Note
Go to the end to download the full example code.
06. Rename BrainVision EEG data files#
According to the EEG extension to BIDS [1], the BrainVision data format is one of the recommended formats to store EEG data within a BIDS dataset.
To organize EEG data in BIDS format, it is often necessary to rename the files. In the case of BrainVision files, we would have to rename multiple files for each recording:
A text header file (
.vhdr
) containing meta dataA text marker file (
.vmrk
) containing information about events in the dataA binary data file (
.eeg
) containing the voltage values of the EEG
Note
The three files contain references that guide the data reading software. Simply renaming the files without adjusting these references will corrupt the dataset! But relax, MNE-BIDS can take care of this for you.
In this example, we use MNE-BIDS to rename BrainVision data files including a repair of the internal file links
For the command line version of this tool, see the cp
tool in the docs
for the Python Command Line Interface.
# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
We are importing everything we need for this example:
import os.path as op
import mne
from mne_bids.copyfiles import copyfile_brainvision
Download some example data#
To demonstrate the MNE-BIDS functions, we need some testing data. Here, we will use the MNE-Python testing data. Feel free to use your own BrainVision data.
Warning
This will download 1.6 GB of data!
data_path = mne.datasets.testing.data_path()
examples_dir = op.join(data_path, "Brainvision")
Rename the recording#
Above, at the top of the example, we imported
mne_bids.copyfiles.copyfile_brainvision()
from
the MNE-BIDS mne_bids/copyfiles.py
module. This function takes two
main inputs:
First, the path to the existing .vhdr
file. And second, the path to
the future .vhdr
file.
With the optional verbose
parameter you can furthermore determine how
much information you want to get during the procedure.
mne_bids.copyfiles.copyfile_brainvision()
will then create three new
files (.vhdr
, .vmrk
, and .eeg
) with the new names as provided
with the second argument.
Here, we rename a test file name:
# Rename the file
vhdr_file = op.join(examples_dir, "Analyzer_nV_Export.vhdr")
vhdr_file_renamed = op.join(examples_dir, "test_renamed.vhdr")
copyfile_brainvision(vhdr_file, vhdr_file_renamed, verbose=True)
# Check that MNE-Python can read in both, the original as well as the renamed
# data (two files: their contents are the same apart from the name)
raw = mne.io.read_raw_brainvision(vhdr_file)
raw_renamed = mne.io.read_raw_brainvision(vhdr_file_renamed)
Created "test_renamed.eeg" in "/home/circleci/mne_data/MNE-testing-data/Brainvision".
Created "test_renamed.vhdr" in "/home/circleci/mne_data/MNE-testing-data/Brainvision".
Created "test_renamed.vmrk" in "/home/circleci/mne_data/MNE-testing-data/Brainvision".
Extracting parameters from /home/circleci/mne_data/MNE-testing-data/Brainvision/Analyzer_nV_Export.vhdr...
Setting channel info structure...
Extracting parameters from /home/circleci/mne_data/MNE-testing-data/Brainvision/test_renamed.vhdr...
Setting channel info structure...
Further information#
For converting data files, or writing new data to the BrainVision format, you
can use mne.export
or have a look at the pybv Python package.
References#
Total running time of the script: (0 minutes 0.021 seconds)