Connected Brains: BrainWave

The Web Connected Brains

BrainWave: a Java based application for functional connectivity and network analysis

BrainWave is an application for the analysis of multivariate neurophysiological data sets, in particular EEG and MEG, although other types of data such as BOLD time series can be studied as well. It was written by Cornelis Jan Stam. The focus of the software is on the analysis of ongoing, resting-state activity, which is analyzed as a series of epochs, with a maximum length of 4096 per epoch, but short epochs can be analyzed as well. Although is not aimed at the analysis of task related experiments, these can be approached with some effort as multiple short epochs or as a block design. BrainWave includes facilities for computing power spectra, several measures of functional connectivity (coherence, phase coherence, imaginary coherence, PLI and synchronization likelihood). Following a basic analysis of functional connectivity, the resulting matrices can be studied with a large variety of graph theoretical measures, based upon unweighted or weighted graphs, using clustering coefficients, path lengths, modularity and graph spectral analysis (eigenvector centrality, spectral radius, spectral gap, eigenratio and algebraic connectivity). The graph spectral analysis in BrainWave is based upon JAMA: A Java Matrix Package by Robert Sedgewick and Kevin Wayne. All results can be viewed in various ways, especially in the case of data obtained with the Neuromag MEG system of Elekta. Imported files should be plain ASCII data, with channels as columns and samples as rows. Results of computations are exported as text files. Almost all analyses can be done in batch mode. BrainWave also contains models of complex networks. The software is Java based, and thus should run on all major operating systems. However, Java and the Jave Runtime Environment has to be installed on your computer. If this is not the case, you can download it for free from the Sun website. BrainWave is the successor of the older application DIGEEGXP, a Windows based package written in Delphi. A useful manual to get started with BrainWave was written by Maria Boersma.

How to obtain a copy of BrainWave

BrainWave is an application for science, not for profit. You can download the BrainWave version 0.9.117. Alternatively, you can obtain a copy for free by sending an e-mail. Please indicate where you are located, what kind of research you do, and what you would like to use the software for. Active participation in the BrainWave users community is encouraged. Please let us know if you publish a paper based upon BrainWave.

Changes in last version of BrainWave

The BrainWave users community

BrainWave is neither perfect nor finished. For further improvement feedback and suggestions from users is invaluable. For convenience of the user community, use comments are shown below, in reverse temporal order. If you have a problem or a question, please have a look at previous users comments below.

For comments and suggestions: send an e-mail

copyright C.J.Stam
Contact information: Department of Clinical Neurophysiology VU University Medical Center
Postal address: De Boelelaan 1118 Postal code: 1081 HV Amsterdam The Netherlands
P.O Box: 7057 Postal code: 1007 MB Amsterdam The Netherlands
Phone: 020 4440727 Fax: 020 4444816