This is a repository for creating BIDS-compatible datasets with MNE.
We recommend the
Anaconda Python distribution.
matplotlib that are included in the standard
anaconda distribution, you will need to install the following dependencies
to be able to use
$ pip install pandas mne
$ pip install git+https://github.com/mne-tools/mne-bids.git#egg=mne-bids
If you do not have administrator privileges on the computer, use the
pip. To upgrade, use the
--upgrade flag provided by
To check if everything worked fine, you can do:
$ python -c 'import mne_bids'
and it should not give any error messages.
Command Line Interface
In addition to
import mne_bids, you can use the command line interface.
$ mne_bids raw_to_bids --subject_id sub01 --task rest --raw_file data.edf --output_path new_path
Contributions are welcome in the form of pull requests.
Once the implementation of a piece of functionality is considered to be bug free and properly documented (both API docs and an example script), it can be incorporated into the master branch.
To help developing
mne-bids, you will need a few adjustments to your
installation as shown below.
To run the tests using
pytest, you need to have the git cloned mne-python
repository with a local pip-install instead of the mne-python package from
pypi. Update your installation as follows.
$ git clone https://github.com/mne-tools/mne-python --depth 1 $ cd mne-python $ pip uninstall mne # uninstall pypi mne $ pip install -e . # use the cloned repo for a local install of mne
Then, install the following python packages:
$ pip install flake8 pytest pytest-cov
Finally, it is necessary to install the BIDS validator. The outputs of MNE-BIDS are run through the BIDS validator to check if the conversion worked.
Building the documentation
The documentation can be built using sphinx. For that, please additionally install the following:
$ pip install sphinx numpydoc sphinx-gallery sphinx_bootstrap_theme pillow
If you use
mne-bids in your work, please cite:
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