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Elektra Beckum MCE manual

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Table of contents for the manual

  • Page 1

    MCE User’s Guide Version 1.3 May 2004[...]

  • Page 2

    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 this document may be copied or changed without the prior c[...]

  • Page 3

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

  • Page 4

    MCE User’ s Guide ii 2004-05-17 NM20600A-A 11.2 Creating movies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 12 MCE windows and dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 12.1 Window menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .[...]

  • Page 5

    MCE User’ s Guide Introduction NM20600A-A 2004-05-17 1 1 Intr oduction 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 Inf or mation This manual contains important hazard information which must be read, under- stood and observed by all us[...]

  • Page 6

    Introduction MCE User’ s Guide 2 2004-05-17 NM20600A-A 1.2 V ersion This manual refers to program version 1.3 patch le vel 18 and later . 1.3 What’ s ne w? • Default directory menu • Export figure menu • Batch calculation error log display • Slo wed down animation • Calculation can be cancelled • Sho wing selected R OI in arrow dis[...]

  • Page 7

    MCE User’ s Guide Getting Started NM20600A-A 2004-05-17 3 2 Getting Star ted T o 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 windo w shown in Figure 1 opens. If you are using a pre viously calculated response, y[...]

  • Page 8

    Selecting the data file and pre-processing MCE User’ s Guide 4 2004-05-17 NM20600A-A 3 Selecting the data file and pre-pr ocessing Select the MEG data file by pressing the [File] button of main windo w (p. 22). Select the data file from the dialog. If the file has se veral data sets, a selection dia- log pops up and you can select the correc[...]

  • Page 9

    MCE User’ s Guide Selecting the data file and pre-processing NM20600A-A 2004-05-17 5 F igure 3 Effect of the baselines 3.2 Decreasing the computing time and file siz es If you do not calculate estimates at all the time points, you can decrease the computing time and sav e disk space. If you lo w-pass filter the data, the data will be smoother [...]

  • Page 10

    Selecting the data file and pre-processing MCE User’ s Guide 6 2004-05-17 NM20600A-A F igure 4 If too str ong down-sampling is applied, the aliasing is reflected in the pr evie w window with the folding fr equency response . Decr ease the filter cutoff fr equency or decimation. 3.3 Bad channels and projections If some of the channels are flat[...]

  • Page 11

    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 [A utomatic] button, and then add bad channels that are not included. Because the selection of the bad channels slightly af fects the projections and the projec- tions af fect the sele[...]

  • Page 12

    Selecting the head model MCE User’ s Guide 8 2004-05-17 NM20600A-A 4 Selecting the head model Y ou can select the head model by pressing the [Head model] b utton in the Main windo w (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 paramet[...]

  • Page 13

    MCE User’ s Guide Selecting the head model NM20600A-A 2004-05-17 9 4.2 P oint set selection F igure 6 P oint 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 [...]

  • Page 14

    Selecting the head model MCE User’ s Guide 10 2004-05-17 NM20600A-A T able 1 Pr operties of the point sets 4.3 Creating BEM files If you hav e MR images of the subject, you can create fif-files describing boundary element models of the brain with MriLab and meshes2fif f programs. See the manu- als of those programs (or Source Modeling manual)[...]

  • Page 15

    MCE User’ s Guide Calculating the estimates NM20600A-A 2004-05-17 11 5 Calculating the estimates Before vie wing the results you hav e to calculate the current estimates for the epoch. Y ou should hav e already selected the MEG data, pre-processed it, and selected the head model (see chapters “Selecting the data file and pre-processing” on p[...]

  • Page 16

    Loading a calculated estimate MCE User’ s Guide 12 2004-05-17 NM20600A-A 6 Loading a calculated estimate If you hav e previously calculated (p. 11) an estimate and sav ed it to a disk file, you can load it by pressing the [Full] button in the Main windo w (p. 22) to open the full calculation dialog (p. 27). If you hav e selected the right fif-?[...]

  • Page 17

    MCE User’ s Guide Selecting the time NM20600A-A 2004-05-17 13 7 Selecting the time Y ou can select a single time point in three ways: • By entering the time (in ms) in the [Time] field in the Main windo w (p. 22). • By using the slider in the Main windo w (p. 22). • By pressing the left mouse button in the Amplitude windo w (p. 31), if a b[...]

  • Page 18

    Region of interest MCE User’ s Guide 14 2004-05-17 NM20600A-A 8 Region of interest Y ou can estimate the activity in certain brain area as a function of time by defining a region of interest (R OI). R OI is actually a weighting function that is used to cal- culate the sum amplitude from the estimate. 8.1 What is R OI? The smoothed weighting is a[...]

  • Page 19

    MCE User’ s Guide Region of interest NM20600A-A 2004-05-17 15 8.3 Selecting a R OI Y ou can select a R OI from the Color display (p. 29). Select a range of nodes with the right mouse button. The program will find the acti ve source points that are contributing to the selected acti vity and calculate the R OI center and extent. The orientation of[...]

  • Page 20

    Predicting MEG wa veforms MCE User’ s Guide 16 2004-05-17 NM20600A-A 9 Predicting MEG wavef orms F igure 7 Pr edicted fields shown with XPlotter. The original measur ement is shown with yellow lines and the waveforms pr edicted with the activity of the selected R OI is shown with r ed lines. T o find out, what part of the measured data is expla[...]

  • Page 21

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

  • Page 22

    Printing MCE User’ s Guide 18 2004-05-17 NM20600A-A The EPS formats suit well the Arro w (p. 30), Amplitude (p. 31), and Region of interest (p. 34) windo ws. In the con version of the color displays (Color display (p. 29), Color scale (p. 33)) some errors may occur; the JPEG or PNG formats are more suitable for them. 10.3 Sa ving with xgifdump co[...]

  • Page 23

    MCE User’ s Guide Creating HTML documents and MPEG movies NM20600A-A 2004-05-17 19 11 Creating HTML documents and MPEG mo vies 11.1 Creating HTML documents F igure 9 An example of a cr eated HTML document Y ou can create HTML documents with the HTML document creation dialog (p. 38). The document will include projected, color coded vie ws of the e[...]

  • Page 24

    Creating HTML documents and MPEG movies MCE User’ s Guide 20 2004-05-17 NM20600A-A T able 2 Default viewing orientations for created HTML documents MPEG movies 11.2 Creating mo vies Y ou can create MPEG movies with the Mo vie creation dialog (p. 39). The movie will sho w projected, color coded views of the estimate from the selected orienta- tion[...]

  • Page 25

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 21 12 MCE windows and dialogs 12.1 Windo w menus F igure 10 Menus of the Main W indow (p. 22) File Windows Opens the dif ferent windows Colors Selects the color map for current windo w Help Options Some windo ws have specific options. Create HTML ... Opens the HTML creation dialog ([...]

  • Page 26

    MCE windows and dialogs MCE User’ s Guide 22 2004-05-17 NM20600A-A 12.2 Main windo w F igure 11 The main window The main windo w is opened when the program starts, and closing it quits the pro- gram. T able 3 Contr ols in the Main window Options menu The [Options] menu in the main windo w includes buttons [MNE options] , [Pre- processing] , and [[...]

  • Page 27

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 23 F igure 12 Minimum norm estimate options dialo g The [Regularization] slider and text field select and sho w the number of singu- lar v alues of the data used in the estimate. If the noise lev el in the measurement is lo w , increase the value to correctly estimate more comple x [...]

  • Page 28

    MCE windows and dialogs MCE User’ s Guide 24 2004-05-17 NM20600A-A F igure 13 The pr e-pr ocessing dialog The left side of the windo w shows controls that you can use to pre-process the data. W ith the filter frame you can lo w-pass filter the data, with the baseline frame you can compensate for the DC le vel and slo w drifts. W ith the pr ojec[...]

  • Page 29

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 25 T able 4 Contr ols in the Pr e-pr ocessing dialog Filter frame The [Lowpass filter] toggle selects the filter . Y ou can select the cutof f frequency or transition width with the corresponding text fields or sliders.The v alues are in Hz. Use the [F req. response] and [Impulse [...]

  • Page 30

    MCE windows and dialogs MCE User’ s Guide 26 2004-05-17 NM20600A-A 12.4 MEG data dialog The MEG data dialog is opened with the [Show all] button of the Pre-processing dialog (p. 23). It sho ws wav eforms of all the channels overlaid based location. Left-clicking zooms in the image, right-clicking sho ws the maximum amplitude and channel in the se[...]

  • Page 31

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 27 12.5 Full calculation dialog F igure 14 The full calculation dialog The full calculation dialog is opened by pressing the [Full] b utton in the Main windo w (p. 22). This windo w is used to calculate (p. 11) or load (p. 12) the minimum norm esti- mates of a whole response. The cal[...]

  • Page 32

    MCE windows and dialogs MCE User’ s Guide 28 2004-05-17 NM20600A-A 12.6 Batch jobs windo w F igure 15 The batc h jobs window This windo w controls the calculation of the estimates. The list shows current batch jobs and their states. The preferred way to start a calculating all the jobs, press the [Star t ser ver] b utton. This will be done in the[...]

  • Page 33

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 29 12.7 Color displa y F igure 16 Color display of the estimate The color display is opened by selecting [Color displa y] in the Windo ws menu (p. 21). The color display sho ws the estimated source distribution projected to the sur- face of the brain. The projection is done along the[...]

  • Page 34

    MCE windows and dialogs MCE User’ s Guide 30 2004-05-17 NM20600A-A 12.8 Arro w display F igure 17 Arr ow display of the estimate The arro w display is opened by selecting [Arrow displa y] in the W indows menu (p. 21). The arro w display shows the 3-dimensional estimated source locations and orienta- tions. If a time period is selected, the a vera[...]

  • Page 35

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 31 12.9 Amplitude windo w F igure 18 The amplitude window with total activity F igure 19 The amplitude window with an oriented R OI The amplitude windo w is opened by selecting [Amplitude] in the W indows menu (p. 21).[...]

  • Page 36

    MCE windows and dialogs MCE User’ s Guide 32 2004-05-17 NM20600A-A The amplitude windo w shows the acti vity of the selected R OI (p. 14) during the whole response. Y ou can also use it to select a time point or time range (p. 13). T o select a time point, use the left mouse button. T o select a time range, drag with the right mouse button. The t[...]

  • Page 37

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 33 12.11 Color scale windo w F igure 21 The color scale window The color scale windo w is opened by selecting [Color scale] in the W indo ws menu (p. 21). Y ou can adjust the color scale of the Color display (p. 29) using the color scale windo w . Constant color mode By pressing the [...]

  • Page 38

    MCE windows and dialogs MCE User’ s Guide 34 2004-05-17 NM20600A-A Things to remember Remember that the Arro w display (p. 30) has different color scale and check that you are using the same color map (p. 21) in dif ferent windows. Remember also, that because the estimation method tries to minimize the current, the absolute scale of the estimate [...]

  • Page 39

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 35 12.13 R OI database window F igure 23 The R OI database The R OI database windo w is opened by selecting [ROI database] in the W in- do ws menu (p. 21). The R OI database windo w is your contains your interface to the database of pre- viously selected brain areas, R OIs (p. 14). T[...]

  • Page 40

    MCE windows and dialogs MCE User’ s Guide 36 2004-05-17 NM20600A-A R OI search T able 8 Contr ols in the upper left corner R OI list The list on the right side sho ws the R OIs matching your specifications. The com- ment, the name of the fif-file the selection is based on, and the name of the creator are sho wn. Select a R OI by pressing the l[...]

  • Page 41

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 37 Current R OI T able 9 Contr ols in the lower left corner Other controls T able 10 Contr ols in the bottom r ow SQL database All the R OI queries are done from an database server using SQL query lan- guage. Some examples ho w to refine your queries: • x<0 • x<0 AND y>[...]

  • Page 42

    MCE windows and dialogs MCE User’ s Guide 38 2004-05-17 NM20600A-A [Options] menu The selected R OI can be exported to a file with the [Expor t new file] button. The [Append] button adds the selected ellipsoid to the pre viously selected output file. 12.14 HTML Creation Dialog F igure 24 The HTML Cr eation Dialog Y ou can open the HTML Creatio[...]

  • Page 43

    MCE User’ s Guide MCE windows and dialogs NM20600A-A 2004-05-17 39 T able 11 Contr ols in the HTML Cr eation Dialog 12.15 Mo vie Creation Dialog F igure 25 The Mo vie Creation Dialo g [File] Select the output file name. The PNG picture files will be created with the same prefix and dif ferent suffix es. [Time periods] Select the time periods [...]

  • Page 44

    MCE windows and dialogs MCE User’ s Guide 40 2004-05-17 NM20600A-A Y ou can open the Movie Creation Dialog from the [File] menu. T able 12 Contr ols in the Movie Cr eation Dialog [File] Select the output file name [Time points] Select the time points with format begin:skip:end For e xample, for a movie from 100 to 300 ms with 10 ms step between [...]

  • Page 45

    MCE User’ s Guide NM20600A-A 2004-05-17 41 Index A Adobe Illustrator 17 amplitude 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 33 detrend 4 batch jobs 11, 28 BEM. See boundary element model boundary element model 8 C calculating 11 color scale consta[...]

  • Page 46

    MCE User’ s Guide 42 2004-05-17 NM20600A-A Q quitting 3 R references 2 region of interest 14, 34 center 37 database 15, 35 definition 14 exporting 15, 38 extent 37 hard 14 orientation 14 selecting 15, 29 smooth 14 regularization 23 ROI. See region of interest S server 11 SQL query language 37 SSP 6 starting the program 3 subject 15 T time 13, 22,[...]