From ERPs to MVPA Using the Amsterdam Decoding and Modeling Toolbox (ADAM)

Frontiers in Neuroscience
Johannes Jacobus FahrenfortChristian N L Olivers

Abstract

In recent years, time-resolved multivariate pattern analysis (MVPA) has gained much popularity in the analysis of electroencephalography (EEG) and magnetoencephalography (MEG) data. However, MVPA may appear daunting to those who have been applying traditional analyses using event-related potentials (ERPs) or event-related fields (ERFs). To ease this transition, we recently developed the Amsterdam Decoding and Modeling (ADAM) toolbox in MATLAB. ADAM is an entry-level toolbox that allows a direct comparison of ERP/ERF results to MVPA results using any dataset in standard EEGLAB or Fieldtrip format. The toolbox performs and visualizes multiple-comparison corrected group decoding and forward encoding results in a variety of ways, such as classifier performance across time, temporal generalization (time-by-time) matrices of classifier performance, channel tuning functions (CTFs) and topographical maps of (forward-transformed) classifier weights. All analyses can be performed directly on raw data or can be preceded by a time-frequency decomposition of the data in which case the analyses are performed separately on different frequency bands. The figures ADAM produces are publication-ready. In the current manuscript, we provide a cookb...Continue Reading

References

May 5, 1998·Electroencephalography and Clinical Neurophysiology·W KlimeschT Pachinger
Feb 4, 1999·Biophysical Journal·P P Mitra, B Pesaran
Nov 27, 1999·Clinical Neurophysiology : Official Journal of the International Federation of Clinical Neurophysiology·G Pfurtscheller, F H Lopes da Silva
Mar 29, 2003·Neural Networks : the Official Journal of the International Neural Network Society·Bjorn O. PetersHenrik Flyvbjerg
May 23, 2007·Journal of Neuroscience Methods·Eric Maris, Robert Oostenveld
Dec 27, 2008·Neuron·Nikolaus KriegeskortePeter A Bandettini
Feb 13, 2009·Frontiers in Neuroinformatics·Michael HankeStefan Pollmann
Apr 28, 2009·Nature Neuroscience·Nikolaus KriegeskorteChris I Baker
Nov 6, 2009·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Gijs Joost Brouwer, David J Heeger
Jul 6, 2010·NeuroImage·Benjamin BlankertzKlaus-Robert Müller
Jan 22, 2011·Computational Intelligence and Neuroscience·Robert OostenveldJan-Mathijs Schoffelen
Sep 1, 2011·Nature Neuroscience·Sander NieuwenhuisEric-Jan Wagenmakers
Oct 11, 2012·NeuroImage·Joachim GrossJan-Mathijs Schoffelen
Dec 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Johannes J FahrenfortVictor A F Lamme
Jun 5, 2013·Frontiers in Neuroinformatics·Ethan M Meyers
Oct 29, 2013·NeuroImage·Alexandre GramfortMatti S Hämäläinen
Jan 28, 2014·Nature Neuroscience·Radoslaw Martin CichyAude Oliva
Mar 7, 2014·Trends in Cognitive Sciences·J-R King, S Dehaene
Nov 21, 2014·Journal of Neurophysiology·Niels A KloostermanTobias H Donner
May 16, 2015·Scientific Data·Daniel G Wakeman, Richard N Henson
Sep 10, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Jing-Hao Xue, Peter Hall
Oct 16, 2015·Journal of Neurophysiology·Joshua J FosterEdward Awh
Dec 17, 2015·Scientific Reports·Pim MostertFloris P de Lange
Aug 9, 2016·Frontiers in Neuroinformatics·Nikolaas N OosterhofJames V Haxby
Oct 14, 2016·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Daniel KaiserMarius V Peelen
Mar 23, 2017·Proceedings of the National Academy of Sciences of the United States of America·Johannes J FahrenfortHinze Hogendoorn
May 17, 2017·Scientific Reports·Johannes Jacobus FahrenfortMartin Eimer
Aug 2, 2017·Consciousness and Cognition·William Francis TurnerStefan Bode
Dec 7, 2017·Nature Communications·Sébastien Marti, Stanislas Dehaene
Dec 8, 2017·Neuron·Padraig GleesonGiorgio A Ascoli

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Citations

Sep 7, 2018·Journal of Cognitive Neuroscience·Andrea De CesareiMaurizio Codispoti
Nov 6, 2018·ELife·Anouk Mariette van LoonChristian Nl Olivers
Aug 28, 2019·ELife·Eduard OrtChristian Nl Olivers
Aug 17, 2019·Journal of Cognitive Neuroscience·Ingmar E J de VriesChristian N L Olivers
Jun 26, 2020·Frontiers in Neuroscience·Matthias S Treder
Dec 29, 2020·Cortex; a Journal Devoted to the Study of the Nervous System and Behavior·Katya Olmos-SolisChristian N L Olivers
Nov 17, 2020·Frontiers in Behavioral Neuroscience·Yadwinder KaurAndrea Hildebrandt
Jul 13, 2021·The European Journal of Neuroscience·Serena DefinaTristan A Bekinschtein
Jul 4, 2021·International Journal of Psychophysiology : Official Journal of the International Organization of Psychophysiology·Fariba SharifianEdmund Wascher
Jul 8, 2021·Journal of Neurophysiology·Astrid ProchnowChristian Beste
Dec 24, 2021·Neuropsychology, Development, and Cognition. Section B, Aging, Neuropsychology and Cognition·Verena R Sommer, Myriam C Sander

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Software Mentioned

MVPA
stats
Matlab
Decision Decoding Toolbox
BrainVision Analyzer
MaxFilter
RAW
Neural Decoding Toolbox
MATLAB Command
Pyt

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