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MNE-BIDS

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

Installation

We recommend the Anaconda Python distribution. Next to numpy, scipy, and matplotlib that are included in the standard anaconda distribution, you will need to install the following dependencies to be able to use mne_bids:

$ pip install pandas mne

Then install mne_bids:

$ 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 --user flag with pip. To upgrade, use the --upgrade flag provided by pip.

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.

Example :

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

Contributions

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.

Running tests

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

Cite

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