<?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_singletrial</title><revhistory><revision><revnumber>2</revnumber><date>2013-03-08 10:02:37</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>1</revnumber><date>2010-07-21 14:53:43</date><authorinitials>YaaraErez</authorinitials></revision></revhistory></articleinfo><section><title>Computing Source Estimates for Single Trials</title><para>Data at the single-trial level are obviously noisier than for evoked responses. You should make sure that your data are appropriately filtered and pre-processed, and bad channels are marked. It is recommended to use empty-room data for the computation of the <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix">covariance matrix</ulink>, and to compute an <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator">inverse operator</ulink> with this new covariance matrix. </para><para>At the single-trial level, MNE allows you to extract source estimates for <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels">ROIs (or labels)</ulink>. Because the inverse operators are specific to invidivual subjects, these ROIs must be defined in the space of the individual MRIs (not the average). </para><para>Morphing of ROIs from the average to the individual space can be done using </para><itemizedlist><listitem><para><emphasis role="strong">mne_morph_labels</emphasis> <emphasis>(options e.g. --from --to --labeldir)</emphasis> </para></listitem></itemizedlist><para>Extracting source estimates for ROIs is done by </para><itemizedlist><listitem><para><emphasis role="strong">mne_compute_raw_inverse</emphasis> <emphasis>(options e.g. --in --inv --labeldir --out)</emphasis> </para></listitem></itemizedlist><para>The output will be a continuous time series for each ROI. </para><para>In order to epoch your data with regard to events/triggers in your data, use </para><itemizedlist><listitem><para><emphasis role="strong">mne_epochs2mat</emphasis> <emphasis>(options e.g. --raw --mat --events --event --tmin --tmax --lowpass)</emphasis> </para></listitem></itemizedlist><para>This will produce a description file and an epoch file. </para><para>From here on, you are on your own... </para></section></article>