eegkit / pybv

A lightweight I/O utility for the BrainVision data format, written in Python.

pybv

pybv is a lightweight I/O utility for the BrainVision data format.

The BrainVision data format is a recommended data format for use in the Brain Imaging Data Structure.

The documentation can be found under the following links:

• for the stable release
• for the latest (development) version

About the BrainVision data format

BrainVision is the name of a file format commonly used for storing electrophysiology data. Originally, it was put forward by the company Brain Products, however the simplicity of the format has allowed for a diversity of tools reading from and writing to the format.

The format consists of three separate files:

1. A text header file (.vhdr) containing meta data
2. A text marker file (.vmrk) containing information about events in the data
3. A binary data file (.eeg) containing the voltage values of the EEG

Both text files are based on the Microsoft Windows INI format consisting of:

• sections marked as [square brackets]
• comments marked as ; comment
• key-value pairs marked as key=value

The binary .eeg data file is written in little-endian format without a Byte Order Mark (BOM), in accordance with the specification by Brain Products. This ensures that the data file is uniformly written irrespective of the native system architecture.

A documentation for the BrainVision file format is provided by Brain Products. You can view the specification as hosted by Brain Products.

Installation

pybv runs on Python version 3.8 or higher.

pybv's only dependency is numpy. However, we currently recommend that you install MNE-Python for reading BrainVision data. See their installation instructions.

After you have a working installation of MNE-Python (or only numpy if you do not want to read data and only write it), you can install pybv through the following:

• pip install --upgrade pybv

or if you use conda:

• conda install --channel conda-forge pybv

Contributing

The development of pybv is taking place on GitHub.

For more information, please see CONTRIBUTING.md

Usage

Writing BrainVision files

The primary functionality provided by pybv is the write_brainvision function. This writes a numpy array of data and provided metadata into a collection of BrainVision files on disk.

from pybv import write_brainvision

# for further parameters see our API documentation
write_brainvision(data=data, sfreq=sfreq, ch_names=ch_names,
                  fname_base=fname, folder_out=tmpdir,
                  events=events)

Reading BrainVision files

Currently, pybv recommends using MNE-Python for reading BrainVision files.

Here is an example of the MNE-Python code required to read BrainVision data:

import mne

# Import the BrainVision data into an MNE Raw object
raw = mne.io.read_raw_brainvision('tmp/test.vhdr', preload=True)

# Reconstruct the original events from our Raw object
events, event_ids = mne.events_from_annotations(raw)

Alternatives

The BrainVision data format is very popular and accordingly there are many software packages to read this format, or write to it. The following table is intended as a quick overview of packages similar to pybv. Please let us know if you know of additional packages that should be listed here.

Name of software	Language	Notes
BioSig Project	miscellaneous	Reading and writing capabilities depend on bindings used, see their overview
Brainstorm	MATLAB	Read and write, search for brainamp in their io functions
BrainVision Analyzer	n/a, GUI for Windows	Read and write, by Brain Products, requires commercial license
brainvisionloader.jl	Julia	Read
EEGLAB	MATLAB / Octave	Read and write via BVA-IO
FieldTrip	MATLAB	Read and write, search for brainvision in their fileio functions
MNE-Python	Python	Read (writing via pybv)

Acknowledgements

This package was originally adapted from the Philistine package by palday. It copies much of the BrainVision exporting code, but removes the dependence on MNE. Several features have been added, such as support for individual units for each channel.