MNE-BIDS

This is a repository for creating BIDS-compatible datasets with MNE.

Installation

We recommend the Anaconda Python distribution. We require that you use Python 3. Besides numpy and scipy (which are included in the standard Anaconda installation), you will need to install the most recent version of MNE using the pip tool:

$ pip install -U mne

Then install mne-bids:

$ pip install -U mne-bids

These 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 pip.

To check if everything worked fine, the following command should not give any error messages:

$ python -c 'import mne_bids'

If you want to use the latest development version, use the following command:

$ pip install https://api.github.com/repos/mne-tools/mne-bids/zipball/master

Quickstart

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', output_path='./bids_dataset')

Command Line Interface

In addition to import mne_bids, you can use the command line interface.

Example:

$ mne_bids raw_to_bids --subject_id sub01 --task rest --raw data.edf --output_path new_path

Bug reports

Use the github issue tracker to report bugs.

Cite

If you use mne-bids in your work, please cite one of the following papers, depending on which modality you used:

MEG

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

EEG

Pernet, C. R., Appelhoff, S., Flandin, G., Phillips, C., Delorme, A., &
Oostenveld, R. (2018, December 6). BIDS-EEG: an extension to the Brain
Imaging Data Structure  (BIDS) Specification for electroencephalography.
https://doi.org/10.31234/osf.io/63a4y

iEEG

Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S.,
David, O., … Hermes, D. (2018, December 13). BIDS-iEEG: an extension to the
brain imaging data structure  (BIDS) specification for human intracranial
electrophysiology. https://doi.org/10.31234/osf.io/r7vc2