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ASA User Manual Version 4.7 September 2009
ANT BV, Enschede, The Netherlands
A.N.T. BV Colosseum 22 7521 PT Enschede Netherlands e-mail phone fax internet
[email protected] +31 (0)53-4365175 +31 (0)53-4303795 http://www.ant-neuro.com
ASA 4.7 User Manual
Table of Contents 1 Introduction ... 7 1.1 Welcome to ASA ... 7 1.2 Installation/Deinstallation of ASA ... 9 1.3 System requirements... 10 1.4 Supported data formats ... 11 1.5 Indications for use ... 14 1.6 Remarks concerning MEG ... 14 2 ASA Workspace ... 15 2.1 Workspace ... 15 2.2 View panel ... 17 2.3 Montage per view ... 19 2.4 Synchronize views ... 23 2.5 Save view layout ... 24 2.6 Workspace view ... 25 2.7 Status view ... 27 2.8 Status bar ... 30 2.9 Event navigation bar ... 31 2.10 Toolbars ... 32 2.10.1 General information about toolbars ... 32 2.10.2 Standard toolbar ... 33 2.10.3 EEG toolbar ... 34 2.10.4 Feature toolbar ... 36 2.10.5 View toolbar ... 37 2.10.6 3D Image toolbar ... 38 2.10.7 Set marker toolbar ... 39 2.10.8 Events toolbar ... 44 2.10.9 Segmentation toolbar ... 45 2.10.10 Macro toolbar ... 46 2.10.11 Video toolbar ... 47 2.11 Views ... 48 2.11.1 Save View Properties ... 50 2.11.2 EEG data view ... 51 2.11.3 CDSA view ... 68 2.11.4 Spectrum view ... 80 2.11.5 3D Mapping views ... 98 2.11.6 3D Coherence view ... 152 9/29/2009
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2.11.7 3D image view ... 159 2.11.8 Dipole waveform view ... 179 2.11.9 List views ... 182 2.11.9.2 Channel list ... 183 2.11.9.3 Group list ... 185 2.11.9.4 Electrode list... 186 2.11.9.5 Spike list ... 187 2.11.9.6 Event list ... 189 2.11.9.7 Epoch event list... 191 2.11.9.8 Patient data list... 193 2.11.9.9 Dipole list ... 194 2.11.9.10 Image marker list... 197 2.11.10 Working with views ... 199 2.11.10.1 View properties ... 199 2.11.10.2 Split the view panel ... 200 2.11.10.3 Change the active view ... 202 3. Working with ASA ... 203 3.1 Study manager ... 203 3.2 Starting a project... 207 3.3 Application Options ... 209 3.4 Navigation in time and frequency ... 224 3.5 Goto time control and functionality... 228 3.6 Shortcuts ... 229 3.7 Events ... 231 3.7.1General Information about Events... 231 3.7.2 Set an event marker ... 232 3.7.3 How to Mark Artefacts ... 236 3.7.4 Generate epoch events... 237 3.7.5 Move events ... 239 3.8 Montages ... 240 3.8.1 What is a Montage? ... 240 3.8.2 Montage editor ... 241 3.8.3 Montage types ... 246 3.8.4 Adjust channel properties ... 247 3.8.5 Create a new montage ... 248 3.8.6 Copy a montage ... 248 3.8.7 Assign channels to a montage ... 249 3.8.8 Define a virtual reference ... 250 3.9 Select objects ... 252 3.9.1 Select channels ... 252 3.9.2 Select electrodes... 253 3.9.3 Select spikes ... 254 3.9.4 Select events ... 255 9/29/2009
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3.9.5 Select dipoles ... 256 3.10 Features ... 257 3.10.1 Reading files ... 258 3.10.1.1 Reading the EEG file ... 258 3.10.1.2 Reading the electrode file... 259 3.10.1.3 Reading the head model file... 260 3.10.1.4 Reading the image file ... 261 3.10.1.5 Reading the spectrum data file ... 262 3.10.1.6 Reading the dipole file ... 263 3.10.2 Saving files and Data export (Writing files) ... 264 3.10.2.1 Saving and sending analysis files ... 264 3.10.2.2 Data export ... 265 3.10.2.3 Export of EEG/MEG files and segments ... 266 3.10.2.4 Export events ... 267 3.10.2.5 Export electrodes ... 268 3.10.2.6 Head model export ... 271 3.10.2.7 FFT analysis export ... 272 3.10.2.8 Coherence analysis export ... 279 3.10.2.9 Export of dipoles ... 282 3.10.2.10 Export of MUSIC and LORETA results ... 283 3.10.2.11 Export of MRI files... 285 3.10.3 Head modeling ... 286 3.10.3.1 Setting image markers ... 286 3.10.3.2 Performing the segmentation ... 292 3.10.3.3 Generate head model ... 295 3.10.3.4 Create Curvilinear Surface ... 298 3.10.3.5 System matrix computation ... 300 3.10.4 Signal processing ... 304 3.10.4.1 Performing the artefact detection ... 304 3.10.4.2 Performing the artefact correction feature ... 308 3.10.4.3 Performing the spike detection feature ... 315 3.10.4.4 Performing the seizure detection feature ... 319 3.10.4.5 Performing the filtering ... 325 3.10.4.6 Performing the Surface Laplacian feature ... 328 3.10.4.7 Performing the resampling of data ... 330 3.10.4.8 Performing the averaging ... 333 3.10.4.9 Performing the FFT analysis ... 335 3.10.4.10 Performing the Wavelet analysis ... 340 3.10.4.11 Phase locking ... 346 3.10.4.12 Performing the coherence analysis... 348 3.10.4.13 Performing the baseline correction ... 352 3.10.4.14 Performing the detrending ... 357 3.10.4.15 Performing the signal subtraction ... 362 9/29/2009
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3.10.4.16 Performing the conditioning ... 366 3.10.4.17 Grand Averaging ... 383 3.10.4.18 Hilbert Filter ... 388 3.10.4.19 ERD / ERS ... 391 3.10.4.20 Merge Channel Sets ... 396 3.10.4.21 Channel Interpolation ... 400 3.10.4.22 Difference of Data Sets ... 404 3.10.4.23 Trigger Extraction ... 405 3.10.4.24 Sensor Manipulation ... 406 3.10.4.25 Rearrange 3D Images ... 409 3.10.4.26 TMS Artefact Correction ... 411 3.10.4.27 R peak detection ... 413 3.10.5 Source reconstruction ... 416 3.10.5.1 Performing the dipole fit ... 416 3.10.5.2 Source reconstruction with MUSIC ... 420 3.10.5.3 Source reconstruction with LORETA ... 424 3.10.5.4 Source reconstruction with sLORETA and swLORETA ... 439 3.10.5.5 Source reconstruction with sLORETA in the frequency domain ... 445 3.10.5.6 Source reconstruction with Cortical Imaging ... 449 3.10.5.7 Forward Simulation ... 455 4. Data Acquisition with ASA ... 458 4.1 Preparation of the ASA Data Acquisition... 459 4.2 Workflow of EEG/ERP Data Acquisition with ASA ... 460 5 Video Recording, Review, and Editing ... 468 5.1 Video View ... 468 5.2 Video data recording ... 469 5.3 Video Review ... 478 5.4 Video Editing ... 481 6 Working with Macros ... 489 6.1 Automating tasks with macros ... 489 6.2 Record macros ... 490 6.3 Stop macros ... 491 6.4 Edit macros ... 492 6.5 Start macros ... 493 6.6 Delete macros ... 493 7. References ... 494 7.1 Frequency band mapping (FFT)... 494 7.2 Dipole source localization (DSL) ... 495 7.3 Coherence Analysis ... 496 7.4 ERD / ERS ... 497 7.5 Filter ... 499 7.6 Phase locking analysis ... 501 7.7 DICOM (Digital Imaging and Communications in Medicine) ... 502 9/29/2009
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7.8 MRI coordinate systems ... 503 7.9 Inverse methods... 536 7.10 Segmentation and head model generation ... 560 7.10.1 Realistic head models ... 560 7.10.2 Segmentation ... 561 7.10.3 Region growing ... 562 7.10.4 Generating realistic head models ... 563 7.11 File formats ... 565 7.11.1 EEG/MEG/Laplacian file format... 565 7.11.2 Electrode file format ... 568 7.11.3 Current dipole file format ... 570 7.11.4 MRI file format ... 574 7.11.5 Boundary file format ... 576 7.11.6 Volume Conductor file format ... 578 7.11.7 Matrix file format ... 579 7.12 Time interval definitions and Time formats ... 580 7.12.1 FFT and coherence interval definitions ... 580 7.12.2 Time basis using event duration (Baseline correction feature) ... 584 7.12.3 User-defined time basis ... 585 7.12.4 Time formats... 586 8. Licensing ... 589 8.1 General information about the licensing system ... 589 8.2 Test license ... 590 8.3 License registration of ASA ... 591 8.4 Import / export a license ... 592 8.5 Problems with licensing ... 593 8.6 License Modules ... 594
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1 Introduction 1.1 Welcome to ASA
ANT b.v. developed ASA 4 in close cooperation with eemagine GmbH, following a new approach of handling data and with a new user interface. The Advanced Source Analysis (ASA) software package is designed for functional brain imaging based on EEG/MEG measurements. Recordings can be visualized in a three-dimensional context together with their sensors, a model of the head and the MRI. The software offers different approaches to source localization based on either spherical or realistic head modeling. MRI can be used to generate surface models of the head, and to provide anatomical information for the visualization of brain activity. ASA Experiment Manager for ERP group analysis is included in the ASA installation. Please refer to the ASA Experiment Manager Reference Manual in order to get detailed information. Version: 4.7
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MANUFACTURER: eemagine Medical Imaging Solutions GmbH Comeniushof (Fabrik) Gubener Str. 47 D-10243 Berlin Germany Phone: Fax: E-Mail:
+49 (0)30 2904-8404 +49 (0)30 2904-8405 [email protected]
DISTRIBUTOR: ANT B.V. (Advanced Neuro Technology) Colosseum 22 NL-7521 PT Enschede Netherlands Phone: Fax: Website: E-Mail:
+31 (0) 53 436 5175 +31 (0) 53 430 3795 http://www.ant-neuro.com [email protected]
DISCLAIMER We have attempted to write this manual as accurately as possible. However, mistakes are bound to occur, and we reserve the right to make changes to ASA, which may render parts of this manual invalid. We assume no liability as a result of the use or application of this product. No part of this manual may be copied or reproduced without the express permission of the authors. Document version: ASA user manual 1.4.0.9 Related ASA version
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1.2 Installation/Deinstallation of ASA In order to install ASA onto your PC, please insert the installation CD in the CD-ROM drive. The installation program starts automatically if the autorun function is enabled. Otherwise, please execute the program setup.exe on the CD. The installation procedure guides you through the necessary steps. When you start ASA for the first time, the dialog "Test License" is displayed. Simply click on the OK button to use the 30-day trial license. The dialog is shown every time you start up ASA, to show the remaining days of use. Please contact us to obtain a permanent license. Add-Ons If you want to use ASA add-ons Data Acquisition and Xensor, you have to select the referring Add-Ons during the installation procedure. Otherwise, toolbars and view layouts for these add-ons will not be available.
Deinstallation ASA supports the deinstallation of the program. To remove ASA, please use the option Add / Remove Programs in the control panel. Note: Windows NT users should be logged in as administrator.
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1.3 System requirements
• • • • • • •
Pentium 900 MHz or higher 128 MB working memory (256 MB RAM recommended, 512 MB RAM for High Speed Recording) Wheel-Mouse recommended MS Windows XP (SP2 recommended) MS Internet Explorer 6.0.26 or higher DirectX 9.0 c or higher Screen resolution: recommended min. 1024 x 768
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1.4 Supported data formats New data formats and features are constantly being added to ASA. If you don't find your data format mentioned here, please contact us. Data formats of major manufacturers of EEG, MEG, and MRI can be imported. ASA file formats are extensively described and can easily be dealt with. In the following tables: Abbreviation EEG MEG PAT EVT MNT
Meaning EEG data MEG data Patient information Events Montages
On the next pages, supported data formats for
EEG EEG data export MEG MRI
are listed in separate tables.
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ASA 4.7 User Manual EEG data importers: The ASA software package can currently be connected to the following data format or systems: Alpha-Trace DigitalEEG (.alp) ASA (ANT Software B.V.) (.msr) BESA BrainVision Curry Deltamed Coherence EBNeuro Galileo DOS (.gtf) EBNeuro Galileo NT (.gnt) EEProbe (ANT Software B.V.) (.avr) Electrical Geodesics (EGI) (.ave) EMS Pegasus 1 and 2, EMS Pegasus (Events) European Data Format (.edf, .rec) Micromed (.trc) MPI Nijmegen (MPIData) (.data) Nation 9128 NCI Uniquant (.sif) Neuroscan AVG, CNT and EEG (.avg, .cnt, .eeg) Nicolet AllianceWorks Intuition (.eeg) Nicolet BMSI 5000 (.eeg) Nicolet BMSI 6000 (.eeg) Nicolet Bravo Intuition Nicolet EEG Vue (.eeg) Nicolet UltraSom NT (.eeg) Nicolet Voyageur (.data) Nihon Kohden 2100 (.eeg) Partig Medical ASPP Persyst Layout (Exported Data) (.lay) Schwarzer/OSG (.sig) Stellate Harmony Stellate Monitor Stellate Rhythm Telefactor (.tmsp, .ref) TMSI SMP (.smp) Vangard (k.*) WalterGraphtek/Dantek PLEEG (.WG1) XLTEK
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EEG, PAT, EVT EEG, MNT EEG EEG EEG EEG, PAT, EVT EEG, PAT, EVT EEG, PAT, EVT EEG, EVT EEG, PAT EEG, PAT EEG, PAT, EVT EEG, PAT, EVT, VIDEO EEG, PAT EEG, PAT EEG, PAT, EVT, VIDEO EEG, PAT, EVT EEG, PAT, EVT EEG, PAT, EVT, VIDEO EEG, PAT, EVT, VIDEO EEG, PAT, EVT EEG, PAT, EVT EEG, PAT, EVT EEG, PAT EEG, PAT, EVT EEG EEG EEG, PAT, EVT EEG, PAT, EVT EEG EEG EEG, PAT EEG, PAT EEG, PAT EEG, PAT EEG, PAT, EVT, MNT, VIDEO
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ASA 4.7 User Manual MEG data importers: Data format
MEG
4D_BTI ASA (.msr) CTF Neuromag (.fif)
X X X X
PAT
EVT
Currently supported data formats for data export: Data format ASA (.msr) European Data Format (.edf, .rec) ASCII EEProbe
EEG 16 bit X X
EEG 32 bit
PAT
EVT
X X
X
X X
MNT
X X
MRI data importers: Data format
MRI
ASA Analyze DICOM NeuromagMRI Nifti
X X X X X
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1.5 Indications for use ASA is not designed for clinical diagnosis and have not FDA pre-market approval. If they are to be used for clinical research, they may require approval by an institution's Institutional Review Board.
1.6 Remarks concerning MEG ASA enables you to analyze EEG data as well as MEG data. If in this manual EEG is mentioned, explanations also refer analogously to MEG data unless other remarks are not given explicitly. Note: Review of MEG data and performing many feature with MEG data can be done with the licenses Basic, Mapping, Signal Processing, and Spectral Analysis. Source localization for MEG data requires the MEG license module.
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2 ASA Workspace 2.1 Workspace The ASA workspace is the screen space occupied by the application. The workspace consists of three elements: I. II. III.
The Status View in the upper left upper portion, The Workspace view in the lower left lower portion, and The View panel in the right portion.
The Status View gives you information about the current project, such as the number of electrodes or events. The Workspace view visualizes your analysis in a comprehensive way. It shows which steps have been performed. The View panel provides visualization of data in different views. The area of the view panel can be subdivided into one, two or four views. You can hide the status view and the workspace view in order to enlarge the area of the view panel at your disposal.
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Figure 1: ASA Workspace
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2.2 View panel The view panel is the area of the workspace that displays data. Since the data shown in ASA are very different in appearance (EEG traces, 3D maps, MRI images, lists, etc.), the display offers different views as well. The view panel can be subdivided into one, two, or four views. The splitting of the view panel into two or four views can be carried out through the menu option Window / Split. Alternatively, you can use the split bars. Please note that every step defines its own view panel. The choice of a particular view depends on the type of data to be shown at a certain stage of the analysis. The predefined default views can be changed interactively. An important detail of ASA is that all views are synchronized with each other through the selection mechanism. If, as shown in the figure below, a dipole is selected in the Dipole list view (top right), then all other views show the data related to this dipole: the dipole and the voltage map that belongs to its latency (3D mapping view, top left), the dipole in the respective MR image (3D image view, bottom left), and the respective page of EEG data with the spike event that belongs to the dipole (EEG data view, bottom right). This works equally in all views, regardless of the view selected. Note: Only one view in the view panel is active at one time. This active view receives the input focus. All keyboard inputs (such as arrow keys or PgUp / PgDn), menu options, and settings in the toolbars are routed to the active view. The active view is marked with a blue rectangle (as the dipole list view shows in the figure below). To change the active view, click with the left mouse button in the area of the desired view. If you want to change the view to another type, use the View menu and choose one of the available options. The new view replaces the active view.
Note: The layout of the view panel can be saved. The view layout in this context means the number and type of views, which are displayed in the view panel. To save the view layout, right-click on the view panel to activate the context menu. Select View Layout / Capture and Save Current Layout. (See the next section 2.3 for details) Note: Full screen mode Select the full screen icon mode.
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in the Views toolbar or press the F11 key to show the view panel in the fullscreen
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Figure 1: View panel showing four views, which are synchronized with each other Note: Views can not only “synchronized” in time mode but also in frequency mode. For example, when you have the 3D frequency view and the spectrum view open in the view panel, you can select “current frequency” from the Bands control in the EEG toolbar. Then, clicking into the spectrum view at a certain frequency results in showing the frequency mapping for this frequency. In a similar way, source localizations can be analyzed in the frequency domain. For this, perform the sLORETA feature in the frequency domain and choose “current frequency” as dipole setting in the 3D image view properties dialog.
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2.3 Montage per view Usually a montage is applied to all views displayed in the view panel. The montage used is shown in the montage control of the EEG toolbar. An additional feature of ASA is that you can see EEG data of different montages at the same type. This is done by specifying the montage in the properties dialog of the view, e.g. the EEG data view.
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ASA 4.7 User Manual Procedure 1. Split the view panel, as a result there are 2 EEG data views. 2. Double-click the second EEG data view to open the properties dialog. Select the Montage tab
Figure 1: Montage tab of the EEG data view properties dialog. The referring view should take the montage "Copy As Recorded". By checking the control, "Show selected montage in view", the montage used will be displayed above the view. 3. Make the settings as shown in Fig. 1. The montage "New Montage" was created before with the Montage editor. 4. Press the OK button to apply the montage settings to the view and to close the properties dialog.
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