Elektra Beckum MCE - Manuals

Page 2 - Copyright and Warranty; Printing History; st edition

MCE User’s Guide NM20600A-A 2004-05-17 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 thisdocument...

Page 3 - Contents

MCE User’s Guide NM20600A-A 2004-05-17 i Contents 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Hazard Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Version . ...

Page 5 - Introduction; Hazard Information

MCE User’s Guide Introduction NM20600A-A 2004-05-17 1 1 Introduction This manual describes the use of MCE program to analyze magnetoencephalo- graphic(MEG) measurements using L1 minimum norm estimates 1,2 (L1 MNE). 1.1 Hazard Information This manual contains important hazard information which must b...

Page 6 - Conventions and typography; User input; bold; NeuroImage

Introduction MCE User’s Guide 2 2004-05-17 NM20600A-A 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 se...

Page 7 - Getting Started; An iconified Matlab console appears on the desktop; Also the main window shown in Figure 1 opens.; Quitting the program; You can quit the program by three alternative ways:

MCE User’s Guide Getting Started NM20600A-A 2004-05-17 3 2 Getting Started To start the program, double click the MCE icon in the Neuromag folder of theApplication 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 us...

Page 8 - Selecting the data file and pre-processing; Figure 2; Setting the filtering and baselines

Selecting the data ﬁle and pre-processing MCE User’s Guide 4 2004-05-17 NM20600A-A 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 pop...

Page 9 - Figure 3; Decreasing the computing time and file sizes; toggle and slider, the estimates will be calculated with

MCE User’s Guide Selecting the data ﬁle and pre-processing NM20600A-A 2004-05-17 5 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 thecomputing time and save disk space. If you low-pass ﬁlter...

Page 10 - Bad channels and projections; MEG

Selecting the data ﬁle and pre-processing MCE User’s Guide 6 2004-05-17 NM20600A-A Figure 4If too strong down-sampling is applied, the aliasing is reﬂected in thepreview window with the folding frequency response. Decrease the ﬁlter cutofffrequency or decimation. 3.3 Bad channels and projections If ...

Page 11 - button, and then add bad channels that are not included. Because

MCE User’s Guide Selecting the data ﬁle and pre-processing NM20600A-A 2004-05-17 7 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 projectio...

Page 12 - Selecting the head model; Figure 5

Selecting the head model MCE User’s Guide 8 2004-05-17 NM20600A-A 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 elementmodel (BEM) (p. 8) describes the shape of the brain and...

Page 13 - Point set selection; Figure 6

MCE User’s Guide Selecting the head model NM20600A-A 2004-05-17 9 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 thecalculations and the parameters of the conductor model used in the forward cal-culations. Eac...

Page 14 - Table 1; Creating BEM files; The triangle meshes used in MCE to describe the shape of the brain; Lattice; The density of the points in the point set (in mm); Min dist; The comment seen in the list; Points; The number of possible source points

Selecting the head model MCE User’s Guide 10 2004-05-17 NM20600A-A Table 1 Properties of the point sets 4.3 Creating BEM files If you have MR images of the subject, you can create ﬁf-ﬁles describing boundaryelement models of the brain with MriLab and meshes2ﬁff programs. See the manu-als of those pr...

Page 15 - Calculating the estimates; wait

MCE User’s Guide Calculating the estimates NM20600A-A 2004-05-17 11 5 Calculating the estimates Before viewing the results you have to calculate the current estimates for theepoch. You should have already selected the MEG data, pre-processed it, and selectedthe head model (see chapters “Selecting th...

Page 16 - Loading a calculated estimate; Otherwise, check that the

Loading a calculated estimate MCE User’s Guide 12 2004-05-17 NM20600A-A 6 Loading a calculated estimate If you have previously calculated (p. 11) an estimate and saved it to a disk ﬁle, youcan load it by pressing the [Full] button in the Main window (p. 22) to open the full calculation dialog (p. 27...

Page 17 - Selecting the time; tmin

MCE User’s Guide Selecting the time NM20600A-A 2004-05-17 13 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 t...

Page 18 - Region of interest; The smoothed weighting is a function of position

Region of interest MCE User’s Guide 14 2004-05-17 NM20600A-A 8 Region of interest You can estimate the activity in certain brain area as a function of time by deﬁninga region of interest (ROI). ROI is actually a weighting function that is used to cal-culate the sum amplitude from the estimate. 8.1 W...

Page 20 - Predicting MEG waveforms; Figure 7

Predicting MEG waveforms MCE User’s Guide 16 2004-05-17 NM20600A-A 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 theselected ROI is shown with red lines. To ﬁnd out, what p...

Page 21 - Printing from the dialog; Figure 8; Saving to an image file; Adobe Illustrator

MCE User’s Guide Printing NM20600A-A 2004-05-17 17 10 Printing You can print the displays or save them as images by using the printing dialog,or with UNIX command /neuro/mce/bin/xgifdump 10.1 Printing from the dialog Figure 8 The printing dialog The [Print] command in the File menu (p. 21) opens the...

Page 22 - xgifdump; The images can be saved in GIF format by giving the command

Printing MCE User’s Guide 18 2004-05-17 NM20600A-A The EPS formats suit well the Arrow (p. 30), Amplitude (p. 31), and Region ofinterest (p. 34) windows. In the conversion of the color displays (Color display (p.29), Color scale (p. 33)) some errors may occur; the JPEG or PNG formats aremore suitabl...

Page 23 - 1 Creating HTML documents and MPEG movies; Creating HTML documents; Figure 9

MCE User’s Guide Creating HTML documents and MPEG movies NM20600A-A 2004-05-17 19 11 Creating HTML documents and MPEG movies 11.1 Creating HTML documents Figure 9 An example of a created HTML document You can create HTML documents with the HTML document creation dialog (p.38). The document will incl...

Page 24 - Table 2

Creating HTML documents and MPEG movies MCE User’s Guide 20 2004-05-17 NM20600A-A Table 2 Default viewing orientations for created HTML documents MPEG movies 11.2 Creating movies You can create MPEG movies with the Movie creation dialog (p. 39). The moviewill show projected, color coded views of the...

Page 25 - 2 MCE windows and dialogs; File; Close

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 21 12 MCE windows and dialogs 12.1 Window menus Figure 10 Menus of the Main Window (p. 22) File Windows Opens the different windows Colors Selects the color map for current window Help Options Some windows have speciﬁc options. Create HT...

Page 26 - Figure 11 The main window; Options menu; The

MCE windows and dialogs MCE User’s Guide 22 2004-05-17 NM20600A-A 12.2 Main window Figure 11 The main window The main window is opened when the program starts, and closing it quits the pro-gram. Table 3 Controls in the Main window Options menu The [Options] menu in the main window includes buttons [...

Page 27 - Figure 12 Minimum norm estimate options dialog

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 23 Figure 12 Minimum norm estimate options dialog The [Regularization] slider and text ﬁeld select and show the number of singu- lar values of the data used in the estimate. If the noise level in the measurementis low, increase the value...

Page 28 - Figure 13 The pre-processing dialog

MCE windows and dialogs MCE User’s Guide 24 2004-05-17 NM20600A-A Figure 13 The pre-processing dialog The left side of the window shows controls that you can use to pre-process the data.With the ﬁlter frame you can low-pass ﬁlter the data, with the baseline frame you can compensate for the DC level ...

Page 29 - Table 4Controls in the Pre-processing dialog; Filter frame

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 25 Table 4Controls in the Pre-processing dialog Filter frame The [Lowpass filter] toggle selects the ﬁlter. You can select the cutoff frequency or transition width with thecorresponding text ﬁelds or sliders.The values are in Hz.Use the ...

Page 31 - Full calculation dialog; Figure 14The full calculation dialog

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 27 12.5 Full calculation dialog Figure 14The full calculation dialog The full calculation dialog is opened by pressing the [Full] button in the Main window (p. 22). This window is used to calculate (p. 11) or load (p. 12) the minimum nor...

Page 32 - Batch jobs window; Figure 15 The batch jobs window

MCE windows and dialogs MCE User’s Guide 28 2004-05-17 NM20600A-A 12.6 Batch jobs window Figure 15 The batch jobs window This window controls the calculation of the estimates. The list shows current batchjobs and their states. The preferred way to start a calculating all the jobs, press the [Start s...

Page 33 - Figure 16 Color display of the estimate

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 29 12.7 Color display Figure 16 Color display of the estimate The color display is opened by selecting [Color display] in the Windows menu (p. 21). The color display shows the estimated source distribution projected to the sur-face of th...

Page 34 - Figure 17 Arrow display of the estimate; not

MCE windows and dialogs MCE User’s Guide 30 2004-05-17 NM20600A-A 12.8 Arrow display Figure 17 Arrow display of the estimate The arrow display is opened by selecting [Arrow display] in the Windows menu (p. 21). The arrow display shows the 3-dimensional estimated source locations and orienta-tions. I...

Page 35 - Amplitude window; Figure 18 The amplitude window with total activity

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 31 12.9 Amplitude window Figure 18 The amplitude window with total activity Figure 19 The amplitude window with an oriented ROI The amplitude window is opened by selecting [Amplitude] in the Windows menu (p. 21).

Page 36 - Amplitude scale window; Figure 20 Amplitude scale window

MCE windows and dialogs MCE User’s Guide 32 2004-05-17 NM20600A-A The amplitude window shows the activity of the selected ROI (p. 14) during thewhole response. You can also use it to select a time point or time range (p. 13). To select a time point, use the left mouse button. To select a time range,...

Page 37 - Figure 21 The color scale window; Constant color mode

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 33 12.11 Color scale window Figure 21 The color scale window The color scale window is opened by selecting [Color scale] in the Windows menu (p. 21). You can adjust the color scale of the Color display (p. 29) using the color scalewindow...

Page 38 - Things to remember; Figure 22 The region of interest

MCE windows and dialogs MCE User’s Guide 34 2004-05-17 NM20600A-A Things to remember Remember that the Arrow display (p. 30) has different color scale and check thatyou are using the same color map (p. 21) in different windows. Remember also, that because the estimation method tries to minimize the ...

Page 39 - Figure 23 The ROI database

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 35 12.13 ROI database window Figure 23 The ROI database The ROI database window is opened by selecting [ROI database] in the Win- dows menu (p. 21). The ROI database window is your contains your interface to the database of pre-viously s...

Page 40 - ROI search; Table 8; ROI list; No ROI

MCE windows and dialogs MCE User’s Guide 36 2004-05-17 NM20600A-A ROI search Table 8 Controls in the upper left corner ROI list The list on the right side shows the ROIs matching your speciﬁcations. The com-ment, the name of the ﬁf-ﬁle the selection is based on, and the name of the creatorare shown....

Page 41 - Current ROI; Table 9; Other controls; Controls in the bottom row; SQL database; The comment used as the name of the ROI

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 37 Current ROI Table 9 Controls in the lower left corner Other controls Table 10 Controls in the bottom row SQL database All the ROI queries are done from an database server using SQL query lan-guage. Some examples how to reﬁne your quer...

Page 42 - The selected ROI can be exported to a file with the

MCE windows and dialogs MCE User’s Guide 38 2004-05-17 NM20600A-A [Options] menu The selected ROI can be exported to a ﬁle with the [Export new file] button. The [Append] button adds the selected ellipsoid to the previously selected output ﬁle. 12.14 HTML Creation Dialog Figure 24The HTML Creation D...

Page 43 - Controls in the HTML Creation Dialog; Movie Creation Dialog; Figure 25 The Movie Creation Dialog

MCE User’s Guide MCE windows and dialogs NM20600A-A 2004-05-17 39 Table 11 Controls in the HTML Creation Dialog 12.15 Movie Creation Dialog Figure 25 The Movie Creation Dialog [File] Select the output ﬁle name. The PNG picture ﬁles willbe created with the same preﬁx and different sufﬁxes. [Time peri...

Page 44 - You can open the Movie Creation Dialog from the

MCE windows and dialogs MCE User’s Guide 40 2004-05-17 NM20600A-A You can open the Movie Creation Dialog from the [File] menu. Table 12 Controls in the Movie Creation Dialog [File] Select the output ﬁle name [Time points] Select the time points with format begin:skip:end For example, for a movie fro...

Page 45 - Index; background calculation 11

MCE User’s Guide NM20600A-A 2004-05-17 41 Index A Adobe Illustrator 17amplitude 14, 31 negative 14 animation 22 B background calculation 11 server 28 bad channels 6, 7, 25 automatic setting 6, 25 baseline 4, 25 color scale 33detrend 4 batch jobs 11, 28BEM. See boundary element modelboundary element ...

Page 46 - quitting 3

MCE User’s Guide 42 2004-05-17 NM20600A-A Q quitting 3 R references 2region of interest 14, 34 center 37database 15, 35definition 14exporting 15, 38extent 37hard 14orientation 14selecting 15, 29smooth 14 regularization 23ROI. See region of interest S server 11SQL query language 37SSP 6starting the p...