brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

Cognitive effects on experienced duration and speed of time, prospectively, retrospectively, in and out of lockdown

Psychological time is influenced by multiple factors such as arousal, emotion, attention and memory. While laboratory observations are well documented, it remains unclear whether cognitive effects on time perception replicate in real-life settings. This study exploits a set of data collected online during the Covid-19 pandemic, where participants completed a verbal working memory (WM) task in which their cognitive load was manipulated using a parametric n-back (1-back, 3-back). At the end of every WM trial, participants estimated the duration of that trial and rated the speed at which they perceived time was passing. In this within-participant design, we initially tested whether the amount of information stored in WM affected time perception in opposite directions depending on whether duration was estimated prospectively (i.e., when participants attend to time) or retrospectively (i.e., when participants do not attend to time). Second, we tested the same working hypothesis for the felt passage of time, which may capture a distinct phenomenology. Third, we examined the link between duration and speed of time, and found that short durations tended to be perceived as fast. Last, we contrasted two groups of individuals tested in and out of lockdown to evaluate the impact of social isolation. We show that duration and speed estimations were differentially affected by social isolation. We discuss and conclude on the influence of cognitive load on various experiences of time.

brainlife.io: A decentralized and open source cloud platform to support neuroscience research

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research.

Psychological Time during the COVID-19 Lockdown: Canadian Data

The COVID-19 pandemic and associated measures have affected routines and mental well-being of people around the world. Research also shows distorted time perception during lockdowns which can partially be explained by compromised well-being. The present study investigates Canadians’ temporal experience and mental well-being at two periods of national lockdown during the COVID-19 pandemic (spring 2020: n = 66; beginning of 2021: n = 100). As results indicate, the only difference between these periods on the investigated variables was the strictness of lockdown measures. Our findings show associations between anxiety, depression, confinement indicators, and time perception (future temporal distance, passage of time judgments). Stepwise regression models indicated that depression and strictness of measures predicted the impression that the next week appeared farther away; one’s loneliness appraisal was associated with a perceived slower time flow. Our findings give a preliminary idea about time perception and mental well-being in the Canadian lockdowns.

The Blursday database as a resource to study subjective temporalities during COVID-19

The COVID-19 pandemic and associated lockdowns triggered worldwide changes in the daily routines of human experience. The Blursday database provides repeated measures of subjective time and related processes from participants in nine countries tested on 14 questionnaires and 15 behavioural tasks during the COVID-19 pandemic. A total of 2,840 participants completed at least one task, and 439 participants completed all tasks in the first session. The database and all data collection tools are accessible to researchers for studying the effects of social isolation on temporal information processing, time perspective, decision-making, sleep, metacognition, attention, memory, self-perception and mindfulness. Blursday includes quantitative statistics such as sleep patterns, personality traits, psychological well-being and lockdown indices. The database provides quantitative insights on the effects of lockdown (stringency and mobility) and subjective confinement on time perception (duration, passage of time and temporal distances). Perceived isolation affects time perception, and we report an inter-individual central tendency effect in retrospective duration estimation.

Does stroke volume influence heartbeat evoked responses?

We know surprisingly little on how heartbeat-evoked responses (HERs) vary with cardiac parameters. Here, we measured both stroke volume, or volume of blood ejected at each heartbeat, with impedance cardiography, and HER amplitude with magneto-encephalography, in 21 male and female participants at rest with eyes open. We observed that HER co-fluctuates with stroke volume on a beat-to-beat basis, but only when no correction for cardiac artifact was performed. This highlights the importance of an ICA correction tailored to the cardiac artifact. We also observed that easy-to-measure cardiac parameters (interbeat intervals, ECG amplitude) are sensitive to stroke volume fluctuations and can be used as proxies when stroke volume measurements are not available. Finally, interindividual differences in stroke volume were reflected in MEG data, but whether this effect is locked to heartbeats is unclear. Altogether, our results question assumptions on the link between stroke volume and HERs.

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.

MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis

The development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al., 2016) gave the neuroscientific community a standard to organize and share data. BIDS prescribes file naming conventions and a folder structure to store data in a set of already existing file formats. Next to rules about organization of the data itself, BIDS provides standardized templates to store associated metadata in the form of Javascript Object Notation (JSON) and tab separated value (TSV) files. It thus facilitates data sharing, eases metadata querying, and enables automatic data analysis pipelines. BIDS is a rich system to curate, aggregate, and annotate neuroimaging databases.

Invisible visual stimuli elicit increases in alpha-band power

The cerebral cortex responds to stimuli of a wide range of intensities. Previous studies have demonstrated that undetectably weak somatosensory stimuli cause a functional deactivation or inhibition in somatosensory cortex. In the present study, we tested whether invisible visual stimuli lead to similar responses, indicated by an increase in EEG alpha-band power—an index of cortical excitability. We presented subliminal and supraliminal visual stimuli after estimating each participant's detection threshold. Stimuli consisted of peripherally presented small circular patches that differed in their contrast to a background consisting of a random white noise pattern. We demonstrate that subliminal and supraliminal stimuli each elicit specific neuronal response patterns. Supraliminal stimuli evoked an early, strongly phase-locked lower-frequency response representing the evoked potential and induced a decrease in alpha-band power from 400 ms on. By contrast, subliminal visual stimuli induced an increase of non-phase-locked power around 300 ms that was maximal within the alpha-band. This response might be due to an inhibitory mechanism, which reduces spurious visual activation that is unlikely to result from external stimuli.

Prestimulus neural oscillations inhibit visual perception via modulation of response gain

The ongoing state of the brain radically affects how it processes sensory information. How does this ongoing brain activity interact with the processing of external stimuli? Spontaneous oscillations in the alpha range are thought to inhibit sensory processing, but little is known about the psychophysical mechanisms of this inhibition. We recorded ongoing brain activity with EEG while human observers performed a visual detection task with stimuli of different contrast intensities. To move beyond qualitative description, we formally compared psychometric functions obtained under different levels of ongoing alpha power and evaluated the inhibitory effect of ongoing alpha oscillations in terms of contrast or response gain models. This procedure opens the way to understanding the actual functional mechanisms by which ongoing brain activity affects visual performance. We found that strong prestimulus occipital alpha oscillations-but not more anterior mu oscillations-reduce performance most strongly for stimuli of the highest intensities tested. This inhibitory effect is best explained by a divisive reduction of response gain. Ongoing occipital alpha oscillations thus reflect changes in the visual system's input/output transformation that are independent of the sensory input to the system. They selectively scale the system's response, rather than change its sensitivity to sensory information.

Visual predictions in the orbitofrontal cortex rely on associative content

Predicting upcoming events from incomplete information is an essential brain function. The orbitofrontal cortex (OFC) plays a critical role in this process by facilitating recognition of sensory inputs via predictive feedback to sensory cortices. In the visual domain, the OFC is engaged by low spatial frequency (LSF) and magnocellular-biased inputs, but beyond this, we know little about the information content required to activate it. Is the OFC automatically engaged to analyze any LSF information for meaning? Or is it engaged only when LSF information matches preexisting memory associations? We tested these hypotheses and show that only LSF information that could be linked to memory associations engages the OFC. Specifically, LSF stimuli activated the OFC in 2 distinct medial and lateral regions only if they resembled known visual objects. More identifiable objects increased activity in the medial OFC, known for its function in affective responses. Furthermore, these objects also increased the connectivity of the lateral OFC with the ventral visual cortex, a crucial region for object identification. At the interface between sensory, memory, and affective processing, the OFC thus appears to be attuned to the associative content of visual information and to play a central role in visuo-affective prediction.

A pool of pairs of related objects (POPORO) for investigating visual semantic integration: behavioral and electrophysiological validation

Semantic processing of verbal and visual stimuli has been investigated in semantic violation or semantic priming paradigms in which a stimulus is either related or unrelated to a previously established semantic context. A hallmark of semantic priming is the N400 event-related potential (ERP)--a deflection of the ERP that is more negative for semantically unrelated target stimuli. The majority of studies investigating the N400 and semantic integration have used verbal material (words or sentences), and standardized stimulus sets with norms for semantic relatedness have been published for verbal but not for visual material. However, semantic processing of visual objects (as opposed to words) is an important issue in research on visual cognition. In this study, we present a set of 800 pairs of semantically related and unrelated visual objects. The images were rated for semantic relatedness by a sample of 132 participants. Furthermore, we analyzed low-level image properties and matched the two semantic categories according to these features. An ERP study confirmed the suitability of this image set for evoking a robust N400 effect of semantic integration. Additionally, using a general linear modeling approach of single-trial data, we also demonstrate that low-level visual image properties and semantic relatedness are in fact only minimally overlapping. The image set is available for download from the authors' website. We expect that the image set will facilitate studies investigating mechanisms of semantic and contextual processing of visual stimuli.

Unconscious learning versus visual perception: dissociable roles for gamma oscillations revealed in MEG

Oscillatory synchrony in the gamma band (30-120 Hz) has been involved in various cognitive functions including conscious perception and learning. Explicit memory encoding, in particular, relies on enhanced gamma oscillations. Does this finding extend to unconscious memory encoding? Can we dissociate gamma oscillations related to unconscious learning and to conscious perception? We investigate these issues in a magnetoencephalographic experiment using a modified version of the contextual cueing paradigm. In this visual search task, repeated presentation of search arrays triggers an unconscious spatial learning process that speeds reaction times but leaves conscious perception unaffected. In addition to a high-frequency perceptual gamma activity present throughout the experiment, we reveal the existence of a fronto-occipital network synchronized in the low gamma range specifically engaged in unconscious learning. This network shows up as soon as a display is searched for the second time and disappears as behavior gets affected. We suggest that oscillations in this network shape neural processing to build an efficient neural route for learned displays. Accordingly, in the last part of the experiment, evoked responses dissociate learned images at early latencies, suggesting that a sharpened representation is activated without resort on learning gamma oscillations, whereas perceptual gamma oscillations remain unaffected.

Unconscious contextual memory affects early responses in the anterior temporal lobe

Memory and perception are two tightly interrelated cognitive processes, but the neural level of their interaction remains a matter of debate. Proponents of a late interaction emphasize feedback memory effects on visual processing, whereas others suggest that feed forward processing is affected by memory. In the visual domain, unconscious memory for stable relations among objects is known to influence visually-guided behavior. Recent evidence suggest an early interaction between this form of unconscious memory and visually-driven neural activity: the brain dissociates stable and unstable spatial relations at surprisingly early latencies, within the first 100 ms of sensory processing. The anatomical localization of this early effect however was still uncertain. In this study, we estimated the sources of the early effect in magnetoencephalographic (MEG) recordings, and analyzed intracranial electroencephalographic (iEEG) signal from seven epileptic patients in the modified version of the contextual cueing paradigm we recently developed. In spite of a lack of behavioral effect in the patient population, the striking agreement between the two electrophysiological datasets suggests that memory for spatial relations leads to differential responses in the anterior temporal lobe before 100 ms. The intracranial data further revealed orbitofrontal and more posterior temporal memory related activities around 100 ms. Altogether, the data point toward an early interaction between contextual memories and perceptual processing. The anterior temporal cortex, in particular appears to play a critical role in merging sensory processing with unconscious memory as soon as it gets activated.

Dynamic properties of the representation of the visual field midline in the visual areas 17 and 18 of the ferret (Mustela putorius)

In mammals, the visual field is split along the midline, each hemisphere representing the contralateral hemifield. We determined that, in the ferret, an 8- to 10-deg-wide strip of visual field near the midline is represented in both hemispheres. Bright squares (1.5 deg) were flashed at different azimuths within the central 20 deg of the visual field. Stimuli were flashed either alone or sequentially, and the responses were analyzed with the voltage-sensitive dye (VSD) RH 795 and/or by recording local field potentials (LFPs). In both VSD and LFP experiments, each stimulus evoked a cortical response field that extended over visual areas 17 and 18 up to a surface of 1-1.5 mm(2) and then shrank again. Amplitude of the responses decreased approaching the visual midline and the latency increased. These positional differences are likely to originate from the spatiotemporal structure of the peripheral response fields (PRFs) that form a mosaic in areas 17 and 18, interrupted near the visual midline. Unexpectedly, interhemispheric connections appear not to modify these PRFs' effects and may not contribute to the responses to discrete, flashed stimuli.

Visual grouping and the focusing of attention induce gamma-band oscillations at different frequencies in human magnetoencephalogram signals

Neural oscillatory synchrony could implement grouping processes, act as an attentional filter, or foster the storage of information in short-term memory. Do these findings indicate that oscillatory synchrony is an unspecific epiphenomenon occurring in any demanding task, or that oscillatory synchrony is a fundamental mechanism involved whenever neural cooperation is requested? If the latter hypothesis is true, then oscillatory synchrony should be specific, with distinct visual processes eliciting different types of oscillations. We recorded magnetoencephalogram (MEG) signals while manipulating the grouping properties of a visual display on the one hand, and the focusing of attention to memorize part of this display on the other hand. Grouping-related gamma oscillations were present in all conditions but modulated by the grouping properties of the stimulus (one or two groups) in the high gamma-band (70-120 Hz) at central occipital locations. Attention-related gamma oscillations appeared as an additional component whenever attentional focusing was requested in the low gamma-band (44-66 Hz) at parietal locations. Our results thus reveal the existence of a functional specialization in the gamma range, with grouping-related oscillations showing up at higher frequencies than attention-related oscillations. The pattern of oscillatory synchrony is thus specific of the visual process it is associated with. Our results further suggest that both grouping processes and focused attention rely on a common implementation process, namely, gamma-band oscillatory synchrony, a finding that could account for the fact that coherent percepts are more likely to catch attention than incoherent ones.