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.

State-dependent effects of neural stimulation on brain function and cognition.

Invasive and non-invasive brain stimulation methods are widely used in neuroscience to establish causal relationships between distinct brain regions and the sensory, cognitive and motor functions they subserve. When combined with concurrent brain imaging, such stimulation methods can reveal patterns of neuronal activity responsible for regulating simple and complex behaviours at the level of local circuits and across widespread networks. Understanding how fluctuations in physiological states and task demands might influence the effects of brain stimulation on neural activity and behaviour is at the heart of how we use these tools to understand cognition. Here we review the concept of such 'state-dependent' changes in brain activity in response to neural stimulation, and consider examples from research on altered states of consciousness (for example, sleep and anaesthesia) and from task-based manipulations of selective attention and working memory. We relate relevant findings from non-invasive methods used in humans to those obtained from direct electrical and optogenetic stimulation of neuronal ensembles in animal models. Given the widespread use of brain stimulation as a research tool in the laboratory and as a means of augmenting or restoring brain function, consideration of the influence of changing physiological and cognitive states is crucial for increasing the reliability of these interventions.

A computational account of transsaccadic attentional allocation based on visual gain fields.

Coordination of goal-directed behavior depends on the brain's ability to recover the locations of relevant objects in the world. In humans, the visual system encodes the spatial organization of sensory inputs, but neurons in early visual areas map objects according to their retinal positions, rather than where they are in the world. How the brain computes world-referenced spatial information across eye movements has been widely researched and debated. Here, we tested whether shifts of covert attention are sufficiently precise in space and time to track an object's real-world location across eye movements. We found that observers' attentional selectivity is remarkably precise and is barely perturbed by the execution of saccades. Inspired by recent neurophysiological discoveries, we developed an observer model that rapidly estimates the real-world locations of objects and allocates attention within this reference frame. The model recapitulates the human data and provides a parsimonious explanation for previously reported phenomena in which observers allocate attention to task-irrelevant locations across eye movements. Our findings reveal that visual attention operates in real-world coordinates, which can be computed rapidly at the earliest stages of cortical processing.

Distinct early and late neural mechanisms regulate feature-specific sensory adaptation in the human visual system.

A canonical feature of sensory systems is that they adapt to prolonged or repeated inputs, suggesting the brain encodes the temporal context in which stimuli are embedded. Sensory adaptation has been observed in the central nervous systems of many animal species, using techniques sensitive to a broad range of spatiotemporal scales of neural activity. Two competing models have been proposed to account for the phenomenon. One assumes that adaptation reflects reduced neuronal sensitivity to sensory inputs over time (the "fatigue" account); the other posits that adaptation arises due to increased neuronal selectivity (the "sharpening" account). To adjudicate between these accounts, we exploited the well-known "tilt aftereffect", which reflects adaptation to orientation information in visual stimuli. We recorded whole-brain activity with millisecond precision from human observers as they viewed oriented gratings before and after adaptation, and used inverted encoding modeling to characterize feature-specific neural responses. We found that both fatigue and sharpening mechanisms contribute to the tilt aftereffect, but that they operate at different points in the sensory processing cascade to produce qualitatively distinct outcomes. Specifically, fatigue operates during the initial stages of processing, consistent with tonic inhibition of feedforward responses, whereas sharpening occurs ~200 ms later, consistent with feedback or local recurrent activity. Our findings reconcile two major accounts of sensory adaptation, and reveal how this canonical process optimizes the detection of change in sensory inputs through efficient neural coding.

Integrated Perceptual Decisions Rely on Parallel Evidence Accumulation.

The ability to make accurate and timely decisions, such as judging when it is safe to cross the road, is the foundation of adaptive behavior. While the computational and neural processes supporting simple decisions on isolated stimuli have been well characterized, decision-making in the real world often requires integration of discrete sensory events over time and space. Most previous experimental work on perceptual decision-making has focused on tasks that involve only a single, task-relevant source of sensory input. It remains unclear, therefore, how such integrative decisions are regulated computationally. Here we used psychophysics, electroencephalography, and computational modeling to understand how the human brain combines visual motion signals across space in the service of a single, integrated decision. To that purpose, we presented two random-dot kinematograms in the left and the right visual hemifields. Coherent motion signals were shown briefly and concurrently in each location, and healthy adult human participants of both sexes reported the average of the two motion signals. We directly tested competing predictions arising from influential serial and parallel accounts of visual processing. Using a biologically plausible model of motion filtering, we found evidence in favor of parallel integration as the fundamental computational mechanism regulating integrated perceptual decisions.

Neurochemical Predictors of Generalized Learning Induced by Brain Stimulation and Training.

Methods of cognitive enhancement for humans are most impactful when they generalize across tasks. However, the extent to which such "transfer" is possible via interventions is widely debated. In addition, the contribution of excitatory and inhibitory processes to such transfer is unknown. Here, in a large-scale neuroimaging individual differences study with humans (both sexes), we paired multitasking training and noninvasive brain stimulation (transcranial direct current stimulation, tDCS) over multiple days and assessed performance across a range of paradigms. In addition, we varied tDCS dosage (1.0 and 2.0 mA), electrode montage (left or right prefrontal regions), and training task (multitasking vs a control task) and assessed GABA and glutamate concentrations via ultrahigh field 7T magnetic resonance spectroscopy. Generalized benefits were observed in spatial attention, indexed by visual search performance, when multitasking training was combined with 1.0 mA stimulation targeting either the left or right prefrontal cortex (PFC). This transfer effect persisted for ∼30 d post intervention. Critically, the transferred benefits associated with right prefrontal tDCS were predicted by pretraining concentrations of glutamate in the PFC. Thus, the effects of this combined stimulation and training protocol appear to be linked predominantly to excitatory brain processes.

Distinct neural markers of evidence accumulation index metacognitive processing before and after simple visual decisions.

Perceptual decision-making is affected by uncertainty arising from the reliability of incoming sensory evidence (perceptual uncertainty) and the categorization of that evidence relative to a choice boundary (categorical uncertainty). Here, we investigated how these factors impact the temporal dynamics of evidence processing during decision-making and subsequent metacognitive judgments. Participants performed a motion discrimination task while electroencephalography was recorded. We manipulated perceptual uncertainty by varying motion coherence, and categorical uncertainty by varying the angular offset of motion signals relative to a criterion. After each trial, participants rated their desire to change their mind. High uncertainty impaired perceptual and metacognitive judgments and reduced the amplitude of the centro-parietal positivity, a neural marker of evidence accumulation. Coherence and offset affected the centro-parietal positivity at different time points, suggesting that perceptual and categorical uncertainty affect decision-making in sequential stages. Moreover, the centro-parietal positivity predicted participants' metacognitive judgments: larger predecisional centro-parietal positivity amplitude was associated with less desire to change one's mind, whereas larger postdecisional centro-parietal positivity amplitude was associated with greater desire to change one's mind, but only following errors. These findings reveal a dissociation between predecisional and postdecisional evidence processing, suggesting that the CPP tracks potentially distinct cognitive processes before and after a decision.

Stimulating prefrontal cortex facilitates training transfer by increasing representational overlap.

A recent hypothesis characterizes difficulties in multitasking as being the price humans pay for our ability to generalize learning across tasks. The mitigation of these costs through training has been associated with reduced overlap of constituent task representations within frontal, parietal, and subcortical regions. Transcranial direct current stimulation, which can modulate functional brain activity, has shown promise in generalizing performance gains when combined with multitasking training. However, the relationship between combined transcranial direct current stimulation and training protocols with task-associated representational overlap in the brain remains unexplored. Here, we paired prefrontal cortex transcranial direct current stimulation with multitasking training in 178 individuals and collected functional magnetic resonance imaging data pre- and post-training. We found that 1 mA transcranial direct current stimulation applied to the prefrontal cortex paired with multitasking training enhanced training transfer to spatial attention, as assessed via a visual search task. Using machine learning to assess the overlap of neural activity related to the training task in task-relevant brain regions, we found that visual search gains were predicted by changes in classification accuracy in frontal, parietal, and cerebellar regions for participants that received left prefrontal cortex stimulation. These findings demonstrate that prefrontal cortex transcranial direct current stimulation may interact with training-related changes to task representations, facilitating the generalization of learning.

Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions.

The mechanisms that enable humans to evaluate their confidence across a range of different decisions remain poorly understood. To bridge this gap in understanding, we used computational modelling to investigate the processes that underlie confidence judgements for perceptual decisions and the extent to which these computations are the same in the visual and auditory modalities. Participants completed two versions of a categorisation task with visual or auditory stimuli and made confidence judgements about their category decisions. In each modality, we varied both evidence strength, (i.e., the strength of the evidence for a particular category) and sensory uncertainty (i.e., the intensity of the sensory signal). We evaluated several classes of computational models which formalise the mapping of evidence strength and sensory uncertainty to confidence in different ways: 1) unscaled evidence strength models, 2) scaled evidence strength models, and 3) Bayesian models. Our model comparison results showed that across tasks and modalities, participants take evidence strength and sensory uncertainty into account in a way that is consistent with the scaled evidence strength class. Notably, the Bayesian class provided a relatively poor account of the data across modalities, particularly in the more complex categorisation task. Our findings suggest that a common process is used for evaluating confidence in perceptual decisions across domains, but that the parameter settings governing the process are tuned differently in each modality. Overall, our results highlight the impact of sensory uncertainty on confidence and the unity of metacognitive processing across sensory modalities.

Neural substrates of individual differences in learning generalization via combined brain stimulation and multitasking training.

A pervasive limitation in cognition is reflected by the performance costs we experience when attempting to undertake two tasks simultaneously. While training can overcome these multitasking costs, the more elusive objective of training interventions is to induce persistent gains that transfer across tasks. Combined brain stimulation and cognitive training protocols have been employed to improve a range of psychological processes and facilitate such transfer, with consistent gains demonstrated in multitasking and decision-making. Neural activity in frontal, parietal, and subcortical regions has been implicated in multitasking training gains, but how the brain supports training transfer is poorly understood. To investigate this, we combined transcranial direct current stimulation of the prefrontal cortex and multitasking training, with functional magnetic resonance imaging in 178 participants. We observed transfer to a visual search task, following 1 mA left or right prefrontal cortex transcranial direct current stimulation and multitasking training. These gains persisted for 1-month post-training. Notably, improvements in visual search performance for the right hemisphere stimulation group were associated with activity changes in the right hemisphere dorsolateral prefrontal cortex, intraparietal sulcus, and cerebellum. Thus, functional dynamics in these task-general regions determine how individuals respond to paired stimulation and training, resulting in enhanced performance on an untrained task.

White matter microstructure is associated with the precision of visual working memory.

Visual working memory is critical for goal-directed behavior as it maintains continuity between previous and current visual input. Functional neuroimaging studies have shown that visual working memory relies on communication between distributed brain regions, which implies an important role for long-range white matter connections in visual working memory performance. Here, we characterized the relationship between the microstructure of white matter association tracts and the precision of visual working memory representations. To that purpose, we devised a delayed estimation task which required participants to reproduce visual features along a continuous scale. A sample of 80 healthy adults performed the task and underwent diffusion-weighted MRI. We applied mixture distribution modelling to quantify the precision of working memory representations, swap errors, and guess rates, all of which contribute to observed responses. Latent components of microstructural properties in sets of anatomical tracts were identified by principal component analysis. We found an interdependency between fibre coherence in the bilateral superior longitudinal fasciculus (SLF) I, SLF II, and SLF III, on one hand, and the bilateral inferior fronto-occipital fasciculus (IFOF), on the other, in mediating the precision of visual working memory in a functionally specific manner. We also found that individual differences in axonal density in a network comprising the bilateral inferior longitudinal fasciculus (ILF) and SLF III and right SLF II, in combination with a supporting network located elsewhere in the brain, form a common system for visual working memory to modulate response precision, swap errors, and random guess rates.

Stimulus Reliability Automatically Biases Temporal Integration of Discrete Perceptual Targets in the Human Brain.

Many decisions, from crossing a busy street to choosing a profession, require integration of discrete sensory events. Previous studies have shown that integrative decision-making favors more reliable stimuli, mimicking statistically optimal integration. It remains unclear, however, whether reliability biases operate even when they lead to suboptimal performance. To address this issue, we asked human observers to reproduce the average motion direction of two suprathreshold coherent motion signals presented successively and with varying levels of reliability, while simultaneously recording whole-brain activity using electroencephalography. By definition, the averaging task should engender equal weighting of the two component motion signals, but instead we found robust behavioral biases in participants' average decisions that favored the more reliable stimulus. Using population-tuning modeling of brain activity we characterized tuning to the average motion direction. In keeping with the behavioral biases, the neural tuning profiles also exhibited reliability biases. A control experiment revealed that observers were able to reproduce motion directions of low and high reliability with equal precision, suggesting that unbiased integration in this task was not only theoretically optimal but demonstrably possible. Our findings reveal that temporal integration of discrete sensory events in the brain is automatically and suboptimally weighted according to stimulus reliability.SIGNIFICANCE STATEMENT Many everyday decisions require integration of several sources of information. To safely cross a busy road, for example, one must consider the movement of vehicles with different speeds and trajectories. Previous research has shown that individual stimuli are weighted according to their reliability. Whereas reliability biases typically yield performance that closely mimics statistically optimal integration, it remains unknown whether such biases arise even when they lead to suboptimal performance. Here we combined a novel integrative decision-making task with concurrent brain recording and modeling to address this question. While unbiased decisions were optimal in the task, observers nevertheless exhibited robust reliability biases in both behavior and brain activity, suggesting that reliability-weighted integration is automatic and dissociable from statistically optimal integration.

Implicit Neurofeedback Training of Feature-Based Attention Promotes Biased Sensory Processing during Integrative Decision-Making.

Complex perceptual decisions, in which information must be integrated across multiple sources of evidence, are ubiquitous but are not well understood. Such decisions rely on sensory processing of each individual source of evidence, and are therefore vulnerable to bias if sensory processing resources are disproportionately allocated among visual inputs. To investigate this, we developed an implicit neurofeedback protocol embedded within a complex decision-making task to bias sensory processing in favor of one source of evidence over another. Human participants of both sexes (N = 30) were asked to report the average motion direction across two fields of oriented moving bars. Bars of different orientations flickered at different frequencies, thus inducing steady-state visual evoked potentials. Unbeknownst to participants, neurofeedback was implemented to implicitly reward attention to a specific "trained" orientation (rather than any particular motion direction). As attentional selectivity for this orientation increased, the motion coherence of both fields of bars increased, making the task easier without altering the relative reliability of the two sources of evidence. Critically, these neurofeedback trials were alternated with "test" trials in which motion coherence was not contingent on attentional selectivity, allowing us to assess the training efficacy. The protocol successfully biased sensory processing, resulting in earlier and stronger encoding of the trained evidence source. In turn, this evidence was weighted more heavily in behavioral and neural representations of the integrated average, although the two sources of evidence were always matched in reliability. These results demonstrate how biases in sensory processing can impact integrative decision-making processes.SIGNIFICANCE STATEMENT Many everyday decisions require active integration of different sources of sensory information, such as deciding when it is safe to cross a road, yet little is known about how the brain prioritizes sensory sources in the service of adaptive behavior, or whether such decisions can be altered through learning. Here we addressed these questions using a novel behavioral protocol that provided observers with real-time feedback of their own brain activity patterns in which sensory processing was implicitly biased toward a subset of the available information. We show that, while such biases are a normal and adaptive mechanism for humans to process complex visual information, they can also contribute to suboptimal decision-making.

Delay activity during visual working memory: A meta-analysis of 30 fMRI experiments.

Visual working memory refers to the temporary maintenance and manipulation of task-related visual information. Recent debate on the underlying neural substrates of visual working memory has focused on the delay period of relevant tasks. Persistent neural activity throughout the delay period has been recognized as a correlate of working memory, yet regions demonstrating sustained hemodynamic responses show inconsistency across individual studies. To develop a more precise understanding of delay-period activations during visual working memory, we conducted a coordinate-based meta-analysis on 30 fMRI experiments involving 515 healthy adults with a mean age of 25.65 years. The main analysis revealed a widespread frontoparietal network associated with delay-period activity, as well as activation in the right inferior temporal cortex. These findings were replicated using different meta-analytical algorithms and were shown to be robust against between-study heterogeneity and publication bias. Further meta-analyses on different subgroups of experiments with specific task demands and stimulus types revealed similar delay-period networks, with activations distributed across the frontal and parietal cortices. The roles of prefrontal regions, posterior parietal regions, and inferior temporal areas are reviewed and discussed in the context of content-specific storage. We conclude that cognitive operations that occur during the unfilled delay period in visual working memory tasks can be flexibly expressed across a frontoparietal-temporal network depending on experimental parameters.

On the relationship between GABA+ and glutamate across the brain.

Equilibrium between excitation and inhibition (E/I balance) is key to healthy brain function. Conversely, disruption of normal E/I balance has been implicated in a range of central neurological pathologies. Magnetic resonance spectroscopy (MRS) provides a non-invasive means of quantifying in vivo concentrations of excitatory and inhibitory neurotransmitters, which could be used as diagnostic biomarkers. Using the ratio of excitatory and inhibitory neurotransmitters as an index of E/I balance is common practice in MRS work, but recent studies have shown inconsistent evidence for the validity of this proxy. This is underscored by the fact that different measures are often used in calculating E/I balance such as glutamate and Glx (glutamate and glutamine). Here we used a large MRS dataset obtained at ultra-high field (7 T) measured from 193 healthy young adults and focused on two brain regions - prefrontal and occipital cortex - to resolve this inconsistency. We find evidence that there is an inter-individual common ratio between GABA+ (γ-aminobutyric acid and macromolecules) and Glx in the occipital, but not prefrontal cortex. We further replicate the prefrontal result in a legacy dataset (n = 78) measured at high-field (3 T) strength. By contrast, with ultra-high field MRS data, we find extreme evidence that there is a common ratio between GABA+ and glutamate in both prefrontal and occipital cortices, which cannot be explained by participant demographics, signal quality, fractional tissue volume, or other metabolite concentrations. These results are consistent with previous electrophysiological and theoretical work supporting E/I balance. Our findings indicate that MRS-detected GABA+ and glutamate (but not Glx), are a reliable measure of E/I balance .

Attention promotes the neural encoding of prediction errors.

The encoding of sensory information in the human brain is thought to be optimised by two principal processes: 'prediction' uses stored information to guide the interpretation of forthcoming sensory events, and 'attention' prioritizes these events according to their behavioural relevance. Despite the ubiquitous contributions of attention and prediction to various aspects of perception and cognition, it remains unknown how they interact to modulate information processing in the brain. A recent extension of predictive coding theory suggests that attention optimises the expected precision of predictions by modulating the synaptic gain of prediction error units. Because prediction errors code for the difference between predictions and sensory signals, this model would suggest that attention increases the selectivity for mismatch information in the neural response to a surprising stimulus. Alternative predictive coding models propose that attention increases the activity of prediction (or 'representation') neurons and would therefore suggest that attention and prediction synergistically modulate selectivity for 'feature information' in the brain. Here, we applied forward encoding models to neural activity recorded via electroencephalography (EEG) as human observers performed a simple visual task to test for the effect of attention on both mismatch and feature information in the neural response to surprising stimuli. Participants attended or ignored a periodic stream of gratings, the orientations of which could be either predictable, surprising, or unpredictable. We found that surprising stimuli evoked neural responses that were encoded according to the difference between predicted and observed stimulus features, and that attention facilitated the encoding of this type of information in the brain. These findings advance our understanding of how attention and prediction modulate information processing in the brain, as well as support the theory that attention optimises precision expectations during hierarchical inference by increasing the gain of prediction errors.

Correction: Attention promotes the neural encoding of prediction errors.

[This corrects the article DOI: 10.1371/journal.pbio.2006812.].

Slow-oscillatory tACS does not modulate human motor cortical response to repeated plasticity paradigms.

Previous history of activity and learning modulates synaptic plasticity and can lead to saturation of synaptic connections. According to the synaptic homeostasis hypothesis, neural oscillations during slow-wave sleep play an important role in restoring plasticity within a functional range. However, it is not known whether slow-wave oscillations-without the concomitant requirement of sleep-play a causal role in human synaptic homeostasis. Here, we aimed to answer this question using transcranial alternating current stimulation (tACS) to induce slow-oscillatory activity in awake human participants. tACS was interleaved between two plasticity-inducing interventions: motor learning, and paired associative stimulation (PAS). The hypothesis tested was that slow-oscillatory tACS would prevent homeostatic interference between motor learning and PAS, and facilitate plasticity from these successive interventions. Thirty-six participants received sham and active fronto-motor tACS in two separate sessions, along with electroencephalography (EEG) recordings, while a further 38 participants received tACS through a control montage. Motor evoked potentials (MEPs) were recorded throughout the session to quantify plasticity changes after the different interventions, and the data were analysed with Bayesian statistics. As expected, there was converging evidence that motor training led to excitatory plasticity. Importantly, we found moderate evidence against an effect of active tACS in restoring PAS plasticity, and no evidence of lasting entrainment of slow oscillations in the EEG. This suggests that, under the conditions tested here, slow-oscillatory tACS does not modulate synaptic homeostasis in the motor system of awake humans.

Cerebellum and Emotion Processing.

Clinical examinations and neuroimaging investigations have dramatically changed the prevailing view of human cerebellar function and suggest contributions beyond movement control. Of these new views, perhaps the most intriguing proposal is that the cerebellum plays a key role in regulating emotion. According to the dysmetria of thought theory, the cerebellum provides accuracy, consistency and appropriateness to cognitive and affective functions, as it does for movement-related operations. Despite the value of a universal theory on cerebellar function, it is also essential to consider its unique contributions to specific functional domains. This chapter aims to provide an accentuated account of the cerebellar role in emotion processing by separately evaluating its impact for sub-components of emotion processing. These include physiological responses that contribute to the subjective or "feeling" component of emotion, emotional expressions that serve essential social-communicative functions, and the cognitive appraisal process that determines the emotional significance of events and therefore affects the generation and modulation of emotions.

Spatial structure, phase, and the contrast of natural images.

The sensitivity of the human visual system is thought to be shaped by environmental statistics. A major endeavor in vision science, therefore, is to uncover the image statistics that predict perceptual and cognitive function. When searching for targets in natural images, for example, it has recently been proposed that target detection is inversely related to the spatial similarity of the target to its local background. We tested this hypothesis by measuring observers' sensitivity to targets that were blended with natural image backgrounds. Targets were designed to have a spatial structure that was either similar or dissimilar to the background. Contrary to masking from similarity, we found that observers were most sensitive to targets that were most similar to their backgrounds. We hypothesized that a coincidence of phase alignment between target and background results in a local contrast signal that facilitates detection when target-background similarity is high. We confirmed this prediction in a second experiment. Indeed, we show that, by solely manipulating the phase of a target relative to its background, the target can be rendered easily visible or undetectable. Our study thus reveals that, in addition to its structural similarity, the phase of the target relative to the background must be considered when predicting detection sensitivity in natural images.