SEREEGA: Simulating event-related EEG activity

STARTS: A Self-Adapted Spatio-Temporal Framework for Automatic E/MEG Source Imaging

To obtain accurate brain source activities, the highly ill-posed source imaging of electro- and magneto-encephalography (E/MEG) requires proficiency in incorporation of biophysiological constraints and signal-processing techniques. Here, we propose a spatio-temporal-constrainted E/MEG source imaging framework-STARTS that can reconstruct the source in a fully automatic way. Specifically, a block-diagonal covariance was adopted to reconstruct the source extents while maintain spatial homogeneity. Temporal basis functions (TBFs) of both sources and noise were estimated and updated in a data-driven fashion to alleviate the influence of noises and further improve source localization accuracy. The performance of the proposed STARTS was quantitatively assessed through a series of simulation experiments, wherein superior results were obtained in comparison with the benchmark ESI algorithms (including LORETA, EBI-Convex, BESTIES & SI-STBF). Additional validations on epileptic and resting-state EEG data further indicate that the STARTS can produce neurophysiologically plausible results. Moreover, a computationally efficient version of STARTS: smooth STARTS was also introduced with an elementary spatial constraint, which exhibited comparable performance and reduced execution cost. In sum, the proposed STARTS, with its advanced spatio-temporal constraints and self-adapted update operation, provides an effective and efficient approach for E/MEG source imaging.

Comprehensive analysis of supervised learning methods for electrical source imaging

Electroencephalography source imaging (ESI) is an ill-posed inverse problem: an additional constraint is needed to find a unique solution. The choice of this constraint, or prior, remains a challenge for most ESI methods. This work explores the application of supervised learning methods for spatio-temporal ESI, where the relationship between measurements and sources is learned directly from the data. Three neural networks were trained on synthetic data and compared with non-learning based methods. Two distinct types of simulation, each based on different models of brain electrical activity, were employed to quantitatively assess the generalization capabilities of the neural networks and the impact of training data on their performances, using five complementary metrics. The results demonstrate that, with appropriately designed simulations, neural networks can be competitive with non-learning-based approaches, even when applied to previously unseen data.

Brain Evoked Response Qualification Using Multi-Set Consensus Clustering: Toward Single-Trial EEG Analysis

In event-related potential (ERP) analysis, it is commonly assumed that individual trials from a subject share similar properties and originate from comparable neural sources, allowing reliable interpretation of group-averages. Nevertheless, traditional group-level ERP analysis methods, including cluster analysis, often overlook critical information about individual subjects' neural processes due to using fixed measurement intervals derived from averaging. We developed a multi-set consensus clustering pipeline to examine cognitive processes at the individual subject level. Initially, consensus clustering from diverse methods was applied to single-trial EEG epochs of individual subjects. Subsequently, a second level of consensus clustering was performed across the trials of each subject. A newly modified time window determination method was then employed to identify individual subjects' ERP(s) of interest. We validated our method with simulated data for ERP components N2 and P3, and real data from a visual oddball task to confirm the P3 component. Our findings revealed that estimated time windows for individual subjects provide precise ERP identification compared to fixed time windows across all subjects. Additionally, Monte Carlo simulations with synthetic single-trial data demonstrated stable scores for the N2 and P3 components, confirming the reliability of our method. The proposed method enhances the examination of brain-evoked responses at the individual subject level by considering single-trial EEG data, thereby extracting mutual information relevant to the neural process. This approach offers a significant improvement over conventional ERP analysis, which relies on the averaging mechanism and fixed measurement interval.

A generic error-related potential classifier based on simulated subjects

Error-related potentials (ErrPs) are brain signals known to be generated as a reaction to erroneous events. Several works have shown that not only self-made errors but also mistakes generated by external agents can elicit such event-related potentials. The possibility of reliably measuring ErrPs through non-invasive techniques has increased the interest in the brain-computer interface (BCI) community in using such signals to improve performance, for example, by performing error correction. Extensive calibration sessions are typically necessary to gather sufficient trials for training subject-specific ErrP classifiers. This procedure is not only time-consuming but also boresome for participants. In this paper, we explore the effectiveness of ErrPs in closed-loop systems, emphasizing their dependency on precise single-trial classification. To guarantee the presence of an ErrPs signal in the data we employ and to ensure that the parameters defining ErrPs are systematically varied, we utilize the open-source toolbox SEREEGA for data simulation. We generated training instances and evaluated the performance of the generic classifier on both simulated and real-world datasets, proposing a promising alternative to conventional calibration techniques. Results show that a generic support vector machine classifier reaches balanced accuracies of 72.9%, 62.7%, 71.0%, and 70.8% on each validation dataset. While performing similarly to a leave-one-subject-out approach for error class detection, the proposed classifier shows promising generalization across different datasets and subjects without further adaptation. Moreover, by utilizing SEREEGA, we can systematically adjust parameters to accommodate the variability in the ErrP, facilitating the systematic validation of closed-loop setups. Furthermore, our objective is to develop a universal ErrP classifier that captures the signal's variability, enabling it to determine the presence or absence of an ErrP in real EEG data.

Optimizing EEG ICA decomposition with data cleaning in stationary and mobile experiments

Electroencephalography (EEG) studies increasingly utilize more mobile experimental protocols, leading to more and stronger artifacts in the recorded data. Independent Component Analysis (ICA) is commonly used to remove these artifacts. It is standard practice to remove artifactual samples before ICA to improve the decomposition, for example using automatic tools such as the sample rejection option of the AMICA algorithm. However, the effects of movement intensity and the strength of automatic sample rejection on ICA decomposition have not been systematically evaluated. We conducted AMICA decompositions on eight open-access datasets with varying degrees of motion intensity using varying sample rejection criteria. We evaluated decomposition quality using mutual information of the components, the proportion of brain, muscle, and 'other' components, residual variance, and an exemplary signal-to-noise ratio. Within individual studies, increased movement significantly decreased decomposition quality, though this effect was not found across different studies. Cleaning strength significantly improved the decomposition, but the effect was smaller than expected. Our results suggest that the AMICA algorithm is robust even with limited data cleaning. Moderate cleaning, such as 5 to 10 iterations of the AMICA sample rejection, is likely to improve the decomposition of most datasets, regardless of motion intensity.

Optimal filters for ERP research I: A general approach for selecting filter settings

Filtering plays an essential role in event-related potential (ERP) research, but filter settings are usually chosen on the basis of historical precedent, lab lore, or informal analyses. This reflects, in part, the lack of a well-reasoned, easily implemented method for identifying the optimal filter settings for a given type of ERP data. To fill this gap, we developed an approach that involves finding the filter settings that maximize the signal-to-noise ratio for a specific amplitude score (or minimizes the noise for a latency score) while minimizing waveform distortion. The signal is estimated by obtaining the amplitude score from the grand average ERP waveform (usually a difference waveform). The noise is estimated using the standardized measurement error of the single-subject scores. Waveform distortion is estimated by passing noise-free simulated data through the filters. This approach allows researchers to determine the most appropriate filter settings for their specific scoring methods, experimental designs, subject populations, recording setups, and scientific questions. We have provided a set of tools in ERPLAB Toolbox to make it easy for researchers to implement this approach with their own data.

An evaluation of inter-brain EEG coupling methods in hyperscanning studies

EEG-based hyperscanning technology has been increasingly applied to analyze interpersonal interactions in social neuroscience in recent years. However, different methods are employed in various of studies without a complete investigation of the suitability of these methods. Our study aimed to systematically compare typical inter-brain EEG coupling methods, with simulated EEG data generated by real EEG data. In particular, two critical metrics of noise level and time delay were manipulated, and three different coupling models were tested. The results revealed that: (1) under certain conditions, various methods were leveraged by noise level and time delay, leading to different performances; (2) most algorithms achieved better experimental results and performance under high coupling degree; (3) with our simulation process, temporal and spectral models showed relatively good results, while data simulated with phase coupling model performed worse. This is the first systematic comparison of typical inter-brain EEG coupling methods, with simulated EEG data generated by real EEG data from different subjects. Existing methods mainly focused on intra-brain coupling. To our knowledge, there was only one previous study that compared five inter-brain EEG coupling methods (Burgess in Front Human Neurosci 7:881, 2013). However, the simulated data used in this study were generated time series with varied degrees of phase coupling without considering any EEG characteristics. For future research, appropriate methods need to be selected based on possible underlying mechanisms (temporal, spectral and phase coupling model hypothesis) of a specific study, as well as the expected coupling degree and conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11571-022-09911-1.

lmeEEG: Mass linear mixed-effects modeling of EEG data with crossed random effects

BACKGROUND

Mixed-effects models are the current standard for the analysis of behavioral studies in psycholinguistics and related fields, given their ability to simultaneously model crossed random effects for subjects and items. However, they are hardly applied in neuroimaging and psychophysiology, where the use of mass univariate analyses in combination with permutation testing would be too computationally demanding to be practicable with mixed models.

NEW METHOD

Here, we propose and validate an analytical strategy that enables the use of linear mixed models (LMM) with crossed random intercepts in mass univariate analyses of EEG data (lmeEEG). It avoids the unfeasible computational costs that would arise from massive permutation testing with LMM using a simple solution: removing random-effects contributions from EEG data and performing mass univariate linear analysis and permutations on the obtained marginal EEG.

RESULTS

lmeEEG showed excellent performance properties in terms of power and false positive rate.

COMPARISON WITH EXISTING METHODS

lmeEEG overcomes the computational costs of standard available approaches (our method was indeed more than 300 times faster).

CONCLUSIONS

lmeEEG allows researchers to use mixed models with EEG mass univariate analyses. Thanks to the possibility offered by the method described here, we anticipate that LMM will become increasingly important in neuroscience. Data and codes are available at osf.io/kw87a. The codes and a tutorial are also available at github.com/antovis86/lmeEEG.

Optimal Filters for ERP Research I: A General Approach for Selecting Filter Settings

Filtering plays an essential role in event-related potential (ERP) research, but filter settings are usually chosen on the basis of historical precedent, lab lore, or informal analyses. This reflects, in part, the lack of a well-reasoned, easily implemented method for identifying the optimal filter settings for a given type of ERP data. To fill this gap, we developed an approach that involves finding the filter settings that maximize the signal-to-noise ratio for a specific amplitude score (or minimizes the noise for a latency score) while minimizing waveform distortion. The signal is estimated by obtaining the amplitude score from the grand average ERP waveform (usually a difference waveform). The noise is estimated using the standardized measurement error of the single-subject scores. Waveform distortion is estimated by passing noise-free simulated data through the filters. This approach allows researchers to determine the most appropriate filter settings for their specific scoring methods, experimental designs, subject populations, recording setups, and scientific questions. We have provided a set of tools in ERPLAB Toolbox to make it easy for researchers to implement this approach with their own data.

μ-STAR: A novel framework for spatio-temporal M/EEG source imaging optimized by microstates

Source imaging of Electroencephalography (EEG) and Magnetoencephalography (MEG) provides a noninvasive way of monitoring brain activities with high spatial and temporal resolution. In order to address this highly ill-posed problem, conventional source imaging models adopted spatio-temporal constraints that assume spatial stability of the source activities, neglecting the transient characteristics of M/EEG. In this work, a novel source imaging method μ-STAR that includes a microstate analysis and a spatio-temporal Bayesian model was introduced to address this problem. Specifically, the microstate analysis was applied to achieve automatic determination of time window length with quasi-stable source activity pattern for optimal reconstruction of source dynamics. Then a user-specific spatial prior and data-driven temporal basis functions were utilized to characterize the spatio-temporal information of sources within each state. The solution of the source reconstruction was obtained through a computationally efficient algorithm based upon variational Bayesian and convex analysis. The performance of the μ-STAR was first assessed through numerical simulations, where we found that the determination and inclusion of optimal temporal length in the spatio-temporal prior significantly improved the performance of source reconstruction. More importantly, the μ-STAR model achieved robust performance under various settings (i.e., source numbers/areas, SNR levels, and source depth) with fast convergence speed compared with five widely-used benchmark models (including wMNE, STV, SBL, BESTIES, & SI-STBF). Additional validations on real data were then performed on two publicly-available datasets (including block-design face-processing ERP and continuous resting-state EEG). The reconstructed source activities exhibited spatial and temporal neurophysiologically plausible results consistent with previously-revealed neural substrates, thereby further proving the feasibility of the μ-STAR model for source imaging in various applications.

An empirical comparison of deep learning explainability approaches for EEG using simulated ground truth

Recent advancements in machine learning and deep learning (DL) based neural decoders have significantly improved decoding capabilities using scalp electroencephalography (EEG). However, the interpretability of DL models remains an under-explored area. In this study, we compared multiple model explanation methods to identify the most suitable method for EEG and understand when some of these approaches might fail. A simulation framework was developed to evaluate the robustness and sensitivity of twelve back-propagation-based visualization methods by comparing to ground truth features. Multiple methods tested here showed reliability issues after randomizing either model weights or labels: e.g., the saliency approach, which is the most used visualization technique in EEG, was not class or model-specific. We found that DeepLift was consistently accurate as well as robust to detect the three key attributes tested here (temporal, spatial, and spectral precision). Overall, this study provides a review of model explanation methods for DL-based neural decoders and recommendations to understand when some of these methods fail and what they can capture in EEG.

Decoding Multi-Class Motor Imagery and Motor Execution Tasks Using Riemannian Geometry Algorithms on Large EEG Datasets

The use of Riemannian geometry decoding algorithms in classifying electroencephalography-based motor-imagery brain-computer interfaces (BCIs) trials is relatively new and promises to outperform the current state-of-the-art methods by overcoming the noise and nonstationarity of electroencephalography signals. However, the related literature shows high classification accuracy on only relatively small BCI datasets. The aim of this paper is to provide a study of the performance of a novel implementation of the Riemannian geometry decoding algorithm using large BCI datasets. In this study, we apply several Riemannian geometry decoding algorithms on a large offline dataset using four adaptation strategies: baseline, rebias, supervised, and unsupervised. Each of these adaptation strategies is applied in motor execution and motor imagery for both scenarios 64 electrodes and 29 electrodes. The dataset is composed of four-class bilateral and unilateral motor imagery and motor execution of 109 subjects. We run several classification experiments and the results show that the best classification accuracy is obtained for the scenario where the baseline minimum distance to Riemannian mean has been used. The mean accuracy values up to 81.5% for motor execution, and up to 76.4% for motor imagery. The accurate classification of EEG trials helps to realize successful BCI applications that allow effective control of devices.

Enhanced external counterpulsation modulates the heartbeat evoked potential

Introduction: Accumulating evidence suggests that enhanced external counterpulsation (EECP) influences cardiac functions, hemodynamic characteristics and cerebral blood flow. However, little is known about whether or how the EECP affects the brain-heart coupling to produce these physiological and functional changes. We aimed to determine if the brain-heart coupling is altered during or after EECP intervention by assessing the heartbeat evoked potential (HEP) in healthy adults.

Methods: Based on a random sham-controlled design, simultaneous electroencephalography and electrocardiography signals as well as blood pressure and flow status data were recorded before, during and after two consecutive 30-min EECP in 40 healthy adults (female/male: 17/23; age: 23.1 ± 2.3 years). HEP amplitude, frequency domain heart rate variability, electroencephalographic power and hemodynamic measurements of 21 subjects (female/male: 10/11; age: 22.7 ± 2.1 years) receiving active EECP were calculated and compared with those of 19 sham control subjects (female/male: 7/12; age: 23.6 ± 2.5 years).

Results: EECP intervention caused immediate obvious fluctuations of HEP from 100 to 400 ms after T-peak and increased HEP amplitudes in the (155–169) ms, (354–389) ms and (367–387) ms time windows after T-peak in the region of the frontal pole lobe. The modifications in HEP amplitude were not associated with changes in the analyzed significant physiological measurements and hemodynamic variables.

Discussion: Our study provides evidence that the HEP is modulated by immediate EECP stimuli. We speculate that the increased HEP induced by EECP may be a marker of enhanced brain-heart coupling. HEP may serve as a candidate biomarker for the effects and responsiveness to EECP.

HArtMuT-modeling eye and muscle contributors in neuroelectric imaging

Objective.Magneto- and electroencephalography (M/EEG) measurements record a mix of signals from the brain, eyes, and muscles. These signals can be disentangled for artifact cleaning e.g. using spatial filtering techniques. However, correctly localizing and identifying these components relies on head models that so far only take brain sources into account.Approach.We thus developed the Head Artifact Model using Tripoles (HArtMuT). This volume conduction head model extends to the neck and includes brain sources as well as sources representing eyes and muscles that can be modeled as single dipoles, symmetrical dipoles, and tripoles. We compared a HArtMuT four-layer boundary element model (BEM) with the EEGLAB standard head model on their localization accuracy and residual variance (RV) using a HArtMuT finite element model (FEM) as ground truth. We also evaluated the RV on real-world data of mobile participants, comparing different HArtMuT BEM types with the EEGLAB standard head model.Main results.We found that HArtMuT improves localization for all sources, especially non-brain, and localization error and RV of non-brain sources were in the same range as those of brain sources. The best results were achieved by using cortical dipoles, muscular tripoles, and ocular symmetric dipoles, but dipolar sources alone can already lead to convincing results.Significance.We conclude that HArtMuT is well suited for modeling eye and muscle contributions to the M/EEG signal. It can be used to localize sources and to identify brain, eye, and muscle components. HArtMuT is freely available and can be integrated into standard software.

The HAPPE plus Event-Related (HAPPE+ER) software: A standardized preprocessing pipeline for event-related potential analyses

Event-Related Potential (ERP) designs are a common method for interrogating neurocognitive function with electroencephalography (EEG). However, the traditional method of preprocessing ERP data is manual-editing - a subjective, time-consuming processes. A number of automated pipelines have recently been created to address the need for standardization, automation, and quantification of EEG data pre-processing; however, few are optimized for ERP analyses (especially in developmental or clinical populations). We propose and validate the HAPPE plus Event-Related (HAPPE+ER) software, a standardized and automated pre-processing pipeline optimized for ERP analyses across the lifespan. HAPPE+ER processes event-related potential data from raw files through preprocessing and generation of event-related potentials for statistical analyses. HAPPE+ER also includes post-processing reports of both data quality and pipeline quality metrics to facilitate the evaluation and reporting of data processing in a standardized manner. Finally, HAPPE+ER includes post-processing scripts to facilitate validating HAPPE+ER performance and/or comparing to performance of other preprocessing pipelines in users' own data via simulated ERPs. We describe multiple approaches with simulated and real ERP data to optimize pipeline performance and compare to other methods and pipelines. HAPPE+ER software is freely available under the terms of GNU General Public License at https://www.gnu.org/licenses/#GPL.

Adaptable and Robust EEG Bad Channel Detection Using Local Outlier Factor (LOF)

Electroencephalogram (EEG) data are typically affected by artifacts. The detection and removal of bad channels (i.e., with poor signal-to-noise ratio) is a crucial initial step. EEG data acquired from different populations require different cleaning strategies due to the inherent differences in the data quality, the artifacts' nature, and the employed experimental paradigm. To deal with such differences, we propose a robust EEG bad channel detection method based on the Local Outlier Factor (LOF) algorithm. Unlike most existing bad channel detection algorithms that look for the global distribution of channels, LOF identifies bad channels relative to the local cluster of channels, which makes it adaptable to any kind of EEG. To test the performance and versatility of the proposed algorithm, we validated it on EEG acquired from three populations (newborns, infants, and adults) and using two experimental paradigms (event-related and frequency-tagging). We found that LOF can be applied to all kinds of EEG data after calibrating its main hyperparameter: the LOF threshold. We benchmarked the performance of our approach with the existing state-of-the-art (SoA) bad channel detection methods. We found that LOF outperforms all of them by improving the F1 Score, our chosen performance metric, by about 40% for newborns and infants and 87.5% for adults.

IC-U-Net: A U-Net-based Denoising Autoencoder Using Mixtures of Independent Components for Automatic EEG Artifact Removal

Electroencephalography (EEG) signals are often contaminated with artifacts. It is imperative to develop a practical and reliable artifact removal method to prevent the misinterpretation of neural signals and the underperformance of brain-computer interfaces. Based on the U-Net architecture, we developed a new artifact removal model, IC-U-Net, for removing pervasive EEG artifacts and reconstructing brain signals. IC-U-Net was trained using mixtures of brain and non-brain components decomposed by independent component analysis. It uses an ensemble of loss functions to model complex signal fluctuations in EEG recordings. The effectiveness of the proposed method in recovering brain activities and removing various artifacts (e.g., eye blinks/movements, muscle activities, and line/channel noise) was demonstrated in a simulation study and four real-world EEG experiments. IC-U-Net can reconstruct a multi-channel EEG signal and is applicable to most artifact types, offering a promising end-to-end solution for automatically removing artifacts from EEG recordings. It also meets the increasing need to image natural brain dynamics in a mobile setting. The code and pre-trained IC-U-Net model are available at https://github.com/roseDwayane/AIEEG.

Closed-loop motor imagery EEG simulation for brain-computer interfaces

In a brain-computer interface (BCI) system, the testing of decoding algorithms, tasks, and their parameters is critical for optimizing performance. However, conducting human experiments can be costly and time-consuming, especially when investigating broad sets of parameters. Attempts to utilize previously collected data in offline analysis lack a co-adaptive feedback loop between the system and the user present online, limiting the applicability of the conclusions obtained to real-world uses of BCI. As such, a number of studies have attempted to address this cost-wise middle ground between offline and live experimentation with real-time neural activity simulators. We present one such system which generates motor imagery electroencephalography (EEG) via forward modeling and novel motor intention encoding models for conducting sensorimotor rhythm (SMR)-based continuous cursor control experiments in a closed-loop setting. We use the proposed simulator with 10 healthy human subjects to test the effect of three decoder and task parameters across 10 different values. Our simulated approach produces similar statistical conclusions to those produced during parallel, paired, online experimentation, but in 55% of the time. Notably, both online and simulated experimentation expressed a positive effect of cursor velocity limit on performance regardless of subject average performance, supporting the idea of relaxing constraints on cursor gain in online continuous cursor control. We demonstrate the merits of our closed-loop motor imagery EEG simulation, and provide an open-source framework to the community for closed-loop SMR-based BCI studies in the future. All code including the simulator have been made available on GitHub.

Good scientific practice in EEG and MEG research: Progress and perspectives

Good scientific practice (GSP) refers to both explicit and implicit rules, recommendations, and guidelines that help scientists to produce work that is of the highest quality at any given time, and to efficiently share that work with the community for further scrutiny or utilization. For experimental research using magneto- and electroencephalography (MEEG), GSP includes specific standards and guidelines for technical competence, which are periodically updated and adapted to new findings. However, GSP also needs to be regularly revisited in a broader light. At the LiveMEEG 2020 conference, a reflection on GSP was fostered that included explicitly documented guidelines and technical advances, but also emphasized intangible GSP: a general awareness of personal, organizational, and societal realities and how they can influence MEEG research. This article provides an extensive report on most of the LiveMEEG contributions and new literature, with the additional aim to synthesize ongoing cultural changes in GSP. It first covers GSP with respect to cognitive biases and logical fallacies, pre-registration as a tool to avoid those and other early pitfalls, and a number of resources to enable collaborative and reproducible research as a general approach to minimize misconceptions. Second, it covers GSP with respect to data acquisition, analysis, reporting, and sharing, including new tools and frameworks to support collaborative work. Finally, GSP is considered in light of ethical implications of MEEG research and the resulting responsibility that scientists have to engage with societal challenges. Considering among other things the benefits of peer review and open access at all stages, the need to coordinate larger international projects, the complexity of MEEG subject matter, and today's prioritization of fairness, privacy, and the environment, we find that current GSP tends to favor collective and cooperative work, for both scientific and for societal reasons.

Methodological considerations for studying neural oscillations

Neural oscillations are ubiquitous across recording methodologies and species, broadly associated with cognitive tasks, and amenable to computational modelling that investigates neural circuit generating mechanisms and neural population dynamics. Because of this, neural oscillations offer an exciting potential opportunity for linking theory, physiology and mechanisms of cognition. However, despite their prevalence, there are many concerns-new and old-about how our analysis assumptions are violated by known properties of field potential data. For investigations of neural oscillations to be properly interpreted, and ultimately developed into mechanistic theories, it is necessary to carefully consider the underlying assumptions of the methods we employ. Here, we discuss seven methodological considerations for analysing neural oscillations. The considerations are to (1) verify the presence of oscillations, as they may be absent; (2) validate oscillation band definitions, to address variable peak frequencies; (3) account for concurrent non-oscillatory aperiodic activity, which might otherwise confound measures; measure and account for (4) temporal variability and (5) waveform shape of neural oscillations, which are often bursty and/or nonsinusoidal, potentially leading to spurious results; (6) separate spatially overlapping rhythms, which may interfere with each other; and (7) consider the required signal-to-noise ratio for obtaining reliable estimates. For each topic, we provide relevant examples, demonstrate potential errors of interpretation, and offer suggestions to address these issues. We primarily focus on univariate measures, such as power and phase estimates, though we discuss how these issues can propagate to multivariate measures. These considerations and recommendations offer a helpful guide for measuring and interpreting neural oscillations.

Utility of linear mixed effects models for event-related potential research with infants and children

Event-related potentials (ERPs) are advantageous for investigating cognitive development. However, their application in infants/children is challenging given children's difficulty in sitting through the multiple trials required in an ERP task. Thus, a large problem in developmental ERP research is high subject exclusion due to too few analyzable trials. Common analytic approaches (that involve averaging trials within subjects and excluding subjects with too few trials, as in ANOVA and linear regression) work around this problem, but do not mitigate it. Moreover, these practices can lead to inaccuracies in measuring neural signals. The greater the subject exclusion, the more problematic inaccuracies can be. We review recent developmental ERP studies to illustrate the prevalence of these issues. Critically, we demonstrate an alternative approach to ERP analysis-linear mixed effects (LME) modeling-which offers unique utility in developmental ERP research. We demonstrate with simulated and real ERP data from preschool children that commonly employed ANOVAs yield biased results that become more biased as subject exclusion increases. In contrast, LME models yield accurate, unbiased results even when subjects have low trial-counts, and are better able to detect real condition differences. We include tutorials and example code to facilitate LME analyses in future ERP research.

NEAR: An artifact removal pipeline for human newborn EEG data

Electroencephalography (EEG) is arising as a valuable method to investigate neurocognitive functions shortly after birth. However, obtaining high-quality EEG data from human newborn recordings is challenging. Compared to adults and older infants, datasets are typically much shorter due to newborns’ limited attentional span and much noisier due to non-stereotyped artifacts mainly caused by uncontrollable movements. We propose Newborn EEG Artifact Removal (NEAR), a pipeline for EEG artifact removal designed explicitly for human newborns. NEAR is based on two key steps: 1) A novel bad channel detection tool based on the Local Outlier Factor (LOF), a robust outlier detection algorithm; 2) A parameter calibration procedure for adapting to newborn EEG data the algorithm Artifacts Subspace Reconstruction (ASR), developed for artifact removal in mobile adult EEG. Tests on simulated data showed that NEAR outperforms existing methods in removing representative newborn non-stereotypical artifacts. NEAR was validated on two developmental populations (newborns and 9-month-old infants) recorded with two different experimental designs (frequency-tagging and ERP). Results show that NEAR artifact removal successfully reproduces established EEG responses from noisy datasets, with a higher statistical significance than the one obtained by existing artifact removal methods. The EEGLAB-based NEAR pipeline is freely available at https://github.com/vpKumaravel/NEAR.

Sparse algorithms for EEG source localization

Source localization using EEG is important in diagnosing various physiological and psychiatric diseases related to the brain. The high temporal resolution of EEG helps medical professionals assess the internal physiology of the brain in a more informative way. The internal sources are obtained from EEG by an inversion process. The number of sources in the brain outnumbers the number of measurements. In this article, a comprehensive review of the state-of-the-art sparse source localization methods in this field is presented. A recently developed method, certainty-based-reduced-sparse-solution (CARSS), is implemented and is examined. A vast comparative study is performed using a sixty-four-channel setup involving two source spaces. The first source space has 5004 sources and the other has 2004 sources. Four test cases with one, three, five, and seven simulated active sources are considered. Two noise levels are also being added to the noiseless data. The CARSS is also evaluated. The results are examined. A real EEG study is also attempted. Graphical Abstract.

EEGSourceSim: A framework for realistic simulation of EEG scalp data using MRI-based forward models and biologically plausible signals and noise

BACKGROUND

Electroencephalography (EEG) is widely used to investigate human brain function. Simulation studies are essential for assessing the validity of EEG analysis methods and the interpretability of results.

NEW METHOD

Here we present a simulation environment for generating EEG data by embedding biologically plausible signal and noise into MRI-based forward models that incorporate individual-subject variability in structure and function.

RESULTS

The package includes pipelines for the evaluation and validation of EEG analysis tools for source estimation, functional connectivity, and spatial filtering. EEG dynamics can be simulated using realistic noise and signal models with user specifiable signal-to-noise ratio (SNR). We also provide a set of quantitative metrics tailored to source estimation, connectivity and spatial filtering applications.

COMPARISON WITH EXISTING METHOD(S)

We provide a larger set of forward solutions for individual MRI-based head models than has been available previously. These head models are surface-based and include two sets of regions-of-interest (ROIs) that have been brought into registration with the brain of each individual using surface-based alignment - one from a whole brain and the other from a visual cortex atlas. We derive a realistic model of noise by fitting different model components to measured resting state EEG. We also provide a set of quantitative metrics for evaluating source-localization, functional connectivity and spatial filtering methods.

CONCLUSIONS

The inclusion of a larger number of individual head-models, combined with surface-atlas based labeling of ROIs and plausible models of signal and noise, allows for simulation of EEG data with greater realism than previous packages.

Post-hoc Labeling of Arbitrary M/EEG Recordings for Data-Efficient Evaluation of Neural Decoding Methods

Many cognitive, sensory and motor processes have correlates in oscillatory neural source activity, which is embedded as a subspace in the recorded brain signals. Decoding such processes from noisy magnetoencephalogram/electroencephalogram (M/EEG) signals usually requires data-driven analysis methods. The objective evaluation of such decoding algorithms on experimental raw signals, however, is a challenge: the amount of available M/EEG data typically is limited, labels can be unreliable, and raw signals often are contaminated with artifacts. To overcome some of these problems, simulation frameworks have been introduced which support the development of data-driven decoding algorithms and their benchmarking. For generating artificial brain signals, however, most of the existing frameworks make strong and partially unrealistic assumptions about brain activity. This limits the generalization of results observed in the simulation to real-world scenarios. In the present contribution, we show how to overcome several shortcomings of existing simulation frameworks. We propose a versatile alternative, which allows for an objective evaluation and benchmarking of novel decoding algorithms using real neural signals. It allows to generate comparatively large datasets with labels being deterministically recoverable from the arbitrary M/EEG recordings. A novel idea to generate these labels is central to this framework: we determine a subspace of the true M/EEG recordings and utilize it to derive novel labels. These labels contain realistic information about the oscillatory activity of some underlying neural sources. For two categories of subspace-defining methods, we showcase how such labels can be obtained-either by an exclusively data-driven approach (independent component analysis-ICA), or by a method exploiting additional anatomical constraints (minimum norm estimates-MNE). We term our framework post-hoc labeling of M/EEG recordings. To support the adoption of the framework by practitioners, we have exemplified its use by benchmarking three standard decoding methods-i.e., common spatial patterns (CSP), source power-comodulation (SPoC), and convolutional neural networks (ConvNets)-wrt. Varied dataset sizes, label noise, and label variability. Source code and data are made available to the reader for facilitating the application of our post-hoc labeling framework.

HEAR to remove pops and drifts: the high-variance electrode artifact removal (HEAR) algorithm

A high fraction of artifact-free signals is highly desirable in functional neuroimaging and brain-computer interfacing (BCI). We present the high-variance electrode artifact removal (HEAR) algorithm to remove transient electrode pop and drift (PD) artifacts from electroencephalographic (EEG) signals. Transient PD artifacts reflect impedance variations at the electrode scalp interface that are caused by ion concentration changes. HEAR and its online version (oHEAR) are open-source and publicly available. Both outperformed state of the art offline and online transient, high-variance artifact correction algorithms for simulated EEG signals. (o)HEAR attenuated PD artifacts by approx. 25 dB, and at the same time maintained a high SNR during PD artifact-free periods. For real-world EEG data, (o)HEAR reduced the fraction of outlier trials by half and maintained the waveform of a movement related cortical potential during a center-out reaching task. In the case of BCI training, using oHEAR can improve the reliability of the feedback a user receives through reducing a potential negative impact of PD artifacts.

Automated Labeling of Movement- Related Cortical Potentials Using Segmented Regression

The movement-related cortical potential (MRCP) is a brain signal related to planning and execution of motor tasks. From an MRCP, three notable features can be identified: the early Bereitschaftspotential (BP1), the late Bereitschaftspotential (BP2), and the negative peak (PN). These features have been used in past studies to quantify neurophysiological changes in response to motor training. Currently, either manual labeling or a priori specification of time points is used to extract these features. The limitation of these methods is the inability to fully model the features. This paper proposes the segmented regression along with a local peak method for automated labeling of the features. The proposed method derives the onsets, amplitudes at onsets, and slopes of BP1 and BP2 along with time and amplitude of the PN in a typical average MRCP. To choose the most suitable regression technique a bounded segmented regression method, a change point method and multivariate adaptive regression splines were evaluated using the root-mean-square error on a dataset of 6000 simulated MRCPs. The best-performing regression technique combined with the local peak method was then applied to a smaller set of 123 simulated MRCPs. Error in onsets of BP1 and BP2 and time of PN were compared with the errors in manual labeling by an expert. The performance of the proposed method was also evaluated on an experimental dataset of MRCPs derived from electroencephalography (EEG) recorded across two sessions from 22 healthy participants during a lower limb task. The Bland-Altman plots were used to evaluate the absolute reliability of the proposed method. On experimental data, the proposed method was also compared with manual labeling by an expert. Bounded segmented regression produced the smallest error on the simulation data. For the experimental data, our proposed method did not exhibit statistically significant bias in any of the modeled features. Furthermore, its performance was comparable to manual labeling by experts. We conclude that the proposed method can be used to automatically obtain robust estimates for the MRCP features with known measurement error.