This is a repository for creating BIDS-compatible datasets with MNE.
The documentation can be found under the following links:
- for the stable release
- for the latest (development) version
- numpy (>=1.14)
- scipy (>=0.18.1)
- mne (>=0.19.1)
- nibabel (optional)
- pybv (optional)
We recommend the Anaconda Python
distribution. We require that you use Python 3. You may choose to install
mne-bids
via pip or
via conda
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'
For full functionality of mne-bids
, you will also need to pip install
the following packages:
nibabel
, for interacting with MRI datapybv
, 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
following command:
$ pip install https://api.github.com/repos/mne-tools/mne-bids/zipball/master
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 mne-bids
:
$ 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 conda
environment.
Alternatively, you may wish to take advantage of the fact that the
mne-bids
package on conda-forge
in fact depends on mne
,
meaning that a "full" installation of mne-bids
(i.e., including its
dependencies) will provide you with a working copy of of both mne
and
mne-bids
at once:
$ conda create --name mne --channel conda-forge mne-bids
After activating the environment, you should be ready to use mne-bids
:
$ 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', output_path='./bids_dataset')
In addition to import mne_bids
, you can use the command line interface.
Simply type mne_bids
in your command line and press enter, to see the
accepted commands. Then type mne_bids <command> --help
, where <command>
is one of the accepted commands, to get more information about that
<command>
.
Example:
$ mne_bids raw_to_bids --subject_id sub01 --task rest --raw data.edf --output_path new_path
Use the github issue tracker to report bugs.
If you use mne-bids
in your work, please cite 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., โฆ 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