Measuring electrophysiological connectivity by power envelope correlation: a technical review on MEG methods

The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. Healthy brain function relies upon efficient connectivity between these areas and, in recent years, neuroimaging has been revolutionised by an ability to estimate this connectivity. In this paper we discuss measurement of network connectivity using magnetoencephalography (MEG), a technique capable of imaging electrophysiological brain activity with good (~5mm) spatial resolution and excellent (~1ms) temporal resolution. The rich information content of MEG facilitates many disparate measures of connectivity between spatially separate regions and in this paper we discuss a single metric known as power envelope correlation. We review in detail the methodology required to measure power envelope correlation including i) projection of MEG data into source space, ii) removing confounds introduced by the MEG inverse problem and iii) estimation of connectivity itself. In this way, we aim to provide researchers with a description of the key steps required to assess envelope based functional networks, which are thought to represent an intrinsic mode of coupling in the human brain. We highlight the principal findings of the techniques discussed, and furthermore, we show evidence that this method can probe how the brain forms and dissolves multiple transient networks on a rapid timescale in order to support current processing demand. Overall, power envelope correlation offers a unique and verifiable means to gain novel insights into network coordination and is proving to be of significant value in elucidating the neural dynamics of the human connectome in health and disease

Functional brain connectivity analysis based on the solution of the inverse problem and on covariance analysis.

The Linearly Constrained Minimum Variance (LCMV) beamformer is one of the most accepted techniques used to estimate the solution of the inverse problem in functional brain dynamics studies, using magnetoencephalograms (MEG). However, since it is based on the assumption of uncorrelated brain sources, its performance decreases in the presence of correlated brain activity, compromising the accuracy of estimates of brain interactions. This problem has not stopped the use of the beamformer in techniques such as Dynamic Imaging of Coherent Sources (DICS), which estimates the functional brain dynamics in a more direct way than the LCMV, and with less computational cost. In this work it is proposed to use a modified version of the well known Minimum Norm Estimates (MNE) spatial filter to estimate the functional brain dynamics of highly correlated activity. This is achieved by using the filter to estimate the cross-spectral density matrices for the brain activity in the same way that DICS does with the LCMV beamformer. The MNE spatial filter is used as a basis because it is not affected by the presence of correlated brain activity. The results obtained from simulations shown that it is possible to estimate highly correlated brain interactions using the proposed method. However, additional methods and constraints need to be applied because of the distorted and weighted output characteristic of the MNE spatial filter. Methods such as the FOcal Undetermined System Solution (FOCUSS) and Singular Value Decomposition Truncation (SVDT) are used to reduce the distorted output, while the estimation of brain dynamics is limited to cortical surface interactions to avoid weighted solutions

Dynamic electrophysiological connectomics

The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. For a century we have been developing techniques to non-invasively map these areas and their associated functions, a discipline now known as neuroimaging. In recent years the field has undergone a paradigm shift to investigate how the brain communicates with itself; it is widely regarded that healthy brain function relies upon efficient connectivity between different functional areas, and the neuroimaging field has been revolutionised by our ability to estimate this connectivity. Studies into communication between spatially separate locations in the brain have revealed a series of robust functional networks which govern mental processes. However these studies have been based on the temporal averaging of minutes or even hours of data to give us a generalised ’snapshot’ of connectivity. Increasing evidence shows us that these connections are dynamic in space, time and frequency and so the next generation of of neuroimaging methods, which capture this 5-dimensional connectivity will prove to be key tools in the investigation of brain networks and ultimately their breakdown in disease. In this thesis we introduce novel methods to capture non-stationarity using magnetoencephalography (MEG), an imaging modality which measures the changes in extracranial magnetic fields associated with neuronal current flow. MEG is a direct measurement of neural activity and has an excellent temporal resolution, which makes it attractive for non-invasively tracking dynamic functional connections. However there are many technical limitations which can confound assessment of functional connectivity which have to be addressed. In Chapters 2 and 3 we introduce the theory behind MEG; specifically how it is possible to measure the femtoTelsa changes in magnetic field generated by the brain and how to project these data to generate a 3-dimensional picture of current in the brain. Chapter 4 reviews some of popular methods of assessing functional connectivity and how to control for the influence of artefactual functional connections erroneously produced during source projection. Chapter 5 introduces a pipeline to assess functional connections across time, space and frequency and in Chapter 6 we apply this pipeline to show that resting state networks, measured using ’static’ metrics are in fact comprised of a series of rapidly forming and dissolving subnetwork connections. Finally, Chapter 7 introduces a pipeline to track dynamic network behaviour simultaneously across the entire brain volume and shows that networks can be characterised by their temporal signatures of connectivity

Dynamic electrophysiological connectomics

The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. For a century we have been developing techniques to non-invasively map these areas and their associated functions, a discipline now known as neuroimaging. In recent years the field has undergone a paradigm shift to investigate how the brain communicates with itself; it is widely regarded that healthy brain function relies upon efficient connectivity between different functional areas, and the neuroimaging field has been revolutionised by our ability to estimate this connectivity. Studies into communication between spatially separate locations in the brain have revealed a series of robust functional networks which govern mental processes. However these studies have been based on the temporal averaging of minutes or even hours of data to give us a generalised ’snapshot’ of connectivity. Increasing evidence shows us that these connections are dynamic in space, time and frequency and so the next generation of of neuroimaging methods, which capture this 5-dimensional connectivity will prove to be key tools in the investigation of brain networks and ultimately their breakdown in disease. In this thesis we introduce novel methods to capture non-stationarity using magnetoencephalography (MEG), an imaging modality which measures the changes in extracranial magnetic fields associated with neuronal current flow. MEG is a direct measurement of neural activity and has an excellent temporal resolution, which makes it attractive for non-invasively tracking dynamic functional connections. However there are many technical limitations which can confound assessment of functional connectivity which have to be addressed. In Chapters 2 and 3 we introduce the theory behind MEG; specifically how it is possible to measure the femtoTelsa changes in magnetic field generated by the brain and how to project these data to generate a 3-dimensional picture of current in the brain. Chapter 4 reviews some of popular methods of assessing functional connectivity and how to control for the influence of artefactual functional connections erroneously produced during source projection. Chapter 5 introduces a pipeline to assess functional connections across time, space and frequency and in Chapter 6 we apply this pipeline to show that resting state networks, measured using ’static’ metrics are in fact comprised of a series of rapidly forming and dissolving subnetwork connections. Finally, Chapter 7 introduces a pipeline to track dynamic network behaviour simultaneously across the entire brain volume and shows that networks can be characterised by their temporal signatures of connectivity

The association of psychotic disorders, dopaminergic agents and resting-state EEG/MEG functional connectivity

Psychotic disorders are complex and heterogeneous mental disorders with low recovery rates despite a great amount of research on the topic. Various hypotheses exist as to the etiology of psychotic disorders. Amongst these, the dopamine hypothesis and the dysconnectivity hypothesis have been the most enduring in the last six decades. Little is known on how the dopamine and the dysconnectivity hypothesis are associated. The overarching research question of this thesis is to investigate this knowledge gap. Resting-state magneto- and electroencephalography (MEG, EEG) were chosen as non-invasive measurement modalities of dysconnectivity at the source and sensor level of the brain in publication 1. Parameters of resting-state EEG microstate classes A-D were used as a global analysis method of functional connectivity at the sensor level of the brain in publications 2 and 3. The first research question focused on finding systematic evidence on the association of the two hypotheses and was addressed by means of a systematic review (publication 1) of 20 studies published since 2000. Based on the review, no definite conclusion on the association of antipsychotic medication (that mainly acts on the dopamine system) and source- and sensor-level EEG/MEG functional connectivity could be drawn. The second research question focused on whether differences in parameters of resting-state EEG microstate classes A-D are associated to antipsychotic medication. It was addressed by a study (publication 2) that compared 19-channel clinical EEG recordings of medicated (mFEP, n = 17) and medication-naïve (untreated; uFEP, n = 30) patients with first-episode psychotic disorders (FEP). The study results revealed significant decrease of microstate class A and significant increase of microstate class B to differentiate mFEP from uFEP. The third research question focused on whether differences in parameters of resting-state EEG microstate classes A-D are associated with psychosis illness progression and transition to psychosis in FEP and ultra-high-risk (UHR) patients. It was addressed by a study (publication 3) that found significantly increased microstate class A to differentiate a combined group of medication-naïve FEP (n = 29) and UHR patients (n = 54) together from healthy controls (HC, n = 25); significantly decreased microstate class B to differentiate FEP from all UHR patients combined; and significantly decreased microstate class D to differentiate UHR-T patients with (n = 20) from UHR-NT patients without (n = 34) later transition to psychotic disorders using 19-channel EEG recordings. In conclusion across all three publications, an association between the dopamine and the dysconnectivity hypothesis could be demonstrated by means of resting-state EEG microstates assessed in publication 2 and 3. No definite conclusion could be drawn by the systematic review (publication 1). More studies with longitudinal designs are needed to rule-out between-subject differences, track response trajectories, pre-post effects of antipsychotic medication and their association with dysconnectivity. With increased effort, resting-state EEG microstates could contribute to establishing a robust biomarker in a multi- domain approach in order to inform clinicians for the diagnosis, treatment and outcome prediction of psychotic disorders

Revealing Distinct Neural Signatures in Magnetoencephalography with Hidden Markov Models

Magnetoencephalography (MEG) is a functional neuroimaging method which measures the magnetic fields produced by neural communication in the brain. Specifically, the fields induced by dendritic current flow in assemblies of pyramidal neurons. Because these magnetic fields are generated directly by brain electrophysiology, and are mostly unperturbed by the skull, MEG data are rich in spatial and temporal information. This thesis is chiefly concerned with interpreting these data in a way that produces useful results whilst minimising bias. Hidden Markov modelling (HMM) is a robust statistical method which has been applied to fields as diverse as speech recognition and financial market prediction. It parses data into a number of ‘hidden states’, each with their own unique characteristics, in an unsupervised way. Because it is data-driven, it can create a model unique to each participant’s brain activity and specific to each task. In addition, the HMM framework itself is flexible so it can be applied to both sensor and source-space data and can be applied to multiple channels (multivariate) or to a single time course (univariate). Choice of an observation model allows states to be characterised by amplitude, spatial, or spectral content depending on the research question. The aim of this thesis is to apply hidden Markov modelling (HMM) to whole head MEG data to identify repeated patterns of transient neural activity occurring throughout the brain. Once these patterns were identified, the interaction between these short ‘bursts’ of activity across the cortex was established which provided a unique measure of functional connectivity. Three studies were undertaken: The role of transient spectral bursts in MEG functional connectivity: In recent years, the smoothly varying neural oscillations often studied in MEG (such as those trial-averaged responses in the traditional neurophysiological (such as alpha/beta) frequency bands) have been shown to be made up of single-trial high-amplitude ‘bursts’ of activity. These bursts can be observed in the beta frequency band and are therefore often referred to as beta bursts. In this study, a novel time-delay embedded HMM was used to identif bursts in broadband data based on their spectral content for MEG data from 66 healthy adult participants. The burst amplitude, duration and frequency of occurrence were characterised across the cortex in resting state data, and in a motor task the classic movement-related beta desynchronisation and post movement beta rebound were shown to be made up of changes in burst occurrence. A novel functional connectivity metric was then introduced based on the coincidence of bursts from distal brain regions, allowing the known beta band functional connectome to be reproduced. Bursts coincident across spatially separate brain regions were also shown to correspond to periods of heightened coherence, lending evidence to the communication by coherence (Fries 2005, 2015) hypothesis. Post-stimulus responses across the cortex: During a motor task, both primary (during stimulation) and post stimulus responses (PSR) can be observed. These are well characterised in the literature, but little is known about their functional significance. The PSR in particular is modified in a range of seemingly unrelated neurological conditions with variable symptoms, such as schizophrenia (Robson et al. 2016), autism spectrum disorder (Gaetz et al. 2020) and multiple sclerosis (Barratt et al. 2017), indicating that the PSR is a fundamental neurophysiological process, the disturbance of which has implications on both healthy and pathological brain function. This work therefore tested the hypothesis that the PSR is present across the cortex. MEG data were acquired and analysed from two experiments with 15 healthy adult volunteers each – the first was a right-hand grip task with visual feedback, the second involved passive left visual field stimulation. Both experiments varied stimulus duration (2s, 5s and 10s) with a 30s rest-period between trials to allow characterisation of the full PSR. A univariate 3-state time-delay-embedded hidden Markov model (HMM) was used to characterise the spatial distributions of the primary and PSR across the cortex for both tasks. Results showed that for both tasks, the primary response state was more bilateral over the sensorimotor or visual areas (depending on task) where the PSR state was more unilateral and confined to the contralateral sensorimotor or visual areas (again, dependant on task). A state coincidence metric was then used to investigate the integration of the primary and PSR states across brain regions as a measure of task-related functional connectivity. Hidden Markov modelling of the interictal brain: Epilepsy is a highly heterogeneous disease with variations in the temporal morphology and localisation of epileptiform activity across patients. Unsupervised machine learning techniques like the HMM allow us to take into account this variability and ensure that every model is tailored to each individual. In this work, a multivariate time-delay embedded HMM was used to identify brain states based on their spatial and spectral properties in sensor-level MEG data acquired as part of standard clinical care for patients at the Children’s Hospital of Philadelphia. State allocations were used together with a linearly constrained minimum variance (LCMV) beamformer to produce a 3D map of state variance, hence localising probable epileptogenic foci. Clinical MEG epilepsy data are routinely analysed by excess kurtosis mapping (EKM) and so the performance of the HMM was assessed against this for three patient groups, each with increasingly complex epilepsy manifestation (10 patients in total). The difference in localization of epileptogenic foci for the two methods was 7 ± 2mm (mean ± SD over all 10 patients); and 94 ± 13% of EKM temporal markers were matched by an HMM state visit. It is therefore clear that this method localizes epileptogenic areas in agreement with EKM and in patients with more than one focus the HMM provides additional information about the relationship between them

Revealing Distinct Neural Signatures in Magnetoencephalography with Hidden Markov Models

Magnetoencephalography (MEG) is a functional neuroimaging method which measures the magnetic fields produced by neural communication in the brain. Specifically, the fields induced by dendritic current flow in assemblies of pyramidal neurons. Because these magnetic fields are generated directly by brain electrophysiology, and are mostly unperturbed by the skull, MEG data are rich in spatial and temporal information. This thesis is chiefly concerned with interpreting these data in a way that produces useful results whilst minimising bias. Hidden Markov modelling (HMM) is a robust statistical method which has been applied to fields as diverse as speech recognition and financial market prediction. It parses data into a number of ‘hidden states’, each with their own unique characteristics, in an unsupervised way. Because it is data-driven, it can create a model unique to each participant’s brain activity and specific to each task. In addition, the HMM framework itself is flexible so it can be applied to both sensor and source-space data and can be applied to multiple channels (multivariate) or to a single time course (univariate). Choice of an observation model allows states to be characterised by amplitude, spatial, or spectral content depending on the research question. The aim of this thesis is to apply hidden Markov modelling (HMM) to whole head MEG data to identify repeated patterns of transient neural activity occurring throughout the brain. Once these patterns were identified, the interaction between these short ‘bursts’ of activity across the cortex was established which provided a unique measure of functional connectivity. Three studies were undertaken: The role of transient spectral bursts in MEG functional connectivity: In recent years, the smoothly varying neural oscillations often studied in MEG (such as those trial-averaged responses in the traditional neurophysiological (such as alpha/beta) frequency bands) have been shown to be made up of single-trial high-amplitude ‘bursts’ of activity. These bursts can be observed in the beta frequency band and are therefore often referred to as beta bursts. In this study, a novel time-delay embedded HMM was used to identif bursts in broadband data based on their spectral content for MEG data from 66 healthy adult participants. The burst amplitude, duration and frequency of occurrence were characterised across the cortex in resting state data, and in a motor task the classic movement-related beta desynchronisation and post movement beta rebound were shown to be made up of changes in burst occurrence. A novel functional connectivity metric was then introduced based on the coincidence of bursts from distal brain regions, allowing the known beta band functional connectome to be reproduced. Bursts coincident across spatially separate brain regions were also shown to correspond to periods of heightened coherence, lending evidence to the communication by coherence (Fries 2005, 2015) hypothesis. Post-stimulus responses across the cortex: During a motor task, both primary (during stimulation) and post stimulus responses (PSR) can be observed. These are well characterised in the literature, but little is known about their functional significance. The PSR in particular is modified in a range of seemingly unrelated neurological conditions with variable symptoms, such as schizophrenia (Robson et al. 2016), autism spectrum disorder (Gaetz et al. 2020) and multiple sclerosis (Barratt et al. 2017), indicating that the PSR is a fundamental neurophysiological process, the disturbance of which has implications on both healthy and pathological brain function. This work therefore tested the hypothesis that the PSR is present across the cortex. MEG data were acquired and analysed from two experiments with 15 healthy adult volunteers each – the first was a right-hand grip task with visual feedback, the second involved passive left visual field stimulation. Both experiments varied stimulus duration (2s, 5s and 10s) with a 30s rest-period between trials to allow characterisation of the full PSR. A univariate 3-state time-delay-embedded hidden Markov model (HMM) was used to characterise the spatial distributions of the primary and PSR across the cortex for both tasks. Results showed that for both tasks, the primary response state was more bilateral over the sensorimotor or visual areas (depending on task) where the PSR state was more unilateral and confined to the contralateral sensorimotor or visual areas (again, dependant on task). A state coincidence metric was then used to investigate the integration of the primary and PSR states across brain regions as a measure of task-related functional connectivity. Hidden Markov modelling of the interictal brain: Epilepsy is a highly heterogeneous disease with variations in the temporal morphology and localisation of epileptiform activity across patients. Unsupervised machine learning techniques like the HMM allow us to take into account this variability and ensure that every model is tailored to each individual. In this work, a multivariate time-delay embedded HMM was used to identify brain states based on their spatial and spectral properties in sensor-level MEG data acquired as part of standard clinical care for patients at the Children’s Hospital of Philadelphia. State allocations were used together with a linearly constrained minimum variance (LCMV) beamformer to produce a 3D map of state variance, hence localising probable epileptogenic foci. Clinical MEG epilepsy data are routinely analysed by excess kurtosis mapping (EKM) and so the performance of the HMM was assessed against this for three patient groups, each with increasingly complex epilepsy manifestation (10 patients in total). The difference in localization of epileptogenic foci for the two methods was 7 ± 2mm (mean ± SD over all 10 patients); and 94 ± 13% of EKM temporal markers were matched by an HMM state visit. It is therefore clear that this method localizes epileptogenic areas in agreement with EKM and in patients with more than one focus the HMM provides additional information about the relationship between them

Statistical causality in the EEG for the study of cognitive functions in healthy and pathological brains

Understanding brain functions requires not only information about the spatial localization of neural activity, but also about the dynamic functional links between the involved groups of neurons, which do not work in an isolated way, but rather interact together through ingoing and outgoing connections. The work carried on during the three years of PhD course returns a methodological framework for the estimation of the causal brain connectivity and its validation on simulated and real datasets (EEG and pseudo-EEG) at scalp and source level. Important open issues like the selection of the best algorithms for the source reconstruction and for time-varying estimates were addressed. Moreover, after the application of such approaches on real datasets recorded from healthy subjects and post-stroke patients, we extracted neurophysiological indices describing in a stable and reliable way the properties of the brain circuits underlying different cognitive states in humans (attention, memory). More in detail: I defined and implemented a toolbox (SEED-G toolbox) able to provide a useful validation instrument addressed to researchers who conduct their activity in the field of brain connectivity estimation. It may have strong implication, especially in methodological advancements. It allows to test the ability of different estimators in increasingly less ideal conditions: low number of available samples and trials, high inter-trial variability (very realistic situations when patients are involved in protocols) or, again, time varying connectivity patterns to be estimate (where stationary hypothesis in wide sense failed). A first simulation study demonstrated the robustness and the accuracy of the PDC with respect to the inter-trials variability under a large range of conditions usually encountered in practice. The simulations carried on the time-varying algorithms allowed to highlight the performance of the existing methodologies in different conditions of signals amount and number of available trials. Moreover, the adaptation of the Kalman based algorithm (GLKF) I implemented, with the introduction of the preliminary estimation of the initial conditions for the algorithm, lead to significantly better performance. Another simulation study allowed to identify a tool combining source localization approaches and brain connectivity estimation able to provide accurate and reliable estimates as less as possible affected to the presence of spurious links due to the head volume conduction. The developed and tested methodologies were successfully applied on three real datasets. The first one was recorded from a group of healthy subjects performing an attention task that allowed to describe the brain circuit at scalp and source level related with three important attention functions: alerting, orienting and executive control. The second EEG dataset come from a group of healthy subjects performing a memory task. Also in this case, the approaches under investigation allowed to identify synthetic connectivity-based descriptors able to characterize the three main memory phases (encoding, storage and retrieval). For the last analysis I recorded EEG data from a group of stroke patients performing the same memory task before and after one month of cognitive rehabilitation. The promising results of this preliminary study showed the possibility to follow the changes observed at behavioural level by means of the introduced neurophysiological indices

Electrostimulation Contingencies and Attention, Electrocortical Activity and Neurofeedback

There is a growing body of evidence for diverse ways of modulating neuronal processing to improve cognitive performance. These include brain-based feedback, self-regulation techniques such as EEG-neurofeedback, and stimulation strategies, alone or in combination. The thesis goal was to determine whether a combined strategy would have advantages for normal cognitive function; specifically operant control of EEG activity in combination with transcutaneous electro-acustimulation. In experiment one the association between transcutaneous electroacustimulation (EA) and improved perceptual sensitivity was demonstrated with a visual GO/NOGO attention task (Chen et al, 2011). Furthermore reduced commission errors were related to an electrocortical motor inhibition component during and after alternating high and low frequency EA, whereas habituation in the control group with sham stimulation was related to different independent components. Experiment two applied frequency-domain ICA to detect changes in EEG power spectra from the eyes-closed to the eyes-open state (Chen et al, 2012). A multiple step approach was provided for analysing the spatiotemporal dynamics of default mode and resting state networks of cerebral EEG sources, preferable to conventional scalp EEG data analysis. Five regions were defined, compatible with fMRI studies. In experiment three the EA approach of Exp I was combined with sensorimotor rhythm (SMR) neurofeedback. SMR training improved perceptual sensitivity, an effect not found in a noncontingent feedback group. However, non-significant benefits resulted from EA. With ICA spectral power analysis changes in frontal beta power were associated with contingent SMR training. Possible long-term effects on an attention network in the resting EEG were also found after SMR training, compared with mock SMR training. In conclusion, this thesis has supplied novel evidence for significant cognitive and electrocortical effects of neurofeedback training and transcutaneous electro-acustimulation in healthy humans. Possible implications of these findings and suggestions for future research are considered

Investigating the role of Gamma-aminobutyric acid (GABA) in sedation: a combinedelectrophysiological, haemodynamicand spectroscopic study in humans

A better understanding of the mechanisms of anaesthesia and sedation are expected not only to improve the understanding of the neural correlates of consciousness but also to help improve safety from the complications of anaesthesia/ sedation and develop safer drugs and objective brain function monitoring systems. Neuroimaging modalities such as functional MRI, magnetoencephalography and MR spectroscopy provide complimentary information about brain functions and can help interrogate brain activity in a living human brain. Most anaesthetic drugs act by enhancing the inhibitory actions of GABA in the brain. Most neuroimaging research has focused on anaesthetic-induced unconsciousness, with only few investigating the earliest levels of sedation-induced altered consciousness. The work in this thesis used a range of advanced neuroimaging modalities to investigate the role of GABA (through a GABA-ergic drug, propofol), during mild sedation, in humans. This was performed as a series of experiments within two, sequential, scanning sessions, MEG followed by fMRI, in the same participants. Propofol resulted in a dissociation of the visual gamma band response (decreased evoked, increased induced power). This was related to a reduced BOLD fMRI response but there were no changes in MRS detectable GABA concentration. Response to multisensory stimulation also revealed interesting changes with MEG and fMRI. Functional connectivity analyses showed changes in connectivities of the posterior cingulate cortex (key hub of default-mode network) and thalamus with each other and other key brain regions. Resting state networks were identified with MEG too, which revealed interesting increases in connectivity in certain band- limited networks while motor networks showed no change. Perfusion fMRI using arterial spin labelling revealed a global and regional reduction in perfusion, highlighting some of the key regions (frontal cortex, precuenus, PCC and thalamus) involved in sedation