https://github.com/alexrockhill/mne-bids-pipeline

Automatically process entire electrophysiological datasets using MNE-Python.

https://github.com/alexrockhill/mne-bids-pipeline

Repository

Automatically process entire electrophysiological datasets using MNE-Python.

https://github.com/alexrockhill/mne-bids-pipeline/blob/main/

#  MNE-BIDS-Pipeline




**MNE-BIDS-Pipeline is a full-flegded processing pipeline for your MEG and
EEG data.**

* It operates on data stored according to the [Brain Imaging Data
Structure (BIDS)](https://bids.neuroimaging.io/).
* Under the hood, it uses [MNE-Python](https://mne.tools).



##  Basic concepts and features



*  Automated processing of MEG and EEG data from raw data to inverse solutions.
*  Configuration via a simple text file.
*  Extensive processing and analysis summary reports.
*  Process just a single participant, or as many as several hundreds of participants  in parallel.
*  Execution via an easy-to-use command-line utility.
*  Helpful error messages in case something goes wrong.
*  Data processing as a sequence of standard processing steps.
*  Steps are cached to avoid unnecessary recomputation.
*  Data can be "ejected" from the pipeline at any stage. No lock-in!
*  Runs on your laptop, on a powerful server, or on a high-performance cluster via Dash.



##  Installation and usage instructions

Please find the documentation at
[**mne.tools/mne-bids-pipeline**](https://mne.tools/mne-bids-pipeline).

##  Acknowledgments

The original pipeline for MEG/EEG data processing with MNE-Python was built
jointly by the [Cognition and Brain Dynamics Team](https://brainthemind.com/)
and the [MNE Python Team](https://mne.tools), based on scripts originally
developed for this publication:

> M. Jas, E. Larson, D. A. Engemann, J. Leppkangas, S. Taulu, M. Hmlinen,
> A. Gramfort (2018). A reproducible MEG/EEG group study with the MNE software:
> recommendations, quality assessments, and good practices. Frontiers in
> neuroscience, 12. https://doi.org/10.3389/fnins.2018.00530

The current iteration is based on BIDS and relies on the extensions to BIDS
for EEG and MEG. See the following two references:

> 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

> 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.
> https://doi.org/10.1038/sdata.2018.110

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