Elektra Beckum NM20600A-A, MCE User Manual
MCE User’s Guide
Version 1.3
May 2004
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 Temperature Laboratory in
Helsinki University of Technology.
The commercial distribution of the product for MEG analysis is exclusively licensed to Elekta
Neuromag Oy.
Included with the software are public domain software components:
• mysql_mex by Kimmo Uutela
• lpsolve_mex by Kimmo Uutela, Michel Berkelaar, and Jeroen Dirks
• Perl 5 by Larry Wall
• DBI by Tim Bunce
• DBD:mysql by Perl Jochen Wiedmann
• Berkeley MPEG Tools by The Regents of the University of California
See the source code of these programs provided with the software for copyright details those
components.
Printing History Neuromag p/n Software Date
1st edition NM20600A 1.3 March 2000
2nd edition NM20600A-A 1.3 May 2004
NM20600A-A 2004-05-17
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 Conventions and typography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.5 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.1 Analyzing data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Quitting the program. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
3 Selecting the data file and pre-processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.1 Setting the filtering and baselines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3.2 Decreasing the computing time and file sizes. . . . . . . . . . . . . . . . . . . . . . 5
3.3 Bad channels and projections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
4 Selecting the head model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
4.1 BEM selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
4.2 Point set selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4.3 Creating BEM files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5 Calculating the estimates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 Loading a calculated estimate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
7 Selecting the time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
8 Region of interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
8.1 What is ROI?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
8.2 What is the orientation of a ROI? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
8.3 Selecting a ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
8.4 ROI database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
8.5 Exporting ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
9 Predicting MEG waveforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
10 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
10.1 Printing from the dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
10.2 Saving to an image file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
10.3 Saving with xgifdump command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
11 Creating HTML documents and MPEG movies. . . . . . . . . . . . . . . . . . . . . . . . . 19
11.1 Creating HTML documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
NM20600A-A 2004-05-17 i
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
12.4 MEG data dialog. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
12.5 Full calculation dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
12.6 Batch jobs window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
12.7 Color display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
12.8 Arrow display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
12.9 Amplitude window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
12.10 Amplitude scale window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
12.11 Color scale window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
12.12 Region of interest window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
12.13 ROI database window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
12.14 HTML Creation Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
12.15 Movie Creation Dialog. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
ii 2004-05-17 NM20600A-A
MCE User’s Guide Introduction
1 Introduction
This manual describes the use of MCE program to analyze magnetoencephalo-
graphic (MEG) measurements using L1 minimum norm estimates
1.1 Hazard Information
This manual contains important hazard information which must be read, understood 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 infinitely many different possible ones. The results
!
must be interpreted and reviewed by a person having good understanding of the
capabilities and limitations of the methods being used.
1,2
(L1 MNE).
Warning: This program should only be used with hardware and software given
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in the specifications listed in the Release Notes of the release being used.
Warning: On some platforms other programs can affect the colors in the
windows of the MCE program. In such cases other programs using colored
windows should be stopped to ensure correct colors on the displays.
Warning: The triangle meshes used in MCE to describe the shape of the brain
must be defined in head coordinates. This differs from the recommended
coordinate system usage in dipole modeling program.
Warning: If the regularization parameters are changed from the default ones,
the new values must be validated using known data.
Warning: Region of interest may contain multiple sources whose activities are
mixed together.
Warning: All users that have access to the database can also access the data-
!
NM20600A-A 2004-05-17 1
base entries related to the data of other users.
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 written by the user is shown as
User input
Some important warnings are shown in bold.
1.5 References
1. K. Matsuura and U. Okabe, “Selective minimum-norm solution of the
biomagnetic inverse problem”, IEEE Trans. Biomed. Eng. 42:608-615, 1995.
2. K. Uutela, M. Hämäläinen, and E. Somersalo, “Visualization of
Magnetoencephalographic Data using Minimum Current Estimates”,
NeuroImage, 1999. In press.
2 2004-05-17 NM20600A-A
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
detail on page 22.
Figure 1 The main window
2.1 Analyzing data
To analyze your data with the L1 MNE, first you should calculate the estimates:
1. Load and pre-process the MEG data (p. 4)
2. Select the head model (p. 8)
3. Start the calculation (p. 11)
After you have loaded (p. 12) the calculated estimates, you can proceed by
viewing the results (p. 33) at different times (p. 13) or by studying the temporal
activity of the Regions of Interest (p. 14).
2.2 Quitting the program
You can quit the program by three alternative ways:
1. pressing the [Quit] button in the Main window
2. typing “quit” Matlab command in the terminal window
3. by closing the main window.
NM20600A-A 2004-05-17 3
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 dialog 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 signals are mainly concentrated to the lower frequencies, you
can increase the signal-to-noise ratio with an low-pass filter. Select the [Lowpass
filter] toggle and set appropriate cutoff frequency and transition width of the filter.
After changing the numeric values, press Enter or the Tab key to update the value.
You can view the effect on a single channel by pressing the [Channel] toggle or
the filter response with the [Impulse response] and [Freq. response] buttons.
You can zoom into the preview window with the left mouse button and revert to
automatic scaling with the [rescale] button.
Because most of the channels usually have a non-zero DC-level, you should select
a [Baseline] toggle and select a time period where there should be no real evoked
responses, typically before the stimulus.
If you are analyzing a long period or the data otherwise includes strong artificial
slow drifts, you can select a [Detrend baseline] period after the evoked response.
This is usually a safer way of getting rid of the drifts than, for example, applying
high-pass filter.
The de-trend baseline actually fits a line to the values in the two baselines and subtracts it form the data (see Figure 3).
4 2004-05-17 NM20600A-A
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
constant intervals.
You can select the correct amount of down-sampling by selecting the [Freq.
response] button. If the down-sampling is too strong compared to the filter
pass-band, the higher frequencies will be mapped to the lower frequencies (see
Figure 4). A reasonable down-sampling ratio is the one, for example, having the
cutoff frequency about half way between the zero frequency and the highest
shown frequency. The down-sampling is carried out by selecting single data
points of the filtered response.
If you do not need to analyze the whole epoch, select the interesting time period
with the [Trim] toggle button and text fields.
NM20600A-A 2004-05-17 5
Selecting the data file and pre-processing MCE User’s Guide
Figure 4 If too strong down-sampling is applied, the aliasing is reflected in the
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 [Badchannels] 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
four digits for Elekta Neuromag™ or Vectorview™ data and three digits for Neuromag-122™ data. Use the numbers in the channel names regardless of the channel
order in the fif-file. Wildcards are not supported.
External disturbance fields can be filtered using Signal Space Projection (SSP). If
the fif-datafile has a noise projection specified, you can apply it to the data and cal-
culations by selecting the [Apply projection] toggle. The projection is updated
when you change the bad channels. Normal data files where the projection information is included and the data itself is the original non-projected data should be
used. If projected data is used, the file must also contain the projection vectors that
were used define the removed subspace. Otherwise the results may be distorted.
When you load a new file or press the [Automatic]button, the bad channels are set
automatically. The following channels are set bad:
1. Channels that are marked bad in the fif-file
2. If baseline is used, the channels where the baseline is flat
3. If baseline is used, the channels where the baseline is very noisy
The “flat channels” are the ones where the standard deviation of the raw baseline
activity is less than 10 % of the median value of others. The “noisy channels” are
the ones where the standard deviation of the baseline activity after projections is
over three times the median value. If the data includes both gradiometer and magnetometer data, the values are only compared with the channels with same coil
type.
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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 projections affect the selection of the noisy channels, resetting the projections repeatedly may result in different channels being marked bad at the second time, if
their noise levels are near the limits.
A handy way of screening for possible bad channels is to open the MEG Data
dialog (p. 26) by pressing the [Showall] button. All the channels will be shown,
overlaid based on the location. If one of the waveforms seems to be an outlier,
right-click it at the time of the maximum difference, and the channel ID is
shown.
NM20600A-A 2004-05-17 7
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 shape of the brain. In the current version (1.3), only sphere models are used in the forward calculation, but the
BEM model affects the point set used in the calculation and the images used in the
3D visualization.
The BEM dialog shows a list of existing models associated with the same subject
and some general models. You can select an existing model from the list and accept
it by pressing the [OK] button.
You can add a new BEM model by pressing the [Add new]button. A file selection
box for selecting the fif-file opens up, and after the selection you can select the
associated the subject.
If the BEM model is not used by any point set (p. 9), you can delete it by pressing
the [Delete] button. If it is used by point sets, you should first delete the point sets.
After you have accepted the BEM model by pressing the [OK] button, you should
select the point set.
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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 calculations. Each point set is related with a certain BEM model (p. 8) and a certain 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 by making the full
calculation (p. 11).
You can create a new point set by pressing the [Add new] button and setting
appropriate values to the properties of the point set. If you modify the Origin,
Lattice, or Min dist properties, the point set is recalculated and the number of
points is show. If you accept the new point set by pressing the OK button, it will
take a while to calculate the projection from the point set to the BEM. You can
remove the point sets by pressing the [Delete] button. If several people are
using the point set, it will be deleted only when it is deleted by all its users.
NM20600A-A 2004-05-17 9
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 numerical instability in the calculations.
Comment The comment seen in the list
Points The number of possible source points
4.3 Creating BEM files
If you have MR images of the subject, you can create fif-files describing boundary
element models of the brain with MriLab and meshes2fiff programs. See the manuals of those programs (or Source Modeling manual) for details of using those programs.
When creating the meshes in Mrilab, you must save them in head coordinates
in meters.
Warning: The triangle meshes used in MCE to describe the shape of the brain
must be defined in head coordinates. This differs from the recommended coordi-
!
nate system usage in dipole modeling program.
10 2004-05-17 NM20600A-A
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