FLUX Toolkit

Utilize and interpret MEG data effectively in research and clinical practice

11th-14th June 2024

Centre for Human Brain Health

University of Birmingham

Toolkit Summary

Unlock the power of Magnetoencephalography (MEG) data analysis with the FLUX pipeline - a state-of-the-art analysis pipeline for human electrophysiological data. Whether you are stepping into the field MEG research for the first time or are a healthcare professional looking to integrate MEG into clinical practice, our course is tailored to enhance your skills and support your research.

Join us at the Centre for Human Brain Health University of Birmingham from June 11th to 14th, 2024, for an immersive learning experience designed to benefit newcomers to MEG and clinicians eager to leverage and interpret MEG data effectively.

MEG holds immense promise in cognitive and clinical neuroscience, yet its data analysis poses significant challenges due to its technical complexity and lack of standardized approaches. In response to the growing demand for accessible MEG training we have developed the FLUX toolkit. We have developed a comprehensive analysis pipeline based on MNE-Python, one of the most widely used MEG analysis toolboxes. Throughout the course, participants will delve into the theoretical underpinnings of electrophysiology while gaining hands-on experience in utilizing FLUX to streamline data preprocessing, source modelling, and bast practice in regard to reporting.

This project is supported by

NIHR Oxford Health Biomedical Research Centre (NIHR203316). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care

The Institute for Interdisciplinary Data Science and AI, University of Birmingham

Learning outcomes

Gain fundamental knowledge of electrophysiology and practical expertise in streamlining analysis processes. Utilize a comprehensive analysis pipeline compatible with MNE-Python to master data preprocessing, source modeling, and result reporting, enhancing analytical skills and research proficiency.

Develop Analytical Skills and Research Proficiency

Go beyond basic data analysis by learning to integrate MEG analysis to tackle specific cognitive and clinical questions. Benefit from insights shared by expert researchers who have utilized MEG and advanced analyses in their cutting-edge published research, empowering attendees to develop their own research projects effectively.

Apply MEG Analysis to Address Cognitive and Clinical Neuroscience Questions

Foster open science and reproducible research practices by utilizing pre-registered report templates, enhancing methodology reporting in journals, and implementing standardized data formats such as MEG-BIDS. Equip participants with the tools to conduct robust and reproducible research in cognitive neuroscience.

Champion Open Science and Reproducible Research

Experience dynamic in-person sessions where participants can engage in discussions, interact with instructors and peers, and seek clarification on course material. Maximize learning potential through interactive engagement and direct access to expert guidance.

Engage in Interactive In-Person Sessions

Forge valuable connections with experts from the University of Birmingham and fellow attendees, enriching your professional network. Enjoy socializing opportunities throughout the course to foster collaborations and career advancement, particularly beneficial for researchers from underrepresented groups.

Expand Your Research Network

The programme

The FLUX toolkit course is divided into two sections each day. The morning sessions cover the theoretical background, while the afternoons are reserved for practical, hands-on sessions. During the hands-on sessions, attendees will learn how to apply the analysis methods they have learned to a sample dataset. There will also be an opportunity to practice using their own data. Additionally, there will be a daily special interest talk where researchers from CHBH will showcase their latest MEG research.

Time table

Program in detail

Tuesday 11th June

Morning session (10:00-11:30)
- 10:00-10:15 Meet and greet Ole Jensen
- 10:15-10:45 The physiological basis of MEG Ole Jensen
- 10:45-11:30 Basics of SQUID and OPM MEG Ole Jensen
Hands-on Session (11:30-13:00)
- Data collection & visit MEG & OPM labs Tara Ghafari & Anna Kowalczyk
Lunch & Coffee (13:00-14:15)
Scientific Presentation (14:15-15:15)
- Mixed linear modelling for the analysis of multimodal imaging data

Clayton Hickey, Damiano Grignolio

Hands-on Session (15:15-17:00)
- FLUX: Introduction and installation Tara Ghafari, Tommy Clausner
- FLUX: The dataset Yulia Bezsudnova-Wilson, Arnab Rakshit
- FLUX: A first look at the data Joey Zhou, Oscar Ferrante

Wednesday 12th June

Morning session (10:00-11:30)
10:00-10:30 Brain Imaging Data Structure Tara Ghafari
10:30-11:30 Preprocessing & Event-related Fields Hyojin Park
Lunch (11:30-12:30)
Scientific Presentation (12:30-13:30)
OPMs: the next generation of MEG Anna Kowalczyk, Kyungmin An
Coffee Break (13:30-14:00)
Hands-on Session (14:00-17:00)
FLUX: ICA for attenuating artefacts Yulia Bezsudnova-Wilson, Arnab Rakshit
FLUX: Extracting condition-specific trials Tara Ghafari, Alicia Rybicki
FLUX: Event-related fields Oscar Ferrante, Tommy Clausner
Social Dinner at Akram's (19:00)

Thursday 13th June

Morning session (10:00-11:30)
10:00-10:20 Oscillations in Cognition Ole Jensen
10:20-10:45 The Fourier Transform Andrew Quinn
10:45-11:00 Power Spectrum Andrew Quinn
11:00- 11:30 Time Frequency Representation Andrew Quinn
Lunch (11:30-12:30)
Scientific Presentation (12:30-13:30)
Dissecting skilled motor control Katja Kornysheva
Coffee Break (13:30-14:00)
Hands-on Session (14:00-17:00)
Education: Discrete Fourier Transform Ole Jensen
Education: Time-frequency Representation of Power Ole Jensen
FLUX: Time-frequency representations of power Oscar Ferrante, Tommy Clausner

Friday 14th June

Morning session (10:00-11:30)
10:00-10:15 Forward Model Ole Jensen
10:15-11:00 Beamforming Ole Jensen
11:00-11:15 Minimum Norm Estimate Ole Jensen
11:15- 11:30 Multivariate Pattern Analysis Oscar Ferrante
Lunch (11:30-12:30)
Scientific Presentation (12:30-13:30)
12:30-13:00 Hierarchical processing of orthographic and semantic parafoveal information during natural reading Lijuan Wang
13:00-13:30 An adversarial collaboration to critically evaluate theories of consciousness. Oscar Ferrante
Coffee Break (13:30-14:00)
Hands-on Session (14:00-17:00)
FLUX: Constructing the forward model Oscar Ferrante, Yulia Bezsudnova-Wilson
FLUX: Source modeling using DICS beamforming Oscar Ferrante, Arnab Rakshit

Recommended Reading Materials

(ask us for PDFs you cannot find)

MEG and OPM instrumentation:

Hari, R. (2004) Magnetoencephalography in Clinical Neurophysiological Assessment of Human Cortical Functions. in Niedermeyer's Electroencephalography : Basic Principles, Clinical Applications, and Related Fields by Schomer and Lopes da Silva
Hämäläinen, M., Hari, R., Ilmoniemi, R.J., , Knuutila, J., and Lounasmaa, O.V. (1993) Magnetoencephalography—theory, instrumentation, and applications to noninvasive studies of the working human brain.
Reviews of modern Physics 65 (2), 413
Brookes, M.J., Leggett, J., Rea, M., Hill, R.M., Holmes, N., Boto, E., Bowtell, R. (2022) Magnetoencephalography with optically pumped magnetometers (OPM-MEG): the next generation of functional neuroimaging. Trends Neurosci. 45(8):621-634. doi: 10.1016/j.tins.2022.05.008.
Kowalczyk, A.U., Bezsudnova, Y., Jensen, O., and Barontini, G. (2021) Detection of human auditory evoked brain signals with a resilient nonlinear optically pumped magnetometer. Neuroimage. 226:117497. doi: 10.1016/j.neuroimage.2020.117497.

Physiology:

Lopes da Silva, F.H. (2010) Electrophysiological Basis of MEG Signals. In MEG: An Introduction to Methods, Eds. Hansen, Kringelback and Salmelin, Oxford Academic Books
Buzsáki, G., Anastassiou, C.A., and Koch, C. (2012) The origin of extracellular fields and currents--EEG, ECoG, LFP and spikes. Nat Rev Neurosci. 2012 May 18;13(6):407-20. doi: 10.1038/nrn3241.

Event-related responses in cognition

Woodman G.F. (2010) A brief introduction to the use of event-related potentials in studies of perception and attention. Atten Percept Psychophys. 72(8):2031-46.
Luck, S.J. (2014) An Introduction to the Event-Related Potential Technique, second edition. The MIT Press

Oscillations in cognition:

Jensen, O., and Hanslmayr (2020) The Role of Alpha Oscillations for Attention and Working Memory. In: The Cognitive Neurosciences. The MIT Press
Jensen, O., Spaak, E., and Zumer, J.M. (2014) Human Brain Oscillations: From Physiological Mechanisms to Analysis and Cognition. In Magnetoencephalography. Eds. Supek and Aine. Springer
Jensen, O. (2024) Distractor inhibition by alpha oscillations is controlled by an indirect mechanism governed by goal-relevant information. Commun Psychol. 2024;2(1):36. doi: 10.1038/s44271-024-00081-w.
Buzsaki, G. (2011) Rhythms of the Brain. Oxford University Press
Jensen, O. (2023) Rhythms and Cognition. Brain Inspired 160. Podcast

Spectral analysis

Smith, S.W. (1997) The Discrete Fourier Transform. Chapter 8. In The Scientist and Engineer's Guide to DSP. PDF
Smith, S.W. (1997) Applications of the DFT. Chapter 9. In The Scientist and Engineer's Guide to DSP. PDF
Percival, D.B. and Walden, A.T. (1993) Spectral Analysis for Physical Applications. Cambridge University Press
Bruns, A. (2004) Fourier-, Hilbert- and wavelet-based signal analysis: are they really different approaches? J Neurosci Methods. 137(2):321-32. doi: 10.1016/j.jneumeth.2004.03.002.

Multi-variate pattern analysis

Cichy, R.M., Pantazis, D., and Oliva, A. (2014) Resolving human object recognition in space and time, Nature Neuroscience, 17:455–462.
Guggenmos, M., Sterzer, P., and Cichy, R.M. (2018) Multivariate pattern analysis for MEG: A comparison of dissimilarity measures, NeuroImage, 173:434-447.
King, J.R., and Dehaene, S. (2014) Characterizing the dynamics of mental representations: the temporal generalization method, Trends in Cognitive Sciences, 18(4): 203-210

Source modelling

Baillet, S. (2017) Magnetoencephalography for brain electrophysiology and imaging. Nat Neurosci. 20(3):327-339. doi: 10.1038/nn.4504.
Baillet S, Mosher JC, Leahy RM (2001) Electromagnetic brain mapping, IEEE SP MAG .
Dale, A.M., Liu, A.K., Fischl, B.R., Buckner, R.L., Belliveau, J.W., Lewine, J.D., and Halgren, E. (2000) Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity. Neuron 2000 Apr, 26(1):55-67
Van Veen,B.D., Van Drongelen, W., Yuchtman, M. and Suzuki, A. (1997) Localization of brain electrical activity via linearly constrained minimum variance spatial filtering, IEEE Transactions on Biomedical Engineering 44(9) 867-880
Jensen, O., and Hesse, C. (2001) Estimating Distributed Representation of Evoked Responses and Oscillatory Brain Activity. In MEG: An Introduction to Methods, Eds. Hansen, Kringelback and Salmelin, Oxford Academic Books

Speakers

Prof. Ole Jensen

Professor in Translational Neuroscience

Dr. Andrew Quinn

Assistant Professor in Psychology

Dr. Katja Kornysheva

Asistant Professor in Human Neuroscience

Dr. Yulia Wilson-Bezsudnova

Postdoc

Dr. Tommy Clausner

Postdoc

Dr. Clayton Hickey

Associate Professor in Psychology

Dr. Anna Kowalczyk

Asistant Professor

Dr. Tara Ghafari

Postdoc

Dr. Alicia Rybicki

Postdoc

Lijuan Wang

PhD candidate

Dr. Hyojin Park

Assistant Professor in Psychology

Dr. Kyungmin An

Asistant Professor in Psychology

Dr. Oscar Ferrante

Postdoc

Dr. Arnab Rakshit

Postdoc

Damiano Grignolio

PhD candidate

Led by esteemed MEG experts and seasoned researchers from the University of Birmingham's Centre for Human Brain Health (CHBH), our instructors bring unparalleled expertise to guide you through every step. Our diverse team of instructors represents nine nationalities, ensuring a rich and inclusive learning environment. We're committed to fostering diversity and will prioritize candidates from underrepresented groups and ethnicities to ensure everyone has the opportunity to benefit from this transformative course.

Diversity

Open Science

Inclusivity

Application

* a statement why you want to attend (1500 characters maximum)

The session is anticipated to host 30 participants, primarily early career researchers (including senior PhD students, post-doctoral fellows, and early-stage faculty members) as well as clinicians seeking to utilize and interpret magnetoencephalography (MEG) effectively.

Fee

The registration fee for the FLUX Hands-On Course is £160. The price covers registration, coffee, lunch, and dinner on one night.

We regret to announce that waivers are not applicable.

Important dates

Application (pre-registration) deadline: 20th April 2024, 11:59 pm (GMT)

Decision communicated: 1st May 2024

Course dates: 11th - 14th June

Venue

Elm House,

University of Birmingham,

Edgbaston,
Birmingham,
B15 2TT,
United Kingdom

Transport

By taxi: Edgbaston Park Hotel, B15 2RS.
By car: North East multi-storey car park; 52 Pritchatts Rd, Birmingham B15 2SA . Use the RingGo app for payments.
By train: University Station (1 km; 13 min walk)

Visa

Once your application is successful, please get in touch if you need an invitation letter for your VISA application.

Contact us

If you have any questions regarding the FLUX Hands-On Course or the application, please contact us via q.chen.5@bham.ac.uk