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:

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

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.

References

1

Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al. EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Sci Data 6, 103 (2019). https://doi.org/10.1038/s41597-019-0104-8

# Authors: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: 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)

Out:

Created "test_renamed.eeg" in "/Users/hoechenberger/mne_data/MNE-testing-data/Brainvision".
Created "test_renamed.vhdr" in "/Users/hoechenberger/mne_data/MNE-testing-data/Brainvision".
Created "test_renamed.vmrk" in "/Users/hoechenberger/mne_data/MNE-testing-data/Brainvision".
Extracting parameters from /Users/hoechenberger/mne_data/MNE-testing-data/Brainvision/Analyzer_nV_Export.vhdr...
Setting channel info structure...
Extracting parameters from /Users/hoechenberger/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 the pybv Python package.

There is node JS tool to check the integrity of your BrainVision files. For that, see the BrainVision Validator

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05. BIDS conversion for group studies

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07. Save and load T1-weighted MRI scan along with anatomical landmarks in BIDS