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.

ezBIDS: Guided standardization of neuroimaging data interoperable with major data archives and platforms.

Data standardization promotes a common framework through which researchers can utilize others' data and is one of the leading methods neuroimaging researchers use to share and replicate findings. As of today, standardizing datasets requires technical expertise such as coding and knowledge of file formats. We present ezBIDS, a tool for converting neuroimaging data and associated metadata to the Brain Imaging Data Structure (BIDS) standard. ezBIDS contains four major features: (1) No installation or programming requirements. (2) Handling of both imaging and task events data and metadata. (3) Semi-automated inference and guidance for adherence to BIDS. (4) Multiple data management options: download BIDS data to local system, or transfer to OpenNeuro.org or to brainlife.io. In sum, ezBIDS requires neither coding proficiency nor knowledge of BIDS, and is the first BIDS tool to offer guided standardization, support for task events conversion, and interoperability with OpenNeuro.org and brainlife.io.

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.

Wireless EEG: A survey of systems and studies.

The popular brain monitoring method of electroencephalography (EEG) has seen a surge in commercial attention in recent years, focusing mostly on hardware miniaturization. This has led to a varied landscape of portable EEG devices with wireless capability, allowing them to be used by relatively unconstrained users in real-life conditions outside of the laboratory. The wide availability and relative affordability of these devices provide a low entry threshold for newcomers to the field of EEG research. The large device variety and the at times opaque communication from their manufacturers, however, can make it difficult to obtain an overview of this hardware landscape. Similarly, given the breadth of existing (wireless) EEG knowledge and research, it can be challenging to get started with novel ideas. Therefore, this paper first provides a list of 48 wireless EEG devices along with a number of important-sometimes difficult-to-obtain-features and characteristics to enable their side-by-side comparison, along with a brief introduction to each of these aspects and how they may influence one's decision. Secondly, we have surveyed previous literature and focused on 110 high-impact journal publications making use of wireless EEG, which we categorized by application and analyzed for device used, number of channels, sample size, and participant mobility. Together, these provide a basis for informed decision making with respect to hardware and experimental precedents when considering new, wireless EEG devices and research. At the same time, this paper provides background material and commentary about pitfalls and caveats regarding this increasingly accessible line of research.

Open and reproducible neuroimaging: From study inception to publication.

Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data.

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.

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.

Modulation of the Somatosensory Evoked Potential by Attention and Spinal Cord Stimulation.

Introduction: Spinal Cord Stimulation (SCS) is a last-resort treatment for patients with intractable chronic pain in whom pharmacological and other treatments have failed. Conventional tonic SCS is accompanied by tingling sensations. More recent stimulation protocols like burst SCS are not sensed by the patient while providing similar levels of pain relief. It has been previously reported that conventional tonic SCS can attenuate sensory-discriminative processing in several brain areas, but that burst SCS might have additional effects on the medial, motivational-affective pain system. In this explorative study we assessed the influence of attention on the somatosensory evoked brain responses under conventional tonic SCS as well as burst SCS regime. Methods: Twelve chronic pain patients with an implanted SCS device had 2-weeks evaluation periods with three different SCS settings (conventional tonic SCS, burst SCS, and sham SCS). At the end of each period, an electro-encephalography (EEG) measurement was done, at which patients received transcutaneous electrical pulses at the tibial nerve to induce somatosensory evoked potentials (SEP). SEP data was acquired while patients were attending the applied pulses and while they were mind wandering. The effects of attention as well as SCS regimes on the SEP were analyzed by comparing amplitudes of early and late latencies at the vertex as well as brain activity at full cortical maps. Results: Pain relief obtained by the various SCS settings varied largely among patients. Early SEP responses were not significantly affected by attention nor SCS settings (i.e., burst, tonic, and sham). However, late SEP responses (P300) were reduced with tonic and burst SCS: conventional tonic SCS reduced P300 brain activity in the unattended condition, while burst SCS reduced P300 brain activity in both attended and unattended conditions. Conclusion: Burst spinal cord stimulation for the treatment of chronic pain seems to reduce cortical attention that is or can be directed to somatosensory stimuli to a larger extent than conventional spinal cord stimulation treatment. This is a first step in understanding why in selected chronic pain patients burst SCS is more effective than tonic SCS and how neuroimaging could assist in personalizing SCS treatment.

Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective.

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

#EEGManyLabs: Investigating the replicability of influential EEG experiments.

There is growing awareness across the neuroscience community that the replicability of findings about the relationship between brain activity and cognitive phenomena can be improved by conducting studies with high statistical power that adhere to well-defined and standardised analysis pipelines. Inspired by recent efforts from the psychological sciences, and with the desire to examine some of the foundational findings using electroencephalography (EEG), we have launched #EEGManyLabs, a large-scale international collaborative replication effort. Since its discovery in the early 20th century, EEG has had a profound influence on our understanding of human cognition, but there is limited evidence on the replicability of some of the most highly cited discoveries. After a systematic search and selection process, we have identified 27 of the most influential and continually cited studies in the field. We plan to directly test the replicability of key findings from 20 of these studies in teams of at least three independent laboratories. The design and protocol of each replication effort will be submitted as a Registered Report and peer-reviewed prior to data collection. Prediction markets, open to all EEG researchers, will be used as a forecasting tool to examine which findings the community expects to replicate. This project will update our confidence in some of the most influential EEG findings and generate a large open access database that can be used to inform future research practices. Finally, through this international effort, we hope to create a cultural shift towards inclusive, high-powered multi-laboratory collaborations.

A thalamocortical pathway for fast rerouting of tactile information to occipital cortex in congenital blindness.

In congenitally blind individuals, the occipital cortex responds to various nonvisual inputs. Some animal studies raise the possibility that a subcortical pathway allows fast re-routing of tactile information to the occipital cortex, but this has not been shown in humans. Here we show using magnetoencephalography (MEG) that tactile stimulation produces occipital cortex activations, starting as early as 35 ms in congenitally blind individuals, but not in blindfolded sighted controls. Given our measured thalamic response latencies of 20 ms and a mean estimated lateral geniculate nucleus to primary visual cortex transfer time of 15 ms, we claim that this early occipital response is mediated by a direct thalamo-cortical pathway. We also observed stronger directed connectivity in the alpha band range from posterior thalamus to occipital cortex in congenitally blind participants. Our results strongly suggest the contribution of a fast thalamo-cortical pathway in the cross-modal activation of the occipital cortex in congenitally blind humans.

Older adults exhibit a more pronounced modulation of beta oscillations when performing sustained and dynamic handgrips.

Muscle contractions are associated with a decrease in beta oscillatory activity, known as movement-related beta desynchronization (MRBD). Older adults exhibit a MRBD of greater amplitude compared to their younger counterparts, even though their beta power remains higher both at rest and during muscle contractions. Further, a modulation in MRBD has been observed during sustained and dynamic pinch contractions, whereby beta activity during periods of steady contraction following a dynamic contraction is elevated. However, how the modulation of MRBD is affected by aging has remained an open question. In the present work, we investigated the effect of aging on the modulation of beta oscillations and their putative link with motor performance. We collected magnetoencephalography (MEG) data from younger and older adults during a resting-state period and motor handgrip paradigms, which included sustained and dynamic contractions, to quantify spontaneous and motor-related beta oscillatory activity. Beta power at rest was found to be significantly increased in the motor cortex of older adults. During dynamic hand contractions, MRBD was more pronounced in older participants in frontal, premotor and motor brain regions. These brain areas also exhibited age-related decreases in cortical thickness; however, the magnitude of MRBD and cortical thickness were not found to be associated after controlling for age. During sustained hand contractions, MRBD exhibited a decrease in magnitude compared to dynamic contraction periods in both groups and did not show age-related differences. This suggests that the amplitude change in MRBD between dynamic and sustained contractions is larger in older compared to younger adults. We further probed for a relationship between beta oscillations and motor behaviour and found that greater MRBD in primary motor cortices was related to degraded motor performance beyond age, but our results suggested that age-related differences in beta oscillations were not predictive of motor performance.

Visual and kinesthetic modes affect motor imagery classification in untrained subjects.

The understanding of neurophysiological mechanisms responsible for motor imagery (MI) is essential for the development of brain-computer interfaces (BCI) and bioprosthetics. Our magnetoencephalographic (MEG) experiments with voluntary participants confirm the existence of two types of motor imagery, kinesthetic imagery (KI) and visual imagery (VI), distinguished by activation and inhibition of different brain areas in motor-related α- and ß-frequency regions. Although the brain activity corresponding to MI is usually observed in specially trained subjects or athletes, we show that it is also possible to identify particular features of MI in untrained subjects. Similar to real movement, KI implies muscular sensation when performing an imaginary moving action that leads to event-related desynchronization (ERD) of motor-associated brain rhythms. By contrast, VI refers to visualization of the corresponding action that results in event-related synchronization (ERS) of α- and ß-wave activity. A notable difference between KI and VI groups occurs in the frontal brain area. In particular, the analysis of evoked responses shows that in all KI subjects the activity in the frontal cortex is suppressed during MI, while in the VI subjects the frontal cortex is always active. The accuracy in classification of left-arm and right-arm MI using artificial intelligence is similar for KI and VI. Since untrained subjects usually demonstrate the VI imagery mode, the possibility to increase the accuracy for VI is in demand for BCIs. The application of artificial neural networks allows us to classify MI in raising right and left arms with average accuracy of 70% for both KI and VI using appropriate filtration of input signals. The same average accuracy is achieved by optimizing MEG channels and reducing their number to only 13.

Brainstorm Pipeline Analysis of Resting-State Data From the Open MEG Archive.

We present a simple, reproducible analysis pipeline applied to resting-state magnetoencephalography (MEG) data from the Open MEG Archive (OMEGA). The data workflow was implemented with Brainstorm, which like OMEGA is free and openly accessible. The proposed pipeline produces group maps of ongoing brain activity decomposed in the typical frequency bands of electrophysiology. The procedure is presented as a technical proof of concept for streamlining a broader range and more sophisticated studies of resting-state electrophysiological data. It also features the recently introduced extension of the brain imaging data structure (BIDS) to MEG data, highlighting the scalability and generalizability of Brainstorm analytical pipelines to other, and potentially larger data volumes.

Functional and effective reorganization of the aging brain during unimanual and bimanual hand movements.

Motor performance decline observed during aging is linked to changes in brain structure and function, however, the precise neural reorganization associated with these changes remains largely unknown. We investigated the neurophysiological correlates of this reorganization by quantifying functional and effective brain network connectivity in elderly individuals (n = 11; mean age = 67.5 years), compared to young adults (n = 12; mean age = 23.7 years), while they performed visually-guided unimanual and bimanual handgrips inside the magnetoencephalography (MEG) scanner. Through a combination of principal component analysis and Granger causality, we observed age-related increases in functional and effective connectivity in whole-brain, task-related motor networks. Specifically, elderly individuals demonstrated (i) greater information flow from contralateral parietal and ipsilateral secondary motor regions to the left primary motor cortex during the unimanual task and (ii) decreased interhemispheric temporo-frontal communication during the bimanual task. Maintenance of motor performance and task accuracy in elderly was achieved by hyperactivation of the task-specific motor networks, reflecting a possible mechanism by which the aging brain recruits additional resources to counteract known myelo- and cytoarchitectural changes. Furthermore, resting-state sessions acquired before and after each motor task revealed that both older and younger adults maintain the capacity to adapt to task demands via network-wide increases in functional connectivity. Collectively, our study consolidates functional connectivity and directionality of information flow in systems-level cortical networks during aging and furthers our understanding of neuronal flexibility in motor processes.

MEG/EEG Group Analysis With Brainstorm.

Brainstorm is a free, open-source Matlab and Java application for multimodal electrophysiology data analytics and source imaging [primarily MEG, EEG and depth recordings, and integration with MRI and functional near infrared spectroscopy (fNIRS)]. We also provide a free, platform-independent executable version to users without a commercial Matlab license. Brainstorm has a rich and intuitive graphical user interface, which facilitates learning and augments productivity for a wider range of neuroscience users with little or no knowledge of scientific coding and scripting. Yet, it can also be used as a powerful scripting tool for reproducible and shareable batch processing of (large) data volumes. This article describes these Brainstorm interactive and scripted features via illustration through the complete analysis of group data from 16 participants in a MEG vision study.

Identification of Time-Varying Cortico-cortical and Cortico-Muscular Coherence during Motor Tasks with Multivariate Autoregressive Models.

Neural populations coordinate at fast subsecond time-scales during rest and task execution. As a result, functional brain connectivity assessed with different neuroimaging modalities (EEG, MEG, fMRI) may also change over different time scales. In addition to the more commonly used sliding window techniques, the General Linear Kalman Filter (GLFK) approach has been proposed to estimate time-varying brain connectivity. In the present work, we propose a modification of the GLFK approach to model timevarying connectivity. We also propose a systematic method to select the hyper-parameters of the model. We evaluate the performance of the method using MEG and EMG data collected from 12 young subjects performing two motor tasks (unimanual and bimanual hand grips), by quantifying time-varying cortico-cortical and corticomuscular coherence (CCC and CMC). The CMC results revealed patterns in accordance with earlier findings, as well as an improvement in both time and frequency resolution compared to sliding window approaches. These results suggest that the proposed methodology is able to unveil accurate time-varying connectivity patterns with an excellent time resolution.

MEG-BIDS, the brain imaging data structure extended to magnetoencephalography.

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG measures brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS was a solution to organise magnetic resonance imaging (MRI) data. The nature and acquisition parameters of MRI and MEG data are strongly dissimilar. Although there is no standard data format for MEG, we propose MEG-BIDS as a principled solution to store, organise, process and share the multidimensional data volumes produced by the modality. The standard also includes well-defined metadata, to facilitate future data harmonisation and sharing efforts. This responds to unmet needs from the multimodal neuroimaging community and paves the way to further integration of other techniques in electrophysiology. MEG-BIDS builds on MRI-BIDS, extending BIDS to a multimodal data structure. We feature several data-analytics software that have adopted MEG-BIDS, and a diverse sample of open MEG-BIDS data resources available to everyone.