Presentation by Robert Oostenveld during the pre-workshop symposium on BIDS in Toulouse, prior to the EEGLAB 2019 workshop in Aspet, France.

1. Organizing EEG data using the
Brain Imaging Data Structure
Robert Oostenveld
Donders Institute, Radboud University, Nijmegen, NL
Karolinska Institutet, Stockholm, SE
r.oostenveld@donders.ru.nl

2. https://bids-specification.readthedocs.io/
http://bids.neuroimaging.io
these slides will be shared on https://www.slideshare.net/RobertOostenveld

3. Science – methods and tools are changing

4. Open Science – infrastructure and tools
Git and GitHub, Gitlab, BitBucket
Work together on code for analyses
Open Science Framework (osf.io)
Work together on documenting
DataVerse, Zenodo, etc
Sharing of data
Code Ocean, Microsoft Azure, Anaconda Clould
Cloud-based computational reproducibility platform
Past - Black-and-white version of article printed on paper and stored in library
Present - PDF for download, sometimes online supplementary material
Future - Online notebooks that allow full reproduction of results (and more)
Lab notebook
Science is getting more exiting – but also requires new skills

5. Outline of this talk
How is BIDS extended to EEG?
What is specific for EEG?
File formats
Channels and electrodes
Coordinates
Other details
Re-using BIDS EEG datasets
Creating BIDS EEG datasets

6. Brain Imaging Data Structure
https://www.nature.com/articles/sdata201644
https://www.nature.com/articles/sdata2018110

7. https://psyarxiv.com/63a4y/
https://psyarxiv.com/r7vc2/ Both accepted for publication in Scientific Data and soon to appear

8. BIDS for MRI, MEG, EEG, iEEG,etc.
data/README
CHANGES
dataset_description.json
participants.tsv
/sub-01/anat/…
/sub-01/meg/…
/sub-01/eeg/sub-01_task-auditory_eeg.edf
/sub-01/eeg/sub-01_task-auditory_eeg.json
/sub-01/eeg/sub-01_task-auditory_channels.tsv
/sub-01/eeg/sub-01_task-auditory_events.tsv
/sub-01/eeg/sub-01_electrodes.tsv
/sub-01/eeg/sub-01_coordinates.json
raw EEG data
general
metadata
electrode
positions

9. Fileformats for EEG data in BIDS
Recommended
BrainVision Core file fomat (*.vhdr, *.vmrk, *.eeg)
European Data Format (*.edf)
Allowed
Biosemi (*.bdf)
EEGLAB (*.set) -> MATLAB, HDF5-based
Limited number of formats that should …
1) address the needs of a large portion of the global EEG community
2) be a FAIR format, with a focus on Interoperability
3) meet the technical requirements of neuroscientific workflows
https://www.brainproducts.com/productdetails.php?id=21&tab=5
https://www.biosemi.com/faq/file_format.htm
https://www.edfplus.info
https://www.hdfgroup.org/solutions/hdf5/ and EEGLAB

10. EEG data sidecar file
Capture information that is not present in the data file
• What was the task or instruction to the subject?
• Which electrode cap was used?
• Which amplifier was used?
• Is line noise at 50Hz or 60Hz?
• Where was the reference electrode placed?
• …
Makes some information more easily available
• Number of channels with EEG, EOG, etc.
• …

11. Channels and electrodes
Electrode
A single point of contact between the acquisition
system and the recording site
Channel
A single analog-to-digital converter in the
recording system that regularly samples the value
of a transducer, which results in the signal being
represented as a time series in the digitized data.
Note that GND and REF are electrodes, but usually not
channels.

12. Coordinates
If EEG electrode positions are digitized and specified,
then the coordinate system should also be specified.
Fiducials
objects with a well defined location used to facilitate the localization of electrodes and
co-registration with other geometric data such as the participant's own T1 weighted
magnetic resonance head image, a T1 weighted template head image, or a spherical
head model.
Anatomical landmarks
locations on a research subject such as the nasion, which is the intersection of the
frontal bone and two nasal bones of the human skull.

13. Task and event details
http://www.hedtags.org
http://wiki.cogpo.org
https://www.cognitiveatlas.org

14. Outline of this talk
How is BIDS extended to EEG?
What is specific for EEG?
File formats
Channels and electrodes
Coordinates
Other details
Re-using BIDS EEG datasets
Creating BIDS EEG datasets

15. Re-using BIDS EEG datasets
…. just use your standard tools!
EEG data in BIDS is stored in formats supported by all EEG software.
Metadata is in human and machine-readable format (tsv, json).
In the future it is likely that complete (semi)-automatic analysis
pipelines will be implemented to process complete datasets.

16. Creating BIDS EEG datasets
http://www.fieldtriptoolbox.org/example/bids/
Tools are also currently being developed in
EEGLAB, BrainStorm, SPM, MNE-Python, etc.
BrainVision is also extending their
software to be more BIDS friendly.

17. Quick demo

18. Why share your EEG data BIDS?
Sharing your data (externally) increases your research impact.
Archiving your data properly (internally) increases its future value.
Document for your “future self”, so that you don’t forget the details
(and that others will know them as well).
Plan your experiment, acquire the data, organize it in BIDS,
and only then start analyzing it!

19. Share/publish your research output
Peer-reviewed publication is the primary output!
More details in your analysis than fits in your “Methods” section.
Not possible to describe all details in human-oriented text.
Raw data
EEG, lab notes, etc
Analysis details
MATLAB, Python, R, SPSS, Bash, …
Analysis results
Output of the computations
-> BIDS for raw EEG data
-> BIDS derivatives (work-in-progress)
-> possibly BIDS apps, otherwise
github or similar

20. https://bids-specification.readthedocs.io/
http://bids.neuroimaging.io
these slides will be shared on https://www.slideshare.net/RobertOostenveld