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MCE User’s Guide
Version 1.3
May 2004
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MCE User’s Guide Copyright and Warranty © 2000-2004 Kimmo Uutela. All rights reserved. The author makes no warranty of any kind with regard to this material or the software. This document contains proprietary information, which is protected by copyright. No part of this document may be copied or changed without the prior consent of the author. The information contained in this document is subject to change without notice. This program was developed at the Brain Research Unit of the Low Temperatu
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MCE User’s Guide Contents 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Hazard Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 What’s new? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.4 Convent
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MCE User’s Guide 11.2 Creating movies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 12 MCE windows and dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 12.1 Window menus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 12.2 Main window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 12.3 Pre-processing dialog . . . . . . .
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MCE User’s Guide Introduction 1 Introduction This manual describes the use of MCE program to analyze magnetoencephalo- 1,2 graphic(MEG)measurementsusingL1minimumnormestimates (L1 MNE). 1.1 Hazard Information This manual contains important hazard information which must be read, under- stood and observed by all users, For your convenience all warnings that appear in the manual are presented below. Warning: Like all inverse solutions of MEG, MCE provides a source distribution which is one of infinit
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Introduction MCE User’s Guide 1.2 Version This manual refers to program version 1.3 patch level 18 and later. 1.3 What’s new? • Default directory menu • Export figure menu • Batch calculation error log display • Slowed down animation • Calculation can be cancelled • Showing selected ROI in arrow display • Show subject ID & file name in different figures • Added several warnings to the manual 1.4 Conventions and typography Buttons that can be pressed will be shown in square brackets: [Button] Text w
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MCE User’s Guide Getting Started 2 Getting Started To start the program, double click the MCE icon in the Neuromag folder of the Application manager. An iconified Matlab console appears on the desktop; do not close it! Also the main window shown in Figure 1 opens. If you are using a previously calculated response, you should now load an old calculation (p. 12). Otherwise, you should select a data file using the [File] but- ton and select the head model (p. 8). The main window is described in more
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Selecting the data file and pre-processing MCE User’s Guide 3 Selecting the data file and pre-processing Select the MEG data file by pressing the [File] button of main window (p. 22). Select the data file from the dialog. If the file has several data sets, a selection dia- log pops up and you can select the correct data set. When the you have selected the data, the pre-processing dialog (see Figure 2) will open. Figure 2 The pre-processing dialog 3.1 Setting the filtering and baselines Because the MEG
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MCE User’s Guide Selecting the data file and pre-processing Figure 3 Effect of the baselines 3.2 Decreasing the computing time and file sizes If you do not calculate estimates at all the time points, you can decrease the computing time and save disk space. If you low-pass filter the data, the data will be smoother and it is unnecessary to calculate the estimate at each time point. By selecting a down-sampling ratio with the [Decimate] toggle and slider, the estimates will be calculated with constan
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Selecting the data file and pre-processing MCE User’s Guide Figure 4Iftoostrongdown-samplingisapplied,thealiasingisreflectedinthe preview window with the folding frequency response. Decrease the filter cutoff frequency or decimation. 3.3 Bad channels and projections If some of the channels are flat or bad, you must set the [Bad channels] toggle and write the channel names to the corresponding text field. The format can be “MEG 1112 1113 ...” or “MEG 1112 MEG 1113 ...”, the channels described with fou
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MCE User’s Guide Selecting the data file and pre-processing In practice, you should first specify the baseline period and then press the [Automatic] button, and then add bad channels that are not included. Because the selection of the bad channels slightly affects the projections and the projec- tions affect the selection of the noisy channels, resetting the projections repeat- edly may result in different channels being marked bad at the second time, if their noise levels are near the limits. A h
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Selecting the head model MCE User’s Guide 4 Selecting the head model You can select the head model by pressing the [Head model] button in the Main window (p. 22). The head model consists of two parts: the boundary element model (BEM) (p. 8) describes the shape of the brain and the point set (p. 9) describes the parameters needed in the calculation. First, the BEM model selection window opens up. 4.1 BEM selection Figure 5 BEM model selection dialog The boundary element model (BEM) describes the
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MCE User’s Guide Selecting the head model 4.2 Point set selection Figure 6 Point set selection dialog The point set includes the brain locations that are used as a source space in the calculations and the parameters of the conductor model used in the forward cal- culations. Each point set is related with a certain BEM model (p. 8) and a cer- tain subject. From the Point set dialog you can select an existing set from the list and accept it by pressing the [OK] button. After this you can proceed b
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Selecting the head model MCE User’s Guide Table 1 Properties of the point sets Origin: xyz Sphere model origin (in mm; head coordinates) Lattice The density of the points in the point set (in mm) Min dist The minimum distance to the sphere model origin (in mm). Points deeper than this are excluded from the point set. Very deep source points may lead to numer- ical instability in the calculations. Comment The comment seen in the list Points The number of possible source points 4.3 Creating BEM fil
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MCE User’s Guide Calculating the estimates 5 Calculating the estimates Before viewing the results you have to calculate the current estimates for the epoch. You should have already selected the MEG data, pre-processed it, and selected the head model (see chapters “Selecting the data file and pre-processing” on page 4 and “Selecting the head model” on page 8). If the noise level of the mea- surement is very high or low, you might change the regularization level or if either magnetometers or gradio
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Loading a calculated estimate MCE User’s Guide 6 Loading a calculated estimate If you have previously calculated (p. 11) an estimate and saved it to a disk file, you can load it by pressing the [Full] button in the Main window (p. 22) to open the full calculation dialog (p. 27). If you have selected the right fif-file and have previously saved the corresponding estimate with the default name, the default values in the dialog should be set to load the estimate. Otherwise, check that the [Load] butto
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MCE User’s Guide Selecting the time 7 Selecting the time You can select a single time point in three ways: • By entering the time (in ms) in the [Time] field in the Main window (p. 22). • By using the slider in the Main window (p. 22). • By pressing the left mouse button in the Amplitude window (p. 31), if a batch calculation is loaded. However, because the single estimates are usually noisy, it is usually more fruitful to view the average activity within a time range. You can also select the ran
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Region of interest MCE User’s Guide 8 Region of interest You can estimate the activity in certain brain area as a function of time by defining a region of interest (ROI). ROI is actually a weighting function that is used to cal- culate the sum amplitude from the estimate. 8.1 What is ROI? The smoothed weighting is a function of position r, having form T –r Wr fr() = e but you don't need to be interested in matrix calculation to understand how the ROIs work. The ROI window (p. 34) visualizes the c
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MCE User’s Guide Region of interest 8.3 Selecting a ROI You can select a ROI from the Color display (p. 29). Select a range of nodes with the right mouse button. The program will find the active source points that are contributing to the selected activity and calculate the ROI center and extent. The orientation of the ROI will be the mean orientation of selected currents. After selecting a new ROI, activity weighted with it is shown in the ROI win- dow (p. 34), the time course of activity in the
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Predicting MEG waveforms MCE User’s Guide 9 Predicting MEG waveforms Figure 7 Predicted fields shown with XPlotter. The original measurement is shown with yellow lines and the waveforms predicted with the activity of the selected ROI is shown with red lines. To find out, what part of the measured data is explained with the activity in the selected ROI, you can press the [Show predicted fields] command in the [Options] menu of the Amplitude window (p. 31). The program calculates the magnetic field pr
