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EEG Tutorial using Brain Vision Analyzer

Transcript of EEG Bootcamp

  • S.J. Luck ERP Boot Camp All rights reserved

    ERP Boot Camp: Data Analysis Tutorials (for use with BrainVision Analyzer-2 Software)

    Preparation of these tutorials was made possible by NIH grant R25MH080794

    Emily S. Kappenman, Marissa L. Gamble, and Steven J. Luck

    Center for Mind & Brain and Department of Psychology

    University of California, Davis Contact information for corresponding author: Emily S. Kappenman UC-Davis Center for Mind & Brain 267 Cousteau Place Davis, CA 95618 530-297-4425 (phone) 530-297-4400 (fax)

  • S.J. Luck ERP Boot Camp All rights reserved Activity 1


    Activity 1

    Learning the Boot Camp Data Analysis Software

    Learning Brain Vision Analyzer In the first activity we will overview the basic structure of the Analyzer program, including how to navigate the workspace. There are many features available in Brain Vision Analyzer, but due to time constraints we are only going to review the basic features that are most applicable to the boot camp lectures. You are welcome to work on your own to explore the additional features of Analyzer that we will not cover. To explore these options or for all of your general questions about Analyzer, we have provided the Analyzer manual at: C:\Bootcamp_Analyzer2\Documentation\Analyzer.pdf Workspace Analyzer uses workspaces to keep track of files and analysis steps. Typically, you would create a separate workspace for each experiment you conduct. We have already created a workspace for you with the raw files we will be using for the demos. Launch the Analyzer2 program by double clicking on the Vision Analyzer icon on the desktop. To load the workspace we created, go to File > Workspace > Open and click on Bootcamp_Analyzer2.wksp (located in C:\Bootcamp_Analyzer2). On the far left side of the screen is a list of the main files in the workspace. You should see four items listed, each with a name and an icon that looks like a little book. The first one labeled AnalyzerIntro can be used for this section. Analyzer adds new nodes under the original node for each step in the analysis to create a tree of nodes. In order to expand the tree for a particular item, click on the + sign next to the icon. You can also expand the tree by right clicking and selecting Expand All. Do this now for the AnalyzerIntro tree. You should see a number of nodes that we will now take you through. Your workspace should look like this:

    . First lets make sure that we are viewing the data in the same way. We are a positive-up lab. To properly compare the work that you do and the pictures you see in this manual, you need to have the same polarity configuration. To check the polarity, go to File > Configuration > Preferences and click on the Scaling tab. Make sure the box that says Polarity Positive Down is unchecked.

  • S.J. Luck ERP Boot Camp All rights reserved Activity 1


    Raw Files The first node in the AnalyzerIntro tree is labeled Raw_Data. There will be a node labeled Raw_Data for each of the demos that contains the raw data for that demo collected with the BioSemi system; however, Raw_Data does not contain the correct event code information. In Analyzer, BioSemi data files have to be decoded with a macro in order for the program to reflect the event code information in a numerical way. We have already completed this decoding step for you for each of the Demos. For the present demo, there is a node labeled AnalyzerIntro_Raw below the Raw_Data node. If you double click on this AnalyzerIntro_Raw node you can see the raw EEG data, decoded with numerical event codes (you may have to move forward in the data to see the event codes). We will be ignoring the Raw_Data node for each demo and will instead use this second raw data node for each of the demos (in this case, AnalyzerIntro_Raw). Take a minute to play around with the raw data and become familiar with the information available. The channel labels are on the left side of the screen and event codes appear on the bottom of the screen. You can also see the time relative to the beginning of the data file at the bottom right of the screen. This is important, as many of the demos will require you to find a particular time point in a particular raw file. You can move forward or backward in a raw file by clicking on the blue arrow buttons at the bottom left of the screen. If you place the cursor over a particular point on one of the lines of EEG, you can see the voltage, channel name, and time in seconds of that particular point in the bottom right of the screen. It is always a good idea to fully examine the raw EEG from each of your subjects before performing any filtering, artifact rejection, or data analysis to ensure that there were no problems during recording (we will discuss this more in later tutorials). Segmented Files The third node in the AnalyzerIntro tree is labeled Segmentation1. This node contains segments of data (known as epochs in some analysis programs). These segments correspond to trials from the experiment, and they were created using particular event codes (we will show you how to do this later). If you want to know what processing steps were performed on a particular node in a tree in Analyzer, you can find this information by right clicking on the name of the node and selecting Operation Infos. This will tell you all of the processing steps completed on this node. If you do this for the segmented data node labeled Segmentation1, you should be able to tell which event codes (also known as reference markers) were used to create the segments, the starting point, the ending point, whether or not overlapped segments were allowed and the total number of segments that fit those parameters. If you double click on the node Segmentation1, you can see that each of the channels is displayed in a separate box. If you wish to view a close-up of a given channel, you can double click on the channel name in the upper left part of the box (e.g., C3) and that channel will expand to fill the screen. To view all of the channels simultaneously again, simply double click on the channel name again. Just like you saw with the raw data file, there is information about the segmented data at the bottom of the screen. Here you can see the total number of segments in the node. Right now we are on segment 1 out of 256 segments. To scroll through the segments, you simply click on the arrow buttons, as you did to scroll through the raw EEG data.

  • S.J. Luck ERP Boot Camp All rights reserved Activity 1


    Now go to the next node, BaselineCorrection1. One useful feature of Analyzer is the ability to overlay information from different nodes or different channels. For example, if we want to overlay channels C3 and C4, you can simply drag the C4 box onto the C3 box, and the waveform for channel C4 will appear in a different color overlaid with channel C3. To remove the overlaid waveform, press the Clear Overlays button.

    In addition, Analyzer allows you to overlay waveforms from different nodes in a tree. For example, if we want to overlay two sets of segments (in this case, BaselineCorrection1 and BaselineCorrection2), we first double click to select BaselineCorrection1. The waveforms should now be visible. Next, drag the BaselineCorrection2 node, which can be found under Analyzer Intro -- Raw Data -- AnalyzerIntro_Raw -- Segmentation2 -- BaselineCorrection2, onto the waveforms. The waveforms from these two nodes should now be overlaid. Feel free to go back and right click on the segmentation nodes and select Operation Infos. See if you can figure out what the difference is between the two nodes that you have overlaid. Other Useful Points It can sometimes be a little difficult to select a particular node, so make sure to double click carefully on the node you wish to select. If you perform an operation and the results do not look like the pictures in this manual, it is likely that a different node was selected when you performed the operation.

  • S.J. Luck ERP Boot Camp All rights reserved Activity 1


    If this happens or you make another type of error or wish to delete a step in the analysis tree, you can simply right click on the n2de and select Delete. Lets try this now. Delete the BaselineCorrection2 node by right clicking and selecting Delete. Now lets recreate the node we just deleted. In other words, lets create a baseline correction node for Segmentation2, so that we have the same analysis steps for Segmentation1 and Segmentation2. Analyzer allows you to duplicate operations performed on one node on a second node very easily. This allows you to save a lot of time if you are analyzing multiple subjects or data sets. To do this, simply drag the node that has the operation you want to duplicate onto the node on which you want to perform the operation. For example, to perform the baseline correction we did for Segmentation1 on Segmentation2, we simply drag the BaselineCorrection1 node onto the Segmentation2 node. Do this now. Analyzer performs the operation from the first node on the second node for us. In addition, if there had been subsequent steps after baseline correction, it would have performed all of those as well. Just make sure to rename the new nodes to keep track of them. For example, Analyzer named the new baseline correction node you created, BaselineCorrection1. You should rename this node BaselineCorrection2 by right clicking and selecting Rename, or by clicking once on the name, pausing, and clicking a second time. Most of the activities in this tutorial will require that you use some type of transformation. These can be found underneath the Transformations tab the top of the Analyzer window. The trans