Presentation at the Glioma MR imaging 3rd Annual Meeting in Kusadasi, Turkey.

1. Connecting with the BIDS initiative
(Brain Imaging Data Structure)
Robert Oostenveld
Donders Institute, Radboud University, Nijmegen, NL
Karolinska Institutet, Stockholm, SE
r.oostenveld@donders.ru.nl
Slides available from:

2. Short intro of myself
Physicist and cognitive neuroscientist
MEG and EEG, data analysis, modelling
Donders Institute, Radboud University Nijmegen, NL
Advocate for Open Source (FieldTrip toolbox) and Open Data
Collaborator on the Human Connectome Project (HCP)
Member of the BIDS steering group and co-author on 5 BIDS papers
Architect of the Donders Repository

3. Open Data
Needed for improved reproducibility and replicability.
Contributes to new research and methods.
Strategies for Open Data are similar to
- archiving within a lab
- sharing with collaborators
Machine learning requires lots of data.

4. Open Data
Findable
Make your data available in a catalog or repository
with a persistent identifier (DOI, handle) and metadata
Accessible
Be explicit about data usage terms (agreement with downloader)
Interoperable
Make your data human and machine readable, e.g. BIDS
Reusable
Make sure you document enough details, e.g. “data descriptor” paper
this can be cited, along with citing our data -> measurable impact!

5. What is BIDS?
BIDS is a way to organize your existing raw data
To improve consistent and complete documentation
To facilitate re-use by your future self and others
BIDS is not
A new file format
A search engine
A data sharing platform
http://bids.neuroimaging.io

6. Brain Imaging Data Structure (BIDS)
external reuse: publishing, sharing
internal reuse: archiving, curation, collaborating
Fundamental for OpenNeuro, but also used in Donders Repository and
as the basis for new analysis pipelines and workflow development
https://openneuro.org
https://data.donders.ru.nl

7. Brain Imaging Data Structure
http://bids.neuroimaging.io

8. BIDS for MRI, MEG, EEG, iEEG, PET,
microscopy …
Just a bunch of directories and files on disk
No special software required (although tools are available)

9. BIDS for MRI, MEG, EEG, iEEG, PET,
microscopy …
data/README
CHANGES
dataset_description.json
participants.tsv
/sub-01/beh/…
/sub-01/eeg/…
/sub-01/anat/sub-01_T1w.nii.gz
/sub-01/anat/sub-01_T1w.json
/sub-01/perf/sub-01_asl.nii.gz
/sub-01/perf/sub-01_asl.json
/sub-01/perf/sub-01_aslcontext.tsv
/sub-01/perf/sub-01_asllabeling.jpg
Directory structure
Actual imaging data
Metadata

10. BIDS “sidecar” files for metadata
see also https://github.com/bids-standard/bids-examples
1) represent otherwise missing data
2) make it easier to query/search
As example for EEG:
_participants.tsv and json
_sessions.tsv and json
_scans.tsv and json
_eeg.json
_channels.tsv and json
_electrodes.tsv and json
_coordinates.json
_photos.jpg

11. Findable
The amount of available information is increasing exponentially: that
gives opportunities, but also requires new strategies
Instead of “knowing where it is”, we rely on “knowing that it exists”
and use google.
Information (and data) should be organized and be complemented with
structured metadata so that we can find it.
Finding our data is not only relevant for others, also for ourselves in a
few years from now.

12. BIDS is not a search engine
but it standardizes the metadata
Generic search engines (i.e., web crawlers) will not use BIDS metadata
and structure
Domain specific search engines might use it
https://search.datacite.org
https://datasetsearch.research.google.com
https://ebrains.eu/services/data-and-knowledge

13. BIDS is not a data sharing platform
So where to share?
Institutional repository
Donders https://data.donders.ru.nl
Radboud University http://data.ru.nl
In the UK Oxford, Cambridge, Edinburg
…
National repository (in NL)
https://easy.dans.knaw.nl
https://dataverse.nl
https://data.4tu.nl
Project specific or Domain specific repository
https://openneuro.org
https://ebrains.eu
General repository
https://zenodo.org
https://dataverse.harvard.edu
https://osf.io
Commercial publishers
https://datadryad.org
https://figshare.com

14. BIDS is not a new file format
So which file formats are used?
MRI and PET
NIFTI, not DICOM or Analyze or MINC
MEG
Original manufacturers file formats
EEG
BrainVision Core format
European Data Format (*.edf)
EEGLAB (HDF5 *.mat file that is renamed to *.set)
Biosemi
iEEG
BrainVision, EDF, EEGLAB
Neurodata Without Borders (*.nwb files)
MEF3 (*.mefd directory)

15. So what is BIDS?
BIDS is a way to organize your data
It comes with publications, online specification, examples, tools,
mailing list…
BIDS is also a thriving community project
Well-documented governance structure
Steering and Maintainers group
GitHub and google docs to work together
Community decides on extensions to the standard
http://bids.neuroimaging.io

16. What makes BIDS?
Both human and machine readable.
Simple standards, easy adoption.
Reuse existing solutions.
80/20 pareto principle, focus on what is important.
Tap into the community for expertise and insights.

17. Current relevance for neuro-oncology
Structural MRI (T1w, T2w, ASL, DWI, …)
PET
Microscopy
Genetics
Tabular datafor:
Participants
Sessions (longitudinal, follow-up)
Scans (within a session/visit)

18. Future relevance for neuro-oncology
BIDS Extension Proposals (BEPs) to extend the standard
BEP030 Functional NIRS data
BEP029 Motion capture data
BEP022 MR spectroscopy
BEP011 Structural preproc derivatives
BEP012 Functional preproc derivatives
BEP017 Connectivity
BEP028 Provenance
Extending with new data types might not be needed, but BIDS metadata
might (as of yet) be insufficient for tumor data.
How to proceed…

19. https://bids.neuroimaging.io – the website
https://bids-specification.readthedocs.io – the specification details
https://github.com/bids-standard - the project
https://openneuro.org – many shared datasets
https://osf.io/yn93h and YouTube - more presentations
Connecting with the BIDS initiative
(Brain Imaging Data Structure)
oostenvr
robert.oostenveld@donders.ru.nl
Slides available from: