BCI2000 Wiki - User contributions [en]

Contributions:BCI2000Command

2025-06-19T20:43:27Z

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==Synopsis==
BCI2000Command is a command line program that controls the BCI2000 Operator. It allows remote control of BCI2000 from command interpreters (shells), such as the WIndows CMD interpreter, or the bash or tcsh shells on Unix systems., or any environment that provides access to Windows automation components. It wraps up the functionality of the [[Programming Reference:BCI2000Remote Class|BCI2000Remote]] C++ class. When writing C++ code, you should consider using that class directly rather than BCI2000Command.

Before you can use it, BCI2000Command must be in your operating system's path variable. Typically, you will keep BCI2000Command inside the BCI2000/prog directory, and add that directory to the path variable.

==Location==
http://{{SERVERNAME}}/svn/trunk/src/contrib/ExternalLinks/BCI2000Command

==Versioning==
===Author===
juergen.mellinger@uni-tuebingen.de
===Source Code Revisions===
*Initial development: 3946
*Tested under: 3953

==Functional Description==
BCI2000Command is a command line interface to the BCI2000 Operator module, and allows to start up, configure, and run BCI2000 from the command line, or from command line scripts (batch files).

Calling "BCI2000Command Run" will start up the Operator module residing in the same directory as BCI2000Automation. You may then use "BCI2000 Command StartupModules" in order to start up BCI2000 core modules.

Alternatively, you may specify the path to a BCI2000 batch file in the BCI2000/batch directory in the ''BCI2000OperatorPath'' environment variable. An appropriate batch file should start up Operator and core modules, and needs to forward its command line arguments to the Operator module. All batch files coming with BCI2000 fulfil this condition. When a batch file is specified, there is no need to call the StartupModules command.

As yet another option, you may connect to an Operator module that is already running, e.g., on a remote machine on the network. In this case, set the BCI2000OperatorPath environment variable to an empty string, and the BCI2000TelnetAddress environment variable to the address that the remote Operator module is listening on, i.e. the remote machine's IP address, followed with a colon, and the port specified when starting up the remote Operator module. The remote Operator module must have been started with the --Telnet command line option, followed with the address to listen on. On the remote machine, this would typically be "localhost:3999". Don't use any of the ports between 4000 and 4002, as this will interfere with the communication between the Operator module, and BCI2000 core modules. Depending on whether the remote Operator module has been started up together with its core modules, or not, you may then call "BCI2000Command StartupModules" in order to start up BCI2000 core modules on the remote machine.

Once all BCI2000 modules are running, you may load parameter files locally or remotely using the LoadParametersLocal and LoadParametersRemote commands. Subject ID, Session ID, and data directory are set using the BCI2000SubjectID, BCI2000SessionID, and BCI2000DataDirectory environment variables.

A recording may then be started by calling the Start command. Depending on configuration, the recording will terminate automatically, or needs to be terminated by calling the Stop command.

To run BCI2000 in a different configuration (i.e., with different core modules), it is not necessary to terminate the Operator module. Rather, you may execute StartupModules multiple times in order to terminate currently running core modules, and start different ones.

Once you are done using BCI2000, you may quit the Operator module using "BCI2000Command Quit".

==BCI2000Command vs. BCI2000Shell==
BCI2000Command provides functionality similar to [[User Reference:BCI2000Shell|BCI2000Shell]], which is a shell that executes [[User Reference:Operator Module Scripting|Operator scripting commands]]. The choice between the two is mainly a choice between writing a shell script vs. writing a BCI2000 Operator script. One would choose BCI2000Command to integrate BCI2000 remote control into an existing system of shell scripts, whereas one would choose BCI2000Shell to use Operator scripting as the main language. However, some amount of overlap exists: BCI2000Command is able to execute arbitrary Operator scripting commands, and BCI2000Shell's ''-c'' option allows it to be run within shell scripts in a way similar to BCI2000Command. Still, BCI2000Command provides a higher-level interface than BCI2000Shell does.

==Reference==
BCI2000Command calling syntax is
BCI2000Command [--property1=value1 --property2=value2 ...] command [argument1 argument2 ...]

===Properties===
Properties correspond to the properties of the BCI2000Remote class, and may be given on the command line, or as environment variables named "BCI2000property". Existing properties are:
Timeout
TelnetAddress
OperatorPath
WindowVisible
WindowTitle
SubjectID
SessionID
DataDirectory

===Commands===
Commands are applied to the BCI2000 operator module listening at the address given by the TelnetAddress property (defaults to localhost:3999).
You may use the "Run" command to start up BCI2000 locally with appropriate parameters.
Available commands are:

====Run [<script file 1> <script file 2> ...]====
Makes sure BCI2000 is started up, and optionally executes BCI2000 script files. Script files are local to the system that runs BCI2000Command, and are specified relative to the current directory of the calling script or shell.

====Quit====
Terminates BCI2000.

====StartupModules <module1> <module2> ...====
Starts up BCI2000 modules.

====SetConfig====
Applies the current set of parameters.

====Start====
Starts a new run (recording).

====Stop====
Stops the current run (recording).

====GetParameter <name>====
Returns the value of the specified parameter.

====SetParameter <name> <value>====
Sets the value of the specified parameter. This command fails when the parameter does not exist. Use the ''Execute'' command in conjunction with the INSERT PARAMETER scripting command to add a parameter to the system.

====LoadParametersLocal <parameter file>====
Loads a parameter file relative to the current working directory.

====LoadParametersRemote <parameter file>====
Loads a parameter file relative to BCI2000's working directory.

====AddStateVariable <variable name> <bit width> <initial value>====
Adds a state variable to the system. This is only possible before core modules are connected to the Operator module.

====GetStateVariable <variable name>====
Returns the value of the named BCI2000 state variable.

====SetStateVariable <variable name> <variable value>====
Sets the value of the named BCI2000 state variable.

====GetSystemState====
Returns the current system state (i.e., state of operation). This will be one of Unavailable, Idle, Startup, Initialization, Resting, Suspended, ParamsModified, Running, Termination, Busy.

====GetControlSignal <channel index> <element index>====
Gets the value of the BCI2000 control signal. Indices are 1-based.

====Execute <scripting command>====
Executes a scripting command. Scripting commands with arguments must enclosed in quotes to be seen as a single argument.
The meaning of the return value depends on which command has been executed, and is the ''exit code'' of the command, as defined in the [[Programming_Reference:BCI2000Remote_Class#bool_Execute.28_string_command.2C_int.2A_exitCode_.3D_0_.29|BCI2000Remote Class Document]].

A full documentation of BCI2000 Operator scripting commands is available under [[User Reference:Operator Module Scripting]].

====SetScript <event> <scripting commands>====
Associates [[User Reference:Operator Module Scripting|Operator scripting commands]] with event, which is one of OnConnect, OnSetConfig, OnStart, OnResume, OnStop, OnShutdown.

====GetScript <event>====
Returns [[User Reference:Operator Module Scripting|Operator scripting commands]] associated with event, which is one of OnConnect, OnSetConfig, OnStart, OnResume, OnStop, OnShutdown.

==Examples==
===Windows cmd interpreter===
It is assumed that the BCI2000/prog directory is the current directory, or in the path.
<pre>
@echo off
setlocal
BCI2000Command Run
BCI2000Command StartupModules "SignalGenerator --LogMouse=1" ARSignalProcessing CursorTask || BCI2000Command Quit && exit /b 1
BCI2000Command LoadParametersLocal "path to myfile.prm"
BCI2000Command Start
:loop
BCI2000Command GetControlSignal 1 1
for /f "tokens=*" %%i in ('BCI2000Command GetSystemState') do set state=%%i
if %state%==Running goto loop
BCI2000Command Quit
</pre>

===Linux/Unix bash shell===
It is assumed that the BCI2000/prog directory is in the path.
<pre>#!/bin/sh
BCI2000Command Run || exit
BCI2000Command StartupModules "SignalGenerator --LogMouse=1" ARSignalProcessing CursorTask || ( BCI2000Command Quit && exit )
BCI2000Command LoadParametersLocal "path to myfile.prm"
if BCI2000Command Start; then
while [ `BCI2000Command GetSystemState` = Running ]; do
BCI2000Command GetControlSignal 1 1;
done
fi
BCI2000Command Quit
</pre>

==See also==
[[Programming Reference:BCI2000Remote Class]], [[Contributions:BCI2000PresentationLink]],[[Contributions:BCI2000PythonBindings]], [[User Reference:BCI2000Shell]], [[Contributions:Applications]]

[[Category:Contributions]][[Category:User Application]][[Category:External Interfaces]]

Contributions:Tools

2025-06-19T20:13:39Z

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The following tools are available in the [[Contributions:Contents|Contributions]] section:

*[[Contributions:FilterGUI]]: Apply an IIR filter to an existing BCI2000 data file.

The following are also still available as part of the old BCI2000 2.1 release, although they are no longer being developed:

*[[Contributions:P300GUI]]: Optimize P300 classifier weights in Matlab.
*[[Contributions:Batch]]: A GUI for online system startup.
*[[Contributions:BCIdiff]]: Analyze <tt>.dat</tt> files for differences.
*[[Contributions:BCITimeFrequency]]: Data analysis in time and frequency domains.
*[[Contributions:GenerateCalibration]]: Determine amplifier calibration parameters from a test signal recording.

==See also==
[[User Reference:BCI2000Viewer]], [[User Reference:BCI2000FileInfo]]

[[Category:Data Analysis Tools]][[Category:Contents]]

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Contributions:Extensions

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A framework ''Extension'' is an optional contributed plugin which can affect multiple modules. For example, various manufacturer-specific [[User Reference:Logging Input|input-device loggers]] are provided in the <code>src/contrib/Extensions</code> folder, and these can be optionally added to the BCI2000 framework for SignalSource modules, thereby giving all source modules the ability to log input from the corresponding devices. Selecting a custom Extension, and re-building your modules to include it, requires the use of CMake and a supported C++ compiler: see the [[Programming Howto:Quickstart Guide]] for a walkthrough that shows you how to recompile BCI2000 modules.

The following user extensions are available in the [[Contributions:Contents|Contributions]] section of BCI2000:

*[[Contributions:CyberGloveLogger]]: A logger extension which acquires data from CGI, CGII and CGIII Cybergloves.
*[[Contributions:DataGloveLogger]]: A logger extension which acquires data from the 5DT Data Glove Ultra.
*[[Contributions:EyetrackerLogger]]: A logger extension which acquires data from Tobii eyetrackers.
*[[Contributions:EyetrackerLoggerTobii3]]: A logger extension which acquires data from Tobii eyetrackers using SDK version 3
*[[Contributions:EyetrackerLoggerTobiiPro]]: A logger extension which acquires data from Tobii eyetrackers using Pro SDK
*[[Contributions:EyetrackerLoggerTobiiX]]: A logger extension which acquires data from Tobii Eye X eyetrackers.
*[[Contributions:GazeMonitorFilter]]: An application module filter extension which supports the EyetrackerLogger.
*[[Contributions:WiimoteLogger]]: A logger extension which acquires data from Nintendo Wii Remotes.
*[[Contributions:WebcamLogger]]: A logger extension which allows for synchronizing webcam video.
*[[Contributions:AudioExtension]]: An all purpose audio toolkit which allows for realtime multichannel audio I/O.
*[[Contributions:StimBoxFilter]]: A logger and controller for the gtec g.STIMbox.
*[[Contributions:ParallelPortFilter]]: A logger and controller for communication through parallel ports.

==See also==
[[Programming Reference:EnvironmentExtension Class]]

[[Programming Tutorial:Implementing an Input Logger]][[Category:Contents]]

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== Getting Started with BCI2000 ==

* [[Creating a User Account|Create a User Account]],
* Download [[BCI2000 Binaries]],
* Take the introductory [[User Tutorial:BCI2000 Tour|BCI2000 Tour]]<br />to learn about using BCI2000,
* Get access to the [[Programming Reference:BCI2000 Source Code|BCI2000 Source Code]].
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==User Tutorials==
Tutorial guides to your first successful experiments:
*[[User Tutorial:Mu Rhythm BCI Tutorial|Mu Rhythm BCI Tutorial]],
*[[User Tutorial:P300 BCI Tutorial|P300 BCI Tutorial]].
Introductions to data analysis and interpretation:
*[[User Tutorial:Data Analysis|Data Analysis Tutorials]].
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==User Reference Manual==
The [[User Reference:Contents|User Reference Manual]] describes all details<br />of system configuration and usage:
*Online System Reference,
*Filters and Parameters,
*BCI2000 Tools Reference.
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==Technical Reference==
The [[Technical Reference:Contents|Technical Reference Manual]] contains information on
*BCI2000 Online System Design,
*Transmission Protocol Definition,
*External Interfaces.
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==Programming Reference==
The [[Programming Reference:Contents|Programming Reference]] provides developer information:
*Accessing and Compiling the Source Code,
*Filter Programming Interface,
*Programming Tutorials.

The [[Programming_Howto:Quickstart_Guide|Quickstart Guide]] walks you through the process <br />of building and customizing BCI2000 from source.
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==System Features==
[[System Features|Features supported by BCI2000:]]<br />
*Data Acquisition Systems,
*Brain Signals,
*Paradigms,
* [[Contributions:Contents|User-Contributed BCI2000 Components and Patches]].
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==Additional Information==
* [http://{{SERVERNAME}}/phpbb BCI2000 Community Forum],
* [http://{{SERVERNAME}}/tracproj/newticket Submit a Bug Report] (make sure you log in),
* [[User FAQ|BCI2000 Frequently Asked Questions]],
* [[BCI2000 Glossary]]<br />of terms specific to BCI2000,
* [[BCI2000 Licensing|Licensing Information]].
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==BCI2000 Publications==
* [http://{{SERVERNAME}}/downloads/doc/paper.pdf G. Schalk, D.J. McFarland, T. Hinterberger, N. Birbaumer, and J.R. Wolpaw: ''BCI2000: A General-Purpose Brain-Computer Interface (BCI) System'', IEEE Trans Biomed Eng, 51(6), June 2004.]
* J. Mellinger, G. Schalk: ''BCI2000: A General-Purpose Software Platform for BCI Research,'' In: G. Dornhege, J. del R. Millán, T. Hinterberger, D.J. McFarland, K.-R. Müller (eds.), ''Toward Brain-Computer Interfacing,'' MIT Press, 2007.
* [http://www.amazon.com/Practical-Guide-BrainComputer-Interfacing-BCI2000/dp/1849960917/ G. Schalk, J. Mellinger: "A Practical Guide to Brain-Computer Interfacing with BCI2000", Springer, 2010.]
* J. Mellinger, G. Schalk: "Using BCI2000 in BCI Research," In: B. Graimann, B. Allison, G. Pfurtscheller (eds.), "Brain-Computer Interfaces: Revolutionizing Human-Computer Interaction", Springer, 2010.
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User Tutorial:Performing a P300 Spelling Session

2010-09-27T15:30:46Z

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This step assumes that you created a subject-specific configuration file for the on-line speller, as described in the [[User Tutorial:Obtaining P300 Parameters in a Calibration Session|previous step]] of this tutorial.

==Preparation==
When performing a P300 Spelling Session, start BCI2000 by running <tt>batch/P3Speller_<Your_Amplifier>.bat</tt>, then load the user-specific parameter file created previously.

Click '''Set Config''' to view the EEG signal, and [[User_Tutorial:EEG_Measurement_Setup|prepare the subject for EEG recording]] according to the instructions below.
<br/>''Note:'' When your latency value does not refer to an exact sample position, a warning message will be displayed once you click '''SetConfig'''. You may safely ignore that warning message for now.

==Instructions to the Subject==
On the subject's screen, a speller matrix the subject is already familiar with from the initial session is presented.
Differently from that session, there is no text suggested; rather, the subject may choose freely which letters, words, and sentences to write.

*You will see a speller matrix, containing letters, numbers, and punctuation marks.
*To choose a certain letter, concentrate on it by counting the number of flashes that occur for it.
*After some time, a result will be classified and appended to the text field located at the top of the window.
*If the letter that appeared is not what you intended, concentrate on the "backspace" or "undo" field to remove it.

Additional instructions should be given regarding minimization of
[[User Tutorial:EEG_Measurement_Setup#EEG Artifacts|artifacts]] from
*Contraction of the muscles of the face/head, swallowing;
*Eye blinks and eye movements;
*Motion.

Provided that subjects are asked to minimize artifacts (e.g. asked to try to
swallow only during the pause between letters), he/she should be further
assisted in these efforts by providing a comfortable chair and a dimly lit room.
The
experimenter must carefully monitor the EEG and alert the subject in the case
he/she has forgotten some of the instructions.
When the experimenter is sure that his/her instructions have been well
understood, the recording session may start.

*Click the "Start" button to start the spelling experiment.

==Multiple Sessions==
Once a run has ended, BCI2000 goes into suspended state.
Further runs will be added to the session when you click '''Resume'''.

When starting the next session, don't forget to increment the ''SessionNumber'' parameter on the ''Storage'' tab. Otherwise, new runs will be added to the previous session's directory. Still, as a safety net, BCI2000 will never overwrite existing data files but increment the largest run number that exists in a session directory. Moreover, it documents date and time in the ''StorageTime'' parameter. This allows to later associate data files with multiple sessions by their time and date, even if the ''SessionNumber'' parameter has not been increased.

==Finished==
Here, the P300 speller tutorial is finished.

Congratulations! You are now able to perform [[User Tutorial:P300 BCI Tutorial|P300 spelling experiments]].

==See also==
[[User Tutorial:P300 BCI Tutorial]]

[[Category:Tutorial]]

User Tutorial:Performing a Time-Domain Offline Analysis of ECoG Data

2010-09-27T15:28:42Z

Admin: /* See also */

In this section of the tutorial, we perform a time-domain offline analysis of a dataset recorded using an ECoG. As in the case of EEG data, we expect the basic properties of the P300 evoked potential to be the same for all individuals while the response's latency, width, and spatial pattern may vary. As in [[User Tutorial:Performing a Time-Domain Offline Analysis of EEG Data]], we will use ''BCI2000 Offline Analysis'' to help determine the P300 parameters for a given subject.

== Experimental Design ==
This tutorial will make use of the <tt>ecog2_1.dat</tt> session that is included as part of the supplementary sample files downloadable [http://www.bci2000.org/downloads/bin/sampleFiles.zip here]. Please download this file and extract the contents to <tt>data/samplefiles/</tt>.

In the ecog2 session the subject was placed in front of a monitor displaying a P300 speller matrix. A test sequence, consisting of a string of letters with a single letter highlighted, was also displayed. In each run of the experiment, the subject was asked to focus on the symbol in the speller matrix that was currently highlighted in the test sequence. This way, it was possible to label evoked responses according to whether they occurred for the highlighted symbol or for some other symbol in the matrix. Such labels can be attached to BCI2000 data using state variables. In the case of the ecog2 data, we used the state variable StimulusType such that StimulusType is equal to 1 when the letter that flashes is the letter that the subject is focused on (i.e., the letter that is currently highlighted). When the symbol that flashes is not the symbol of focus, StimulusType will not be equal to 1. If you are relatively new to ''BCI2000'', you may find it helpful to inspect the data files we'll be using with the ''BCI2000 Viewer''. Using this tool, you will be able to see how state variables change with respect to the data over time. For instruction on how to inspect data using the ''BCI2000 Viewer'', please see [[User Reference:BCI2000Viewer]].

==The Results==
In [[User Tutorial:Performing an Offline Analysis of EEG Data]] we manually entered all the analysis parameters. In this tutorial we will make use of the ''BCI2000 Offline Analysis'' "Load Settings" feature that allows us to load previously saved settings. In order to load the settings for this tutorial, please do the following:

# Open BCI2000 Offline Analysis. If this is your first time using BCI2000 Offline Analysis, you may want to review the instructions on how to install and run this application: [[User Reference:BCI2000 Offline Analysis]].
# Click the "Add" button next to "Data Files" and navigate to <tt>data/samplefiles/</tt>. From there, select the file <tt>ecog2_1.dat</tt> and click "Open". If this file isn't present, please download the [http://www.bci2000.org/downloads/bin/sampleFiles.zip supplementary sample files] and extract them to <tt>data/samplefiles/</tt>.
# Click File>Load Settings
# Navigate to <tt>data/samplefiles/</tt>
# Double-click or otherwise open <tt>ecog2Analysis.bws</tt>

At this point ''BCI2000 Offline Analysis'' should look like this:

[[Image:offlineAnalysisEcog2.png]]

Typically in a P300 analysis, we would not use a CAR filter because it would remove too much of the signal. In this case, as we will find later, the response is primarily on a single channel and performing a CAR filter will provide significant noise reduction without sacrificing the signal quality. Now, click "Generate Plots". Once your analysis is complete, you should see feature, waveform and topography plots similar to those below:

[[Image:ecog2Feature.png|600px]]

[[Image:ecog2Waveform.png|600px]]

[[Image:ecog2Topo.png|600px]]

In designing this analysis, we followed a similar procedure to the procedure outlined in [[User Tutorial:Performing a Time-Domain Offline Analysis of EEG Data]]. We begin by looking for clusters of high [[Glossary|r-squared]] values. Again, these clusters are typically the first indication that the time/channel pairs that comprise the cluster may be good features for on-line analysis. In the generated feature plot, we see that one of the clusters with the highest [[Glossary|r-squared]] values is centered around (260 ms, Channel 1). So, we continue by creating a topography at 260 ms and a waveform for channel 1.

==See also==
[[User Tutorial:Obtaining P300 Parameters in a Calibration Session]]

[[Category:Tutorial]]

User Tutorial:Performing a Time-Domain Offline Analysis of EEG Data

2010-09-27T15:28:20Z

Admin: /* See also */

Although the basic properties of the P300 evoked potential are the same for all individuals, the response's latency, width, and spatial pattern are unique for each individual. In order to facilitate P300 classification, we must determine the typical values for these properties. ''BCI2000 Offline Analysis'' is a helpful tool for performing analyses of offline data in order to characterize a given subject.

==Experimental Design==
This tutorial will make use of the <tt>eeg2_1.dat</tt> and <tt>eeg2_2.dat</tt> sessions that are included with BCI2000 which can be found in <tt>data/samplefiles/</tt>. In these sessions, the subject was placed in front of a monitor displaying a P300 speller matrix. A test sequence, consisting of a string of letters with a single letter highlighted, was also displayed. In each run of the experiment, the subject was asked to focus on the symbol in the speller matrix that was currently highlighted in the test sequence. This way, it was possible to label evoked responses according to whether they occurred for the highlighted symbol or for some other symbol in the matrix. Such labels can be attached to ''BCI2000'' data using state variables. In the case of the eeg2 data, we've used the state variable StimulusType such that StimulusType is equal to 1 when the letter that flashes is the letter that the subject is focused on (i.e., the letter that is currently highlighted). When the symbol that flashes is not the symbol of focus, StimulusType will not be equal to 1. If you are relatively new to BCI2000, you may find it helpful to inspect the data files we'll be using with the ''BCI2000 Viewer''. Using this tool, you will be able to see how state variables change with respect to the data over time. For instruction on how to inspect data using the BCI2000 Viewer, please see [[User Reference:BCI2000Viewer]].

==The Feature Plot==
''BCI2000 Offline Analysis'' generates three plots that will aid you in your analyses. One of these plots, the feature plot, provides an overview of the data. Let's begin by generating this plot:

# Open BCI2000 Offline Analysis. If this is your first time using BCI2000 Offline Analysis, you may want to review the instructions on how to install and run this application: [[User Reference:BCI2000 Offline Analysis]].
# Set the analysis parameters as follows:
##'''Analysis Domain:''' Choose "Time (P300)" in order to perform a time-domain analysis
##'''Acquisition Type:''' Choose "EEG" since the data we'll be working with in this section was recorded using an EEG.
##'''Data Files:''' Click the "Add" button and navigate to <tt>data/samplefiles/</tt>. From there, select the files <tt>eeg2_1.dat</tt> and <tt>eeg2_2.dat</tt> and click "Open". To select multiple files, you'll need to first click on any one file and then, while holding down the control button on your keyboard, click the remaining files.
##'''Montage File:''' Leave this blank. The reason for doing so will be explained shortly.
##'''Target Condition 1:''' Enter the MATLAB-syntax statement "(states.StimulusCode > 0) & (states.StimulusType == 1)" which should be the default value after selecting "Time (P300)" as the analysis domain. This statment instructs ''BCI2000 Offline Analysis'' that condition 1 should correspond to the data where the symbol that the subject was focused on corresponded to one of the letters that was flashing.
##'''Target Condition Label 1:''' The text entered here will be used to label data that is specific to condition 1. So, we will enter the string "Correct" as in the correct (i.e., highlighted) letter was one of the letters flashing.
##'''Target Condition 2:''' Enter the MATLAB-syntax statement "(states.StimulusCode > 0) & (states.StimulusType == 0)" which should be the default value after selecting "Time (P300)" as the analysis domain. This instructs ''BCI2000 Offline Analysis'' that condition 2 should correspond to the data where the symbol the subject was focused on did not corresponded to one of the letters that was flashing.
##'''Target Condition Label 2:''' The text entered here will be used to label data that is specific to condition 2. So, we will enter the string "Incorrect" as in the correct (i.e., highlighted) letter was not one of the letters flashing.
##'''Trial Change Condition:''' Enter the value "states.StimulusBegin == 1". This instructs BCI2000 Offline Analysis that the trial edges correspond to data samples where the state variable StimulusBegin becomes 1 or is 1 and becomes something else.
##'''Waveform Channels:''' Leave this blank. The reason for doing so will become clear.
##'''Topo Times:''' Leave this blank. The reason for doing so will become clear.
##'''Spatial Filter:''' Choose "None". Because P300 responses are typically detected on a number of channels, CAR filtering is not typically effective.
##'''Ignore Warnings:''' Leave this field unchecked. For more information on this field, please see User Reference:BCI2000 Offline Analysis.
##'''Overwrite existing plots:''' If you have not yet run any analyses, this field should be disabled. If it is enabled, it is best for the purposes of this tutorial to leave it checked. Unchecking this box will instruct BCI2000 Offline Analysis to open new figures whenever it plots. This is useful if you want to compare the results of one analysis against another.
#Click "Generate Plots".

Once the analysis has completed, you should see a feature plot similar to the one below. This plot displays the [[Glossary|r-squared (coefficient of determination)]] values for the two distributions (i.e., the average signal for condition 1 and the average signal for condition 2) as a function of time and channel.

[[Image:eeg2Feature.png|600px]]

The feature plot is an overview of the possible features. Thus, it is typically the best place to start your analysis. From this plot, we can find the best features by looking for clusters of high [[Glossary|r-squared]] values. In our feature plot, we notice that all of the clusters appear to be aligned at about 503ms. The biggest of these clusters - with the largest [[Glossary|r-squared]] values - appears to be centered over electrode 51. We will now use ''BCI2000 Offline Analysis'' to produce two additional plots that will help us to take a more detailed look at this time and channel.

==Waveform Plots and Topographies==
''BCI2000 Offline Analysis'' provides - in addition to the feature plot - waveform plots and topographies. Waveform plots are useful for investigating specific channels while topographies are useful for investigating specific time windows. In order to generate the topographies we will need to communicate the manner in which the electrodes were arranged. This is done with a montage file. While there is a montage file included with ''BCI2000'' that is suitable for the data we'll be analyzing here, you will likely need to create or modify montage files for future analyses. For that reason, we recommend that you take the time now to familiarize yourself with the ''Eloc Helper'' if you have not already done so. In [[User Tutorial:Designing an Eloc File]], you will learn how to create a new montage file and modify an existing one so that you ultimately have your own montage file to use to complete this analysis. If you prefer not to complete the ''Eloc Helper'' tutorial at this time, you will still be able to complete this tutorial using one of the montage files that comes with ''BCI2000''.

If you have finished designing your montage file or decided to use the one that's provide, please proceed to the steps below. Note that these steps pick up from the steps outlined in the previous section for generating the feature plot:

# Set the analysis parameters as follows:
## Montage File: Click the "Browse" button next to the field labeled "Montage Files" and browse to <tt>data/samplefiles/</tt>. If you completed the Eloc Helper tutorial and would like to use the montage file you created, double-click <tt>myeeg64.loc</tt>. Otherwise, double-click eeg64.loc to use the montage file that comes with ''BCI2000''.
## Waveform Channels: In the previous section we found that channel 51 may be an effective classification feature for facilitating online control. To generate the waveform plot for this channel, enter "51" into this field.
## Topo Times: In the previous section we found that 503 ms may be an effective classification feature for facilitating online control. To generate a topography for this time, enter "503" into this field.
# Click "Generate Plots".

Once the analysis is complete, you will see the same feature plot as was generated in the previous section. Additionally, you will see a waveform plot and topography similar to those below. In the waveform plot, we expect to see a peak response at approximately 300 ms. For this particular subject, however, we can see the peak response at approximately 503 ms as indicated by the feature plot which is reasonably close. In the adjacent [[Glossary|r-squared]] waveform plot we can see that the [[Glossary|r-squared]] values also peak approximately at this time. P300 topographies can vary significantly. In the generated topography, we see that the response is located mainly
over the parietal and temporal lobes, which is consistent with the P300
response found in other studies (Sellers et. al.: A P300 event-related potential brain–computer interface (BCI): The effects of matrix size and inter stimulus interval on performance. Biological Psychology 70(2006):242-252. April 2006). However, there is significant variance in the spatial distribution of the response across different subjects in P300 experiments. Regardless, it appears that the (503 ms, Channel 51) feature would indeed serve as an effective recognition feature for facilitating online control.

[[Image:eeg2Waveform.png|600px]]

[[Image:eeg2Topo.png|600px]]

==Next Step==
At this point you should understand how to use the ''BCI2000 Offline Analysis'' plots to help you choose effective P300 features. You might like to proceed to [[User Tutorial:Performing a Time-Domain Offline Analysis of ECoG Data]] for a similar tutorial using data recorded using an ECoG.

==See also==
[[User Tutorial:Obtaining P300 Parameters in a Calibration Session]]

[[Category:Tutorial]]

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