An Updated Guide to Robust Statistical Methods in Neuroscience.

There is a vast array of new and improved methods for comparing groups and studying associations that offer the potential for substantially increasing power, providing improved control over the probability of false positives, and yielding a deeper and more nuanced understanding of data. These new techniques effectively deal with four insights into when and why conventional methods can be unsatisfactory. But for the non-statistician, this vast array of techniques for comparing groups and studying associations can seem daunting. This article briefly reviews when and why conventional methods can have relatively low power and yield misleading results. The main goal is to suggest guidelines regarding the use of modern techniques that improve upon classic approaches such as Pearson's correlation, ordinary linear regression, ANOVA, and ANCOVA. This updated version includes recent advances dealing with effect sizes, including situations where there is a covariate. The R code, figures, and accompanying notebooks have been updated as well. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Rating norms should be calculated from cumulative link mixed effects models.

Studies which provide norms of Likert ratings typically report per-item summary statistics. Traditionally, these summary statistics comprise the mean and the standard deviation (SD) of the ratings, and the number of observations. Such summary statistics can preserve the rank order of items, but provide distorted estimates of the relative distances between items because of the ordinal nature of Likert ratings. Inter-item relations in such ordinal scales can be more appropriately modelled by cumulative link mixed effects models (CLMMs). In a series of simulations, and with a reanalysis of an existing rating norms dataset, we show that CLMMs can be used to more accurately norm items, and can provide summary statistics analogous to the traditionally reported means and SDs, but which are disentangled from participants' response biases. CLMMs can be applied to solve important statistical issues that exist for more traditional analyses of rating norms.

Dissociable effects of prediction and integration during language comprehension: evidence from a large-scale study using brain potentials.

Composing sentence meaning is easier for predictable words than for unpredictable words. Are predictable words genuinely predicted, or simply more plausible and therefore easier to integrate with sentence context? We addressed this persistent and fundamental question using data from a recent, large-scale (n = 334) replication study, by investigating the effects of word predictability and sentence plausibility on the N400, the brain's electrophysiological index of semantic processing. A spatio-temporally fine-grained mixed-effect multiple regression analysis revealed overlapping effects of predictability and plausibility on the N400, albeit with distinct spatio-temporal profiles. Our results challenge the view that the predictability-dependent N400 reflects the effects of either prediction or integration, and suggest that semantic facilitation of predictable words arises from a cascade of processes that activate and integrate word meaning with context into a sentence-level meaning. This article is part of the theme issue 'Towards mechanistic models of meaning composition'.

Healthy aging delays the neural processing of face features relevant for behavior by 40 ms.

Fast and accurate face processing is critical for everyday social interactions, but it declines and becomes delayed with age, as measured by both neural and behavioral responses. Here, we addressed the critical challenge of understanding how aging changes neural information processing mechanisms to delay behavior. Young (20-36 years) and older (60-86 years) adults performed the basic social interaction task of detecting a face versus noise while we recorded their electroencephalogram (EEG). In each participant, using a new information theoretic framework we reconstructed the features supporting face detection behavior, and also where, when and how EEG activity represents them. We found that occipital-temporal pathway activity dynamically represents the eyes of the face images for behavior ~170 ms poststimulus, with a 40 ms delay in older adults that underlies their 200 ms behavioral deficit of slower reaction times. Our results therefore demonstrate how aging can change neural information processing mechanisms that underlie behavioral slow down.

Large-scale replication study reveals a limit on probabilistic prediction in language comprehension.

Do people routinely pre-activate the meaning and even the phonological form of upcoming words? The most acclaimed evidence for phonological prediction comes from a 2005 Nature Neuroscience publication by DeLong, Urbach and Kutas, who observed a graded modulation of electrical brain potentials (N400) to nouns and preceding articles by the probability that people use a word to continue the sentence fragment ('cloze'). In our direct replication study spanning 9 laboratories (N=334), pre-registered replication-analyses and exploratory Bayes factor analyses successfully replicated the noun-results but, crucially, not the article-results. Pre-registered single-trial analyses also yielded a statistically significant effect for the nouns but not the articles. Exploratory Bayesian single-trial analyses showed that the article-effect may be non-zero but is likely far smaller than originally reported and too small to observe without very large sample sizes. Our results do not support the view that readers routinely pre-activate the phonological form of predictable words.

A Guide to Robust Statistical Methods in Neuroscience.

There is a vast array of new and improved methods for comparing groups and studying associations that offer the potential for substantially increasing power, providing improved control over the probability of a Type I error, and yielding a deeper and more nuanced understanding of data. These new techniques effectively deal with four insights into when and why conventional methods can be unsatisfactory. But for the non-statistician, the vast array of new and improved techniques for comparing groups and studying associations can seem daunting, simply because there are so many new methods that are now available. This unit briefly reviews when and why conventional methods can have relatively low power and yield misleading results. The main goal is to suggest some general guidelines regarding when, how, and why certain modern techniques might be used. © 2018 by John Wiley & Sons, Inc.

Beyond differences in means: robust graphical methods to compare two groups in neuroscience.

If many changes are necessary to improve the quality of neuroscience research, one relatively simple step could have great pay-offs: to promote the adoption of detailed graphical methods, combined with robust inferential statistics. Here, we illustrate how such methods can lead to a much more detailed understanding of group differences than bar graphs and t-tests on means. To complement the neuroscientist's toolbox, we present two powerful tools that can help us understand how groups of observations differ: the shift function and the difference asymmetry function. These tools can be combined with detailed visualisations to provide complementary perspectives about the data. We provide implementations in R and MATLAB of the graphical tools, and all the examples in the article can be reproduced using R scripts.

A statistical framework for neuroimaging data analysis based on mutual information estimated via a gaussian copula.

We begin by reviewing the statistical framework of information theory as applicable to neuroimaging data analysis. A major factor hindering wider adoption of this framework in neuroimaging is the difficulty of estimating information theoretic quantities in practice. We present a novel estimation technique that combines the statistical theory of copulas with the closed form solution for the entropy of Gaussian variables. This results in a general, computationally efficient, flexible, and robust multivariate statistical framework that provides effect sizes on a common meaningful scale, allows for unified treatment of discrete, continuous, unidimensional and multidimensional variables, and enables direct comparisons of representations from behavioral and brain responses across any recording modality. We validate the use of this estimate as a statistical test within a neuroimaging context, considering both discrete stimulus classes and continuous stimulus features. We also present examples of analyses facilitated by these developments, including application of multivariate analyses to MEG planar magnetic field gradients, and pairwise temporal interactions in evoked EEG responses. We show the benefit of considering the instantaneous temporal derivative together with the raw values of M/EEG signals as a multivariate response, how we can separately quantify modulations of amplitude and direction for vector quantities, and how we can measure the emergence of novel information over time in evoked responses. Open-source Matlab and Python code implementing the new methods accompanies this article. Hum Brain Mapp 38:1541-1573, 2017. © 2016 Wiley Periodicals, Inc.

The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres.

A key to understanding visual cognition is to determine "where", "when", and "how" brain responses reflect the processing of the specific visual features that modulate categorization behavior-the "what". The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features.

The time course of visual influences in letter recognition.

This study builds on a specific characteristic of letters of the Roman alphabet-namely, that each letter name is associated with two visual formats, corresponding to their uppercase and lowercase versions. Participants had to read aloud the names of single letters, and event-related potentials (ERPs) for six pairs of visually dissimilar upper- and lowercase letters were recorded. Assuming that the end product of processing is the same for upper- and lowercase letters sharing the same vocal response, ERPs were compared backward, starting from the onset of articulatory responses, and the first significant divergence was observed 120 ms before response onset. Given that naming responses were produced at around 414 ms, on average, these results suggest that letter processing is influenced by visual information until 294 ms after stimulus onset. This therefore provides new empirical evidence regarding the time course and interactive nature of visual letter perception processes.

A robust and representative lower bound on object processing speed in humans.

How early does the brain decode object categories? Addressing this question is critical to constrain the type of neuronal architecture supporting object categorization. In this context, much effort has been devoted to estimating face processing speed. With onsets estimated from 50 to 150 ms, the timing of the first face-sensitive responses in humans remains controversial. This controversy is due partially to the susceptibility of dynamic brain measurements to filtering distortions and analysis issues. Here, using distributions of single-trial event-related potentials (ERPs), causal filtering, statistical analyses at all electrodes and time points, and effective correction for multiple comparisons, we present evidence that the earliest categorical differences start around 90 ms following stimulus presentation. These results were obtained from a representative group of 120 participants, aged 18-81, who categorized images of faces and noise textures. The results were reliable across testing days, as determined by test-retest assessment in 74 of the participants. Furthermore, a control experiment showed similar ERP onsets for contrasts involving images of houses or white noise. Face onsets did not change with age, suggesting that face sensitivity occurs within 100 ms across the adult lifespan. Finally, the simplicity of the face-texture contrast, and the dominant midline distribution of the effects, suggest the face responses were evoked by relatively simple image properties and are not face specific. Our results provide a new lower benchmark for the earliest neuronal responses to complex objects in the human visual system.

Tracing the Flow of Perceptual Features in an Algorithmic Brain Network.

The model of the brain as an information processing machine is a profound hypothesis in which neuroscience, psychology and theory of computation are now deeply rooted. Modern neuroscience aims to model the brain as a network of densely interconnected functional nodes. However, to model the dynamic information processing mechanisms of perception and cognition, it is imperative to understand brain networks at an algorithmic level--i.e. as the information flow that network nodes code and communicate. Here, using innovative methods (Directed Feature Information), we reconstructed examples of possible algorithmic brain networks that code and communicate the specific features underlying two distinct perceptions of the same ambiguous picture. In each observer, we identified a network architecture comprising one occipito-temporal hub where the features underlying both perceptual decisions dynamically converge. Our focus on detailed information flow represents an important step towards a new brain algorithmics to model the mechanisms of perception and cognition.

With age comes representational wisdom in social signals.

In an increasingly aging society, age has become a foundational dimension of social grouping broadly targeted by advertising and governmental policies. However, perception of old age induces mainly strong negative social biases. To characterize their cognitive and perceptual foundations, we modeled the mental representations of faces associated with three age groups (young age, middle age, and old age), in younger and older participants. We then validated the accuracy of each mental representation of age with independent validators. Using statistical image processing, we identified the features of mental representations that predict perceived age. Here, we show that whereas younger people mentally dichotomize aging into two groups, themselves (younger) and others (older), older participants faithfully represent the features of young age, middle age, and old age, with richer representations of all considered ages. Our results demonstrate that, contrary to popular public belief, older minds depict socially relevant information more accurately than their younger counterparts.

Eye coding mechanisms in early human face event-related potentials.

In humans, the N170 event-related potential (ERP) is an integrated measure of cortical activity that varies in amplitude and latency across trials. Researchers often conjecture that N170 variations reflect cortical mechanisms of stimulus coding for recognition. Here, to settle the conjecture and understand cortical information processing mechanisms, we unraveled the coding function of N170 latency and amplitude variations in possibly the simplest socially important natural visual task: face detection. On each experimental trial, 16 observers saw face and noise pictures sparsely sampled with small Gaussian apertures. Reverse-correlation methods coupled with information theory revealed that the presence of the eye specifically covaries with behavioral and neural measurements: the left eye strongly modulates reaction times and lateral electrodes represent mainly the presence of the contralateral eye during the rising part of the N170, with maximum sensitivity before the N170 peak. Furthermore, single-trial N170 latencies code more about the presence of the contralateral eye than N170 amplitudes and early latencies are associated with faster reaction times. The absence of these effects in control images that did not contain a face refutes alternative accounts based on retinal biases or allocation of attention to the eye location on the face. We conclude that the rising part of the N170, roughly 120-170 ms post-stimulus, is a critical time-window in human face processing mechanisms, reflecting predominantly, in a face detection task, the encoding of a single feature: the contralateral eye.

Single-subject analyses of magnetoencephalographic evoked responses to the acoustic properties of affective non-verbal vocalizations.

Magneto-encephalography (MEG) was used to examine the cerebral response to affective non-verbal vocalizations (ANVs) at the single-subject level. Stimuli consisted of non-verbal affect bursts from the Montreal Affective Voices morphed to parametrically vary acoustical structure and perceived emotional properties. Scalp magnetic fields were recorded in three participants while they performed a 3-alternative forced choice emotion categorization task (Anger, Fear, Pleasure). Each participant performed more than 6000 trials to allow single-subject level statistical analyses using a new toolbox which implements the general linear model (GLM) on stimulus-specific responses (LIMO-EEG). For each participant we estimated "simple" models [including just one affective regressor (Arousal or Valence)] as well as "combined" models (including acoustical regressors). Results from the "simple" models revealed in every participant the significant early effects (as early as ~100 ms after onset) of Valence and Arousal already reported at the group-level in previous work. However, the "combined" models showed that few effects of Arousal remained after removing the acoustically-explained variance, whereas significant effects of Valence remained especially at late stages. This study demonstrates (i) that single-subject analyses replicate the results observed at early stages by group-level studies and (ii) the feasibility of GLM-based analysis of MEG data. It also suggests that early modulation of MEG amplitude by affective stimuli partly reflects their acoustical properties.

Early ERPs to faces: aging, luminance, and individual differences.

Recently, Rousselet et al. reported a 1 ms/year delay in visual processing speed in a sample of healthy aged 62 subjects (Frontiers in Psychology 2010, 1:19). Here, we replicate this finding in an independent sample of 59 subjects and investigate the contribution of optical factors (pupil size and luminance) to the age-related slowdown and to individual differences in visual processing speed. We conducted two experiments. In experiment 1 we recorded EEG from subjects aged 18-79. Subjects viewed images of faces and phase scrambled noise textures under nine luminance conditions, ranging from 0.59 to 60.8 cd/m(2). We manipulated luminance using neutral density filters. In experiment 2, 10 young subjects (age < 35) viewed similar stimuli through pinholes ranging from 1 to 5 mm. In both experiments, subjects were tested twice. We found a 1 ms/year slowdown in visual processing that was independent of luminance. Aging effects became visible around 125 ms post-stimulus and did not affect the onsets of the face-texture ERP differences. Furthermore, luminance modulated the entire ERP time-course from 60 to 500 ms. Luminance effects peaked in the N170 time window and were independent of age. Importantly, senile miosis and individual differences in pupil size did not account for aging differences and inter-subject variability in processing speed. The pinhole manipulation also failed to match the ERPs of old subjects to those of young subjects. Overall, our results strongly suggest that early ERPs to faces (<200 ms) are delayed by aging and that these delays are of cortical, rather than optical origin. Our results also demonstrate that even late ERPs to faces are modulated by low-level factors.

Early ERPs to faces and objects are driven by phase, not amplitude spectrum information: evidence from parametric, test-retest, single-subject analyses.

One major challenge in determining how the brain categorizes objects is to tease apart the contribution of low-level and high-level visual properties to behavioral and brain imaging data. So far, studies using stimuli with equated amplitude spectra have shown that the visual system relies mostly on localized information, such as edges and contours, carried by phase information. However, some researchers have argued that some event-related potentials (ERP) and blood-oxygen-level-dependent (BOLD) categorical differences could be driven by nonlocalized information contained in the amplitude spectrum. The goal of this study was to provide the first systematic quantification of the contribution of phase and amplitude spectra to early ERPs to faces and objects. We conducted two experiments in which we recorded electroencephalograms (EEG) from eight subjects, in two sessions each. In the first experiment, participants viewed images of faces and houses containing original or scrambled phase spectra combined with original, averaged, or swapped amplitude spectra. In the second experiment, we parametrically manipulated image phase and amplitude in 10% intervals. We performed a range of analyses including detailed single-subject general linear modeling of ERP data, test-retest reliability, and unique variance analyses. Our results suggest that early ERPs to faces and objects are due to phase information, with almost no contribution from the amplitude spectrum. Importantly, our results should not be used to justify uncontrolled stimuli; to the contrary, our results emphasize the need for stimulus control (including the amplitude spectrum), parametric designs, and systematic data analyses, of which we have seen far too little in ERP vision research.