For EEG</span>
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<span class="nv">H2MM</span><span class="o">=</span>tmp/tmp.h2mm <span class="c"># For MEG</span>
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<span class="nv">DS2MEG</span><span class="o">=</span>tmp/tmp.ds2mm <span class="c"># For MEG</span>
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<span class="nv">EITSM</span><span class="o">=</span>tmp/tmp.eitsm <span class="c"># For EIT</span>
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<span class="nv">IPHM</span><span class="o">=</span>tmp/tmp.iphm <span class="c"># For IP</span>
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<span class="nv">IPSM</span><span class="o">=</span>tmp/tmp.ipsm <span class="c"># For IP</span>
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mkdir -p tmp
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<span class="c"># Compute EEG gain matrix</span>
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om_assemble -HM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">HM</span><span class="k">}</span>
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om_minverser <span class="k">${</span><span class="nv">HM</span><span class="k">}</span> <span class="k">${</span><span class="nv">HMINV</span><span class="k">}</span>
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om_assemble -DSM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">DIPOLES</span><span class="k">}</span> <span class="k">${</span><span class="nv">DSM</span><span class="k">}</span>
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om_assemble -H2EM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">EEG_ELECTRODES</span><span class="k">}</span> <span class="k">${</span><span class="nv">H2EM</span><span class="k">}</span>
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om_gain -EEG <span class="k">${</span><span class="nv">HMINV</span><span class="k">}</span> <span class="k">${</span><span class="nv">DSM</span><span class="k">}</span> <span class="k">${</span><span class="nv">H2EM</span><span class="k">}</span> <span class="k">${</span><span class="nv">EEG_LEADFIELD</span><span class="k">}</span>
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<span class="c"># Compute MEG gain matrix</span>
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om_assemble -H2MM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">SQUIDS</span><span class="k">}</span> <span class="k">${</span><span class="nv">H2MM</span><span class="k">}</span>
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om_assemble -DS2MM <span class="k">${</span><span class="nv">DIPOLES</span><span class="k">}</span> <span class="k">${</span><span class="nv">SQUIDS</span><span class="k">}</span> <span class="k">${</span><span class="nv">DS2MEG</span><span class="k">}</span>
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om_gain -MEG <span class="k">${</span><span class="nv">HMINV</span><span class="k">}</span> <span class="k">${</span><span class="nv">DSM</span><span class="k">}</span> <span class="k">${</span><span class="nv">H2MM</span><span class="k">}</span> <span class="k">${</span><span class="nv">DS2MEG</span><span class="k">}</span> <span class="k">${</span><span class="nv">MEG_LEADFIELD</span><span class="k">}</span>
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<span class="c"># Compute EIT gain matrix</span>
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om_assemble -EITSM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">EEG_ELECTRODES</span><span class="k">}</span> <span class="k">${</span><span class="nv">EITSM</span><span class="k">}</span>
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om_gain -EEG <span class="k">${</span><span class="nv">HMINV</span><span class="k">}</span> <span class="k">${</span><span class="nv">EITSM</span><span class="k">}</span> <span class="k">${</span><span class="nv">H2EM</span><span class="k">}</span> <span class="k">${</span><span class="nv">EIT_LEADFIELD</span><span class="k">}</span>
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<span class="c"># Compute Internal Potential</span>
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om_assemble -H2IPM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">INTERNAL_ELECTRODES</span><span class="k">}</span> <span class="k">${</span><span class="nv">IPHM</span><span class="k">}</span>
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om_assemble -DS2IPM <span class="k">${</span><span class="nv">GEOMETRY</span><span class="k">}</span> <span class="k">${</span><span class="nv">CONDUCTIVITIES</span><span class="k">}</span> <span class="k">${</span><span class="nv">DIPOLES</span><span class="k">}</span> <span class="k">${</span><span class="nv">INTERNAL_ELECTRODES</span><span class="k">}</span> <span class="k">${</span><span class="nv">IPSM</span><span class="k">}</span>
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om_gain -IP <span class="k">${</span><span class="nv">HMINV</span><span class="k">}</span> <span class="k">${</span><span class="nv">DSM</span><span class="k">}</span> <span class="k">${</span><span class="nv">IPHM</span><span class="k">}</span> <span class="k">${</span><span class="nv">IPSM</span><span class="k">}</span> <span class="k">${</span><span class="nv">IP_LEADFIELD</span><span class="k">}</span>
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</pre></div>
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</body>
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</html>

‎examples/compute_leadfields.bat

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set GEOMETRY=head_model.geom
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set CONDUCTIVITIES=head_model.cond
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set DIPOLES=cortex_dipoles_small.txt
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set EEG_ELECTRODES=eeg_channels_locations.txt
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set SQUIDS=meg_channels_locations.squids
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set INTERNAL_ELECTRODES=internal_electrodes_locations.txt
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rem Leadfields
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set EEG_LEADFIELD=eeg_leadfield.mat
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set MEG_LEADFIELD=meg_leadfield.mat
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set EIT_LEADFIELD=eit_leadfield.mat
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set IP_LEADFIELD=ip_leadfield.mat
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rem Name temporary matrices
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rem For EEG and MEG
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set HM=tmp\tmp.hm
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set HMINV=tmp\tmp.hm_inv
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set DSM=tmp\tmp.dsm
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rem For EEG
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set H2EM=tmp\tmp.h2em
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rem for MEG
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set H2MM=tmp\tmp.h2mm
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set DS2MEG=tmp\tmp.ds2mm
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rem for EIT
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set EITSM=tmp\tmp.eitsm
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rem for IP (Internal Potential)
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set IPHM=tmp\tmp.iphm
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set IPSM=tmp\tmp.ipsm
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mkdir tmp
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rem Compute EEG gain matrix
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om_assemble -HM %GEOMETRY% %CONDUCTIVITIES% %HM%
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om_minverser %HM% %HMINV%
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om_assemble -DSM %GEOMETRY% %CONDUCTIVITIES% %DIPOLES% %DSM%
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om_assemble -H2EM %GEOMETRY% %CONDUCTIVITIES% %EEG_ELECTRODES% %H2EM%
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om_gain -EEG %HMINV% %DSM% %H2EM% %EEG_LEADFIELD%
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rem Compute MEG gain matrix
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om_assemble -H2MM %GEOMETRY% %CONDUCTIVITIES% %SQUIDS% %H2MM%
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om_assemble -DS2MM %DIPOLES% %SQUIDS% %DS2MEG%
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om_gain -MEG %HMINV% %DSM% %H2MM% %DS2MEG% %MEG_LEADFIELD%
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rem Compute EIT gain matrix
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om_assemble -EITSM %GEOMETRY% %CONDUCTIVITIES% %EEG_ELECTRODES% %EITSM%
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om_gain -EEG %HMINV% %EITSM% %H2EM% %EIT_LEADFIELD%
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rem Compute Internal Potential
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om_assemble -H2IPM %GEOMETRY% %CONDUCTIVITIES% %INTERNAL_ELECTRODES% %IPHM%
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om_assemble -DS2IPM %GEOMETRY% %CONDUCTIVITIES% %DIPOLES% %INTERNAL_ELECTRODES% %IPSM%
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om_gain -IP %HMINV% %DSM% %IPHM% %IPSM% %IP_LEADFIELD%
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