<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>AnalyzingData/MNE_AllInOne</title><revhistory><revision><revnumber>9</revnumber><date>2013-03-08 10:02:29</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>8</revnumber><date>2013-02-04 15:07:40</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>7</revnumber><date>2010-07-16 16:09:00</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>6</revnumber><date>2010-07-16 16:08:10</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>5</revnumber><date>2010-07-16 13:53:34</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>4</revnumber><date>2010-07-16 13:49:12</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>3</revnumber><date>2010-07-16 13:45:42</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>2</revnumber><date>2010-07-16 13:40:02</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>1</revnumber><date>2010-07-16 13:36:09</date><authorinitials>YaaraErez</authorinitials></revision></revhistory></articleinfo><para><inlinemediaobject><imageobject><imagedata fileref="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_AllInOne?action=AttachFile&amp;do=get&amp;target=mrclogo.gif"/></imageobject><textobject><phrase>mrclogo.gif</phrase></textobject></inlinemediaobject> </para><section><title>Overview of MNE Processing Steps and Commands</title><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing">Pre-processing MRI Data in Freesurfer</ulink>:</emphasis> </para><itemizedlist><listitem><para>mri_convert </para></listitem><listitem><para>recon-all </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing">Segment Head Surfaces</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_watershed_bem </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing">Prepare MRI Data for MNE</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_setup_mri </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing">Prepare Source Space (Cortical Surface) for MNE</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_setup_source_space </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing">Align MEG and MRI coordinate systems</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_analyze </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution">Set Up BEM Information for MNE</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_setup_forward_model </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution">Compute Forward Solution</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_do_forward_solution </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging">Average MEG Data</ulink>, <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix">Compute Covariance Matrix</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_process_raw </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates">Compute Average Cortical Surface</ulink>:</emphasis> </para><itemizedlist><listitem><para>make_average_subject </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator">Create Inverse Operator (from Forward Solution)</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_do_inverse_operator </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates">Compute Source Estimates (Apply Inverse Operator to MEG data)</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_make_movie </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates">Average Source Estimates</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_average_estimates </para></listitem></itemizedlist><para><emphasis role="strong"><ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels">Extract ROI data</ulink>:</emphasis> </para><itemizedlist><listitem><para>mne_make_movie </para></listitem></itemizedlist></section></article>