Slides from talk on COBIDAS MEEG at CuttingEEG 2018 Paris meeting by Aina Puce.

1. COBIDAS MEEG
Aina Puce & Cyril Pernet

2. What is COBIDAS MEEG?
Committee on Best Practices in
Data Analysis and Sharing
[COBIDAS] using MEEG
203 July 2018

3. Roadmap
• the past & present
• COBIDAS MEEG activities: white paper
• the future
303 July 2018

4. The past & present…
03 July 2018 4

5. The changing practice of science
• the reproducibility crisis in science
• the movement for Open Science
– transparency in reporting data acquisition &
analysis parameters
– sharing analysis code & data with others
– open peer review of scientific manuscripts
503 July 2018

6. Activities in the neuroimaging
community
• grassroots discussions on reproducibility &
scientific practice
• editorial level discussions
• June 2014: statement on Neuroimaging Research
& Data Integrity by Council, Organization for
Human Brain Mapping [OHBM]
603 July 2018
‘…as the OHBM embarks on its third decade, it is an appropriate
time for its membership to embrace a collective effort toward
enhancing solid experimental rigor, study management and
provenance practices, and an openness with regards to data
sharing…’

7. 703 July 2018

8. Continuing OHBM activity
• June 2014: Council, Organization for Human
Brain Mapping [OHBM] creates a ‘Committee
on Best Practices in Data Analysis and Sharing
[COBIDAS]’
– creation of a white paper on best practices in MRI-
based data analysis & sharing in the neuroimaging
community
803 July 2018

9. COBIDAS MRI
• June 2016: COBIDAS MRI report submitted as a preprint
[Nichols et al., bioRxiv 2016]
• Feb 2017: published [Nichols et al., Nat Neurosci 2017]
903 July 2018

10. EVOLUTION OF COBIDAS MEEG
• June 2016:
– OHBM ‘Town Hall’ meeting COBIDAS MEEG issue raised in discussion
– Aina Puce & Cyril Pernet designated as Co-Chairs for COBIDAS MEEG by OHBM
Council Chair
• August 2016:
– solicitation to OHBM membership to help create/edit COBIDAS MEEG
document: 115 volunteers respond!
– discussions with IFCN Executive re: common ground
• September 2016:
– Co-Chairs attempt to create a committee with diversity in expertise, gender,
age & nationality/current working location from OHBM volunteer list
• October 2017
– Committee formed & members delegated to work on different sections of
skeleton document
– discussions with IFCN executive
1003 July 2018

11. EVOLUTION OF COBIDAS MEEG
• November 2017 – January 2018
– Committee works to draft document
• February - April 2018
– Co-Chairs edit document; additional edits by Committee members
• May 2018
– Rough 1st draft completed; sent to IFCN executive & > 100 OHBM
volunteers
– Pernet speaks at IFCN annual meeting in Washington DC
• May – June 2018
– Co-Chairs edit document to incorporate edits by OHBM volunteers
– Completed 1st draft sent to OHBM council
– Puce presents at OHBM General Assembly
1103 July 2018

12. Co-chairs: Aina Puce & Cyril Pernet
[USA] [UK]
Marta Garrido [Australia]
Alexandre Gramfort [France]
Natasha Maurits [Netherlands]
Christoph Michel [Switzerland]
Elizabeth Pang [Canada]
Riitta Salmelin [Finland]
Jan Mathijs Schoffelen [Netherlands]
Pedro Valdes-Sosa [Cuba]
COBIDAS MEEG COMMITTEE
1203 July 2018
IFCN guidelines
committee member
BIDS EEG
co-ordinator

13. COBIDAS MEEG
activities: white paper
03 July 2018 13

14. COBIDAS MEEG OBJECTIVES
03 July 2018 14
To a resource for MEEG scientists, whether they
be authors, reviewers [of papers or grants] or
journal editors

15. 1503 July 2018

16. Topic headings
• Experimental design reporting
• Acquisition reporting
• Preprocessing & processing reporting
• Biophysical & statistical analyses
• Results reporting
• Data sharing & reproducibility
• Appendix [tables of parameters to be reported]
• References
1603 July 2018

17. 1703 July 2018

18. Terminology
• The lexicon of MEEG design
– [Experimental design reporting]
• Naming conventions
– [Results reporting]
– Time-domain analysis
– Frequency-domain analysis
1803 July 2018

19. Lexicon of MEEG design
• Session: logical grouping of MEEG & behavioral data consistent
across participants; incl. time involved in completing all experimental
tasks
• Run: an uninterrupted period of continuous data acquisition without
operator involvement [equivalent to a Block]
• Event: isolated occurrence of a presented stimulus or a response;
trigger marking events in MEEG data is essential
• Condition: systematic variation of exptal parameters or
characteristics commonly designed to engage a particular mental
process or state
• Trial: period of time including a sequence of 1 or more events with
prescribed timing; the basic repeating element of an experiment
• Epoch: outcome of a data segmentation process; usually centered on
an event; can include multiple events
1903 July 2018

20. Lexicon of MEEG design
• Sensors: physical objects/transducers used to perform the
analog MEEG recording
• Channels: Refer to digital signals recorded by amplifiers from
sensors
• Fiducials: ‘objects’ used to facilitate localization & co-
registration of sensors with other geometric data
• Anatomical landmarks: physical locations on the head
• Sensor space: MEEG data expressed in their native format
[how they were acquired]
• Source space: MEEG data expressed in a normalized format
2003 July 2018

21. Naming conventions: Time domain
• ‘component’ refers to a functional brain process that has
a characteristic spatial distribution [Donchin et al. 1978]
• consider using ‘deflection’ for describing ERP/ERFs
• ERP: previous & current guidelines propose names
consisting of response polarity & nominal latency [P100,
N400 etc.]
• ERF: either add an ‘m’ to the name [N100m, N170m] or
refer to them as M100, M170 etc.
• ERPs/ERFs: some cases with special names e.g. MMN
[mismatch negativity], CNV [contingent negative
variation] etc.
2103 July 2018

22. Naming conventions: Freq domain
• The canonical MEEG bands
– delta: 0.1 to < 4 Hz;
– theta: 4 to < 8 Hz;
– alpha: 8 to 13 Hz;
– beta: 14 to 30 Hz;
– gamma: > 30 to 80 Hz
2203 July 2018
Consistent with: 1. IFCN guidelines [Kane Clin Neurophysiol Practice 2017]
2. Amzica & Lopes da Silva Niedermeyer’s Electroencephalography [2018]
3. Hari & Puce MEG-EEG Primer [2017]
For frequencies > 80 Hz see Uhlhass et al. Prog Biophys Mol Biol 2011

23. Naming conventions & more
• ‘Oscillation’: describes a spectral peak within a
freq band of interest; not a general increase in
MEEG power within a canonical freq band
[Lopes da Silva 2013]
• Need to distinguish gamma [MEEG activity]
from willful saccadic activity [artifact] –
particularly problematic in EEG studies [Yuval-
Greenberg et al., 2008]
2303 July 2018

24. General data acquisition details
• Provide details of data acquisition systems
[hardware & software]; include [manufacturer]
name & versions
• EEG: Report impedances; timing of impedance
measurement relative to experiment
• Report participant sampling method;
participant demographics; ancillary data
2403 July 2018

25. Reference electrodes, filtering etc.
• Data acquisition: report reference & ground
electrode configurations; analog low & high
pass filtering
– linked earlobe configuration not recommended for
data acquisition
• Data processing: report digital re-referencing &
filtering details
2503 July 2018

26. Statistical power
• No agreed upon single method for computing
statistical power in MEEG data
• Recommendations:
– 1. all decisions related to computing statistical
power be made prior to starting the experiment
– 2. define [from the literature] the main data
feature of interest
– 3. estimate minimal effect size of interest to
determine power
2603 July 2018

27. Some cautions for basic data analyses
• circular analyses are to be avoided [e.g. double
dipping]
• consider analyses of the full data space instead of
ROI analyses
– if need to use ROI approach specify ROIs a priori [on
literature] or via independent data [session or run]
• need to correct for multiple comparisons
2703 July 2018

28. Considerations for spatial analysis &
source modelling
• source modeling: describe expected accuracy of
method [incl. point spread function & localization
error]
• displays of source results
– incl. time courses
– for distributed models show full non-thresholded &
thresholded maps
• tables of results
– incl. contrast/effect tested, anat region, XYZ co-ord,
T/Z/F statistic, P-value (or Bayes factor)
2803 July 2018

29. Connectivity analyses
• the term ‘functional connectivity’ should be used
with caution
– do not use to refer to mere statistical dependence
• justify & clearly describe how results have been
derived [incl. data reduction strategies and/or
space selection]
• statistical evaluation needs to be clearly reported
2903 July 2018

30. Replicability & data sharing
• encourage the community to:
– adopt BIDS [Brain Imaging Data Structure]
format for MEG [Niso et al, bioRxiv 2017; Niso
et al., Nature 2018] & EEG data [Pernet et al,
in prep]
– share derived data & analysis scripts
[pipelines]
– facilitates meta-analyses
– improves training of new investigators
3003 July 2018

31. The future
03 July 2018 31

32. COBIDAS MEEG: future action plan
• July 2018: Co-Chairs incorporate feedback from OHBM
Council & COBIDAS MEEG Committee edits; 2nd draft
completed
• Aug-Sep 2018: 2nd draft made available to general OHBM
membership, journal editors etc. for comment
• Oct-Nov 2018: Co-Chairs incorporate feedback from OHBM
membership into 3rd draft; Committee’s final edits; 3rd draft
completed; seek OHBM Council & IFCN Executive official
approval
• Dec 2018: Submit pre-print & publish on OHBM website;
seek appropriate journal to publish report
3203 July 2018

33. ACKNOWLEDGEMENT
03 July 2018 33
 COBIDAS MEEG Committee Members
 > 100 OHBM volunteers who
edited/commented on the 1st draft
 future: OHBM community, OHBM Council &
IFCN Executive will provide edits & comments
on the next draft of COBIDAS MEEG