BIDS (Brain Imaging Data Structure) is a standard to organize data according to a set of rules that describe:
- how to name your files
- where to place your files within a directory structure
- what additional metadata to store, and how to store it in sidecar json and tsv files
MNE-Python is a software package for analyzing neurophysiology data.
MNE-BIDS links BIDS and MNE with the goal to make your analyses faster to code, more robust to errors, and easily sharable with colleagues.
The documentation can be found under the following links:
- numpy (>=1.14)
- scipy (>=0.18.1)
- mne (>=0.19.1)
- nibabel (optional)
- pybv (optional)
Installation via pip
scipy (which are included in the standard Anaconda
installation), you will need to install the most recent version of
$ pip install -U mne
$ pip install -U mne-bids
pip commands also work if you want to upgrade if a newer version of
mne-bids is available. If you do not have administrator privileges on the
computer, use the
--user flag with
To check if everything worked fine, the following command should not give any error messages:
$ python -c 'import mne_bids'
For full functionality of
mne-bids, you will also need to
the following packages:
nibabel, for interacting with MRI data
pybv, to convert EEG data to BrainVision if input format is not valid according to EEG BIDS specifications
If you want to use the latest development version of
mne-bids, use the
$ pip install https://api.github.com/repos/mne-tools/mne-bids/zipball/master
Installation via conda
If you have followed the
MNE-Python installation instructions,
all that's left to do is to install
mne-bids without its dependencies, as
they've already been installed during the
MNE installation process.
Activate the correct
conda environment and install
$ conda activate mne $ conda install --channel conda-forge --no-deps mne-bids
This approach ensures that the installation of
mne-bids doesn't alter any
other packages in your existing
Alternatively, you may wish to take advantage of the fact that the
mne-bids package on
conda-forge in fact depends on
meaning that a "full" installation of
mne-bids (i.e., including its
dependencies) will provide you with a working copy of of both
mne-bids at once:
$ conda create --name mne --channel conda-forge mne-bids
After activating the environment, you should be ready to use
$ conda activate mne $ python -c 'import mne_bids'
Currently, we support writing of BIDS datasets for MEG and EEG. Support for iEEG is experimental at the moment.
>>> from mne import io >>> from mne_bids import write_raw_bids >>> raw = io.read_raw_fif('my_old_file.fif') >>> write_raw_bids(raw, 'sub-01_ses-01_run-05', bids_root='./bids_dataset')
Command Line Interface
In addition to
import mne_bids, you can use the command line interface.
mne_bids in your command line and press enter, to see the
accepted commands. Then type
mne_bids <command> --help, where
is one of the accepted commands, to get more information about that
$ mne_bids raw_to_bids --subject_id sub01 --task rest --raw data.edf --bids_root new_path
Use the github issue tracker to report bugs.
Please see our contributing guide.
If you use
mne-bids in your work, please cite:
Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896).
and one of the following papers, depending on which modality you used:
Niso, G., Gorgolewski, K. J., Bock, E., Brooks, T. L., Flandin, G., Gramfort, A., Henson, R. N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J., Tadel, F., Wexler, J., Baillet, S. (2018). MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific Data, 5, 180110. http://doi.org/10.1038/sdata.2018.110
Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103. https://doi.org/10.1038/s41597-019-0104-8
Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7