Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging.

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

From Motion to Emotion: Visual Pathways and Potential Interconnections.

The two visual pathway description of [Ungerleider, L. G., & Mishkin, M. Two cortical visual systems. In D. J. Dingle, M. A. Goodale, & R. J. W. Mansfield (Eds.), Analysis of visual behavior (pp. 549-586). Cambridge, MA: MIT, 1982] changed the course of late 20th century systems and cognitive neuroscience. Here, I try to reexamine our laboratory's work through the lens of the [Pitcher, D., & Ungerleider, L. G. Evidence for a third visual pathway specialized for social perception. Trends in Cognitive Sciences, 25, 100-110, 2021] new third visual pathway. I also briefly review the literature related to brain responses to static and dynamic visual displays, visual stimulation involving multiple individuals, and compare existing models of social information processing for the face and body. In this context, I examine how the posterior STS might generate unique social information relative to other brain regions that also respond to social stimuli. I discuss some of the existing challenges we face with assessing how information flow progresses between structures in the proposed functional pathways and how some stimulus types and experimental designs may have complicated our data interpretation and model generation. I also note a series of outstanding questions for the field. Finally, I examine the idea of a potential expansion of the third visual pathway, to include aspects of previously proposed "lateral" visual pathways. Doing this would yield a more general entity for processing motion/action (i.e., "[inter]action") that deals with interactions between people, as well as people and objects. In this framework, a brief discussion of potential hemispheric biases for function, and different forms of neuropsychological impairments created by focal lesions in the posterior brain is highlighted to help situate various brain regions into an expanded [inter]action pathway.

Advances in human intracranial electroencephalography research, guidelines and good practices.

Since the second-half of the twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into the human brain. At the interface between fundamental research and the clinic, iEEG provides both high temporal resolution and high spatial specificity but comes with constraints, such as the individual's tailored sparsity of electrode sampling. Over the years, researchers in neuroscience developed their practices to make the most of the iEEG approach. Here we offer a critical review of iEEG research practices in a didactic framework for newcomers, as well addressing issues encountered by proficient researchers. The scope is threefold: (i) review common practices in iEEG research, (ii) suggest potential guidelines for working with iEEG data and answer frequently asked questions based on the most widespread practices, and (iii) based on current neurophysiological knowledge and methodologies, pave the way to good practice standards in iEEG research. The organization of this paper follows the steps of iEEG data processing. The first section contextualizes iEEG data collection. The second section focuses on localization of intracranial electrodes. The third section highlights the main pre-processing steps. The fourth section presents iEEG signal analysis methods. The fifth section discusses statistical approaches. The sixth section draws some unique perspectives on iEEG research. Finally, to ensure a consistent nomenclature throughout the manuscript and to align with other guidelines, e.g., Brain Imaging Data Structure (BIDS) and the OHBM Committee on Best Practices in Data Analysis and Sharing (COBIDAS), we provide a glossary to disambiguate terms related to iEEG research.

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.

Statistical power: Implications for planning MEG studies.

Statistical power is key for robust, replicable science. Here, we systematically explored how numbers of trials and subjects affect statistical power in MEG sensor-level data. More specifically, we simulated "experiments" using the MEG resting-state dataset of the Human Connectome Project (HCP). We divided the data in two conditions, injected a dipolar source at a known anatomical location in the "signal condition", but not in the "noise condition", and detected significant differences at sensor level with classical paired t-tests across subjects, using amplitude, squared amplitude, and global field power (GFP) measures. Group-level detectability of these simulated effects varied drastically with anatomical origin. We thus examined in detail which spatial properties of the sources affected detectability, looking specifically at the distance from closest sensor and orientation of the source, and at the variability of these parameters across subjects. In line with previous single-subject studies, we found that the most detectable effects originate from source locations that are closest to the sensors and oriented tangentially with respect to the head surface. In addition, cross-subject variability in orientation also affected group-level detectability, boosting detection in regions where this variability was small and hindering detection in regions where it was large. Incidentally, we observed a considerable covariation of source position, orientation, and their cross-subject variability in individual brain anatomical space, making it difficult to assess the impact of each of these variables independently of one another. We thus also performed simulations where we controlled spatial properties independently of individual anatomy. These additional simulations confirmed the strong impact of distance and orientation and further showed that orientation variability across subjects affects detectability, whereas position variability does not. Importantly, our study indicates that strict unequivocal recommendations as to the ideal number of trials and subjects for any experiment cannot be realistically provided for neurophysiological studies and should be adapted according to the brain regions under study.

Differential effects of propofol and ketamine on critical brain dynamics.

Whether the brain operates at a critical "tipping" point is a long standing scientific question, with evidence from both cellular and systems-scale studies suggesting that the brain does sit in, or near, a critical regime. Neuroimaging studies of humans in altered states of consciousness have prompted the suggestion that maintenance of critical dynamics is necessary for the emergence of consciousness and complex cognition, and that reduced or disorganized consciousness may be associated with deviations from criticality. Unfortunately, many of the cellular-level studies reporting signs of criticality were performed in non-conscious systems (in vitro neuronal cultures) or unconscious animals (e.g. anaesthetized rats). Here we attempted to address this knowledge gap by exploring critical brain dynamics in invasive ECoG recordings from multiple sessions with a single macaque as the animal transitioned from consciousness to unconsciousness under different anaesthetics (ketamine and propofol). We use a previously-validated test of criticality: avalanche dynamics to assess the differences in brain dynamics between normal consciousness and both drug-states. Propofol and ketamine were selected due to their differential effects on consciousness (ketamine, but not propofol, is known to induce an unusual state known as "dissociative anaesthesia"). Our analyses indicate that propofol dramatically restricted the size and duration of avalanches, while ketamine allowed for more awake-like dynamics to persist. In addition, propofol, but not ketamine, triggered a large reduction in the complexity of brain dynamics. All states, however, showed some signs of persistent criticality when testing for exponent relations and universal shape-collapse. Further, maintenance of critical brain dynamics may be important for regulation and control of conscious awareness.

Something to sink your teeth into: The presence of teeth augments ERPs to mouth expressions.

If the whites of the sclera can impact neural processing of eye expressions (Hardee, Thompson, & Puce, 2008; Whalen et al., 1998), do seen teeth affect neural responses to mouth expressions? Twenty participants (10 females; ages 22-31) viewed avatar mouth images depicting grimaces, smiles and open mouth expressions that were presented with and without teeth. A continuous 256 channel electroencephalogram (EEG) was recorded while subjects completed two tasks: an implicit task evaluating stimulus color and an explicit task evaluating mouth expression valence. Event related potential (ERP) peak amplitudes and latencies and area under the curve (AUC) were measured in individual subject averaged ERPs. Statistical testing revealed a main effect of the presence of Teeth for P100, N170, and vertex positive potential (VPP) amplitudes and for slow positive wave (SPW) AUC. Task by teeth interactions occurred for P250 amplitude, underscoring how explicit task demands can influence neural processing. Arousal ratings co-varied with teeth presence, suggesting that low-level visual features such as teeth may drive the saliency of emotional expressions, and lie at the core of differences in neural processing to different emotional expressions.

Neural correlates of apparent motion perception of impoverished facial stimuli: a comparison of ERP and ERSP activity.

Our brains readily decode human movements, as shown by neural responses to face and body motion. N170 event-related potentials (ERPs) are earlier and larger to mouth opening movements relative to closing in both line-drawn and natural faces, and gaze aversions relative to direct gaze in natural faces (Puce and Perrett, 2003; Puce et al., 2000). Here we extended this work by recording both ERP and oscillatory EEG activity (event-related spectral perturbations, ERSPs) to line-drawn faces depicting eye and mouth movements (Eyes: Direct vs Away; Mouth: Closed vs Open) and non-face motion controls. Neural activity was measured in 2 occipito-temporal clusters of 9 electrodes, one in each hemisphere. Mouth opening generated larger N170s than mouth closing, replicating earlier work. Eye motion elicited robust N170s that did not differ between gaze conditions. Control condition differences were seen, and generated the largest N170. ERSP difference plots across conditions in the occipito-temporal electrode clusters (Eyes: Direct vs Away; Mouth: Closed vs Open) showed statistically significant differences in beta and gamma bands for gaze direction changes and mouth opening at similar post-stimulus times and frequencies. In contrast, control stimuli showed activity in the gamma band with a completely different time profile and hemispheric distribution to facial stimuli. ERSP plots were generated in two 9 electrode clusters centered on central sites, C3 and C4. In the left cluster for all stimulus conditions, broadband beta suppression persisted from about 250ms post-motion onset. In the right cluster, beta suppression was seen for control conditions only. Statistically significant differences between conditions were confined between 4 and 15Hz, unlike the occipito-temporal sites where differences occurred at much higher frequencies (high beta/gamma). Our data indicate that N170 amplitude is sensitive to the amount of movement in the visual field, independent of stimulus type. In contrast, occipito-temporal beta and gamma activity differentiates between facial and non-facial motion. Context and stimulus configuration likely plays a role in shaping neural responses, based on comparisons of the current data to previously reported studies. Broadband suppression of central beta activity, and significant low frequency differences were likely stimulus driven and not contingent on behavioral responses.

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging.

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

Inverse effectiveness and multisensory interactions in visual event-related potentials with audiovisual speech.

In recent years, it has become evident that neural responses previously considered to be unisensory can be modulated by sensory input from other modalities. In this regard, visual neural activity elicited to viewing a face is strongly influenced by concurrent incoming auditory information, particularly speech. Here, we applied an additive-factors paradigm aimed at quantifying the impact that auditory speech has on visual event-related potentials (ERPs) elicited to visual speech. These multisensory interactions were measured across parametrically varied stimulus salience, quantified in terms of signal to noise, to provide novel insights into the neural mechanisms of audiovisual speech perception. First, we measured a monotonic increase of the amplitude of the visual P1-N1-P2 ERP complex during a spoken-word recognition task with increases in stimulus salience. ERP component amplitudes varied directly with stimulus salience for visual, audiovisual, and summed unisensory recordings. Second, we measured changes in multisensory gain across salience levels. During audiovisual speech, the P1 and P1-N1 components exhibited less multisensory gain relative to the summed unisensory components with reduced salience, while N1-P2 amplitude exhibited greater multisensory gain as salience was reduced, consistent with the principle of inverse effectiveness. The amplitude interactions were correlated with behavioral measures of multisensory gain across salience levels as measured by response times, suggesting that change in multisensory gain associated with unisensory salience modulations reflects an increased efficiency of visual speech processing.

Cortical networks representing object categories and high-level attributes of familiar real-world action sounds.

In contrast to visual object processing, relatively little is known about how the human brain processes everyday real-world sounds, transforming highly complex acoustic signals into representations of meaningful events or auditory objects. We recently reported a fourfold cortical dissociation for representing action (nonvocalization) sounds correctly categorized as having been produced by human, animal, mechanical, or environmental sources. However, it was unclear how consistent those network representations were across individuals, given potential differences between each participant's degree of familiarity with the studied sounds. Moreover, it was unclear what, if any, auditory perceptual attributes might further distinguish the four conceptual sound-source categories, potentially revealing what might drive the cortical network organization for representing acoustic knowledge. Here, we used functional magnetic resonance imaging to test participants before and after extensive listening experience with action sounds, and tested for cortices that might be sensitive to each of three different high-level perceptual attributes relating to how a listener associates or interacts with the sound source. These included the sound's perceived concreteness, effectuality (ability to be affected by the listener), and spatial scale. Despite some variation of networks for environmental sounds, our results verified the stability of a fourfold dissociation of category-specific networks for real-world action sounds both before and after familiarity training. Additionally, we identified cortical regions parametrically modulated by each of the three high-level perceptual sound attributes. We propose that these attributes contribute to the network-level encoding of category-specific acoustic knowledge representations.

Action expertise reduces brain activity for audiovisual matching actions: an fMRI study with expert drummers.

When we observe someone perform a familiar action, we can usually predict what kind of sound that action will produce. Musical actions are over-experienced by musicians and not by non-musicians, and thus offer a unique way to examine how action expertise affects brain processes when the predictability of the produced sound is manipulated. We used functional magnetic resonance imaging to scan 11 drummers and 11 age- and gender-matched novices who made judgments on point-light drumming movements presented with sound. In Experiment 1, sound was synchronized or desynchronized with drumming strikes, while in Experiment 2 sound was always synchronized, but the natural covariation between sound intensity and velocity of the drumming strike was maintained or eliminated. Prior to MRI scanning, each participant completed psychophysical testing to identify personal levels of synchronous and asynchronous timing to be used in the two fMRI activation tasks. In both experiments, the drummers' brain activation was reduced in motor and action representation brain regions when sound matched the observed movements, and was similar to that of novices when sound was mismatched. This reduction in neural activity occurred bilaterally in the cerebellum and left parahippocampal gyrus in Experiment 1, and in the right inferior parietal lobule, inferior temporal gyrus, middle frontal gyrus and precentral gyrus in Experiment 2. Our results indicate that brain functions in action-sound representation areas are modulated by multimodal action expertise.

EEG measures for clinical research in major vascular cognitive impairment: recommendations by an expert panel.

Vascular contribution to cognitive impairment (VCI) and dementia is related to etiologies that may affect the neurophysiological mechanisms regulating brain arousal and generating electroencephalographic (EEG) activity. A multidisciplinary expert panel reviewed the clinical literature and reached consensus about the EEG measures consistently found as abnormal in VCI patients with dementia. As compared to cognitively unimpaired individuals, those VCI patients showed (1) smaller amplitude of resting state alpha (8-12 Hz) rhythms dominant in posterior regions; (2) widespread increases in amplitude of delta (< 4 Hz) and theta (4-8 Hz) rhythms; and (3) delayed N200/P300 peak latencies in averaged event-related potentials, especially during the detection of auditory rare target stimuli requiring participants' responses in "oddball" paradigms. The expert panel formulated the following recommendations: (1) the above EEG measures are not specific for VCI and should not be used for its diagnosis; (2) they may be considered as "neural synchronization" biomarkers to enlighten the relationships between features of the VCI-related cerebrovascular lesions and abnormalities in neurophysiological brain mechanisms; and (3) they may be tested in future clinical trials as prognostic biomarkers and endpoints of interventions aimed at normalizing background brain excitability and vigilance in wakefulness.

Issues and recommendations from the OHBM COBIDAS MEEG committee for reproducible EEG and MEG research.

The Organization for Human Brain Mapping (OHBM) has been active in advocating for the instantiation of best practices in neuroimaging data acquisition, analysis, reporting and sharing of both data and analysis code to deal with issues in science related to reproducibility and replicability. Here we summarize recommendations for such practices in magnetoencephalographic (MEG) and electroencephalographic (EEG) research, recently developed by the OHBM neuroimaging community known by the abbreviated name of COBIDAS MEEG. We discuss the rationale for the guidelines and their general content, which encompass many topics under active discussion in the field. We highlight future opportunities and challenges to maximizing the sharing and exploitation of MEG and EEG data, and we also discuss how this 'living' set of guidelines will evolve to continually address new developments in neurophysiological assessment methods and multimodal integration of neurophysiological data with other data types.

Different categories of living and non-living sound-sources activate distinct cortical networks.

With regard to hearing perception, it remains unclear as to whether, or the extent to which, different conceptual categories of real-world sounds and related categorical knowledge are differentially represented in the brain. Semantic knowledge representations are reported to include the major divisions of living versus non-living things, plus more specific categories including animals, tools, biological motion, faces, and places-categories typically defined by their characteristic visual features. Here, we used functional magnetic resonance imaging (fMRI) to identify brain regions showing preferential activity to four categories of action sounds, which included non-vocal human and animal actions (living), plus mechanical and environmental sound-producing actions (non-living). The results showed a striking antero-posterior division in cortical representations for sounds produced by living versus non-living sources. Additionally, there were several significant differences by category, depending on whether the task was category-specific (e.g. human or not) versus non-specific (detect end-of-sound). In general, (1) human-produced sounds yielded robust activation in the bilateral posterior superior temporal sulci independent of task. Task demands modulated activation of left lateralized fronto-parietal regions, bilateral insular cortices, and sub-cortical regions previously implicated in observation-execution matching, consistent with "embodied" and mirror-neuron network representations subserving recognition. (2) Animal action sounds preferentially activated the bilateral posterior insulae. (3) Mechanical sounds activated the anterior superior temporal gyri and parahippocampal cortices. (4) Environmental sounds preferentially activated dorsal occipital and medial parietal cortices. Overall, this multi-level dissociation of networks for preferentially representing distinct sound-source categories provides novel support for grounded cognition models that may underlie organizational principles for hearing perception.

Neuronal oscillations and visual amplification of speech.

It is widely recognized that viewing a speaker's face enhances vocal communication, although the neural substrates of this phenomenon remain unknown. We propose that the enhancement effect uses the ongoing oscillatory activity of local neuronal ensembles in the primary auditory cortex. Neuronal oscillations reflect rhythmic shifting of neuronal ensembles between high and low excitability states. Our hypothesis holds that oscillations are 'predictively' modulated by visual input, so that related auditory input arrives during a high excitability phase and is thus amplified. We discuss the anatomical substrates and key timing parameters that enable and constrain this effect. Our hypothesis makes testable predictions for future studies and emphasizes the idea that 'background' oscillatory activity is instrumental to cortical sensory processing.

Serial functional imaging poststroke reveals visual cortex reorganization.

PURPOSE: Visual cortical reorganization following injury remains poorly understood. The authors performed serial functional magnetic resonance imaging (fMRI) on patients with visual cortex infarction to evaluate early and late striate, ventral, and dorsal extrastriate cortical activation. METHODS: Patients were studied with fMRI within 10 days and at 6 months. The authors used a high-level visual activation task designed to activate the ventral extrastriate cortex. These data were compared to those of age-appropriate healthy control participants. RESULTS: The results from 24 healthy control individuals (mean age 65.7 +/- SE 3.6 years, range 32-89) were compared to those from 5 stroke patients (mean age 73.8 +/- SE 7 years, range 49-86). Patients had infarcts involving the striate and ventral extrastriate cortex. Patient activation patterns were markedly different to controls. Bilateral striate and ventral extrastriate activation was reduced at both sessions, but dorsal extrastriate activated voxel counts remained comparable to controls. Conversely, mean percent magnetic resonance signal change increased in dorsal sites. CONCLUSIONS: These data provide strong evidence of bilateral poststroke functional depression of striate and ventral extrastriate cortices. Possible utilization or surrogacy of the dorsal visual system was demonstrated following stroke. This activity could provide a target for novel visual rehabilitation therapies.

Multisensory integration of drumming actions: musical expertise affects perceived audiovisual asynchrony.

We investigated the effect of musical expertise on sensitivity to asynchrony for drumming point-light displays, which varied in their physical characteristics (Experiment 1) or in their degree of audiovisual congruency (Experiment 2). In Experiment 1, 21 repetitions of three tempos x three accents x nine audiovisual delays were presented to four jazz drummers and four novices. In Experiment 2, ten repetitions of two audiovisual incongruency conditions x nine audiovisual delays were presented to 13 drummers and 13 novices. Participants gave forced-choice judgments of audiovisual synchrony. The results of Experiment 1 show an enhancement in experts' ability to detect asynchrony, especially for slower drumming tempos. In Experiment 2 an increase in sensitivity to asynchrony was found for incongruent stimuli; this increase, however, is attributable only to the novice group. Altogether the results indicated that through musical practice we learn to ignore variations in stimulus characteristics that otherwise would affect our multisensory integration processes.