Algorithmic procedures for Bayesian MEG/EEG source reconstruction in SPM

AbstractThe MEG/EEG inverse problem is ill-posed, giving different source reconstructions depending on the initial assumption sets. Parametric Empirical Bayes allows one to implement most popular MEG/EEG inversion schemes (Minimum Norm, LORETA, etc.) within the same generic Bayesian framework. It also provides a cost-function in terms of the variational Free energy—an approximation to the marginal likelihood or evidence of the solution. In this manuscript, we revisit the algorithm for MEG/EEG source reconstruction with a view to providing a didactic and practical guide. The aim is to promote and help standardise the development and consolidation of other schemes within the same framework. We describe the implementation in the Statistical Parametric Mapping (SPM) software package, carefully explaining each of its stages with the help of a simple simulated data example. We focus on the Multiple Sparse Priors (MSP) model, which we compare with the well-known Minimum Norm and LORETA models, using the negative variational Free energy for model comparison. The manuscript is accompanied by Matlab scripts to allow the reader to test and explore the underlying algorithm

Testing covariance models for MEG source reconstruction of hippocampal activity

Beamforming is one of the most commonly used source reconstruction methods for magneto- and electroencephalography (M/EEG). One underlying assumption, however, is that distant sources are uncorrelated and here we tested whether this is an appropriate model for the human hippocampal data. We revised the Empirical Bayesian Beamfomer (EBB) to accommodate specific a-priori correlated source models. We showed in simulation that we could use model evidence (as approximated by Free Energy) to distinguish between different correlated and uncorrelated source scenarios. Using group MEG data in which the participants performed a hippocampal-dependent task, we explored the possibility that the hippocampus or the cortex or both were correlated in their activity across hemispheres. We found that incorporating a correlated hippocampal source model significantly improved model evidence. Our findings help to explain why, up until now, the majority of MEG-reported hippocampal activity (typically making use of beamformers) has been estimated as unilateral

The impact of MEG source reconstruction method on source-space connectivity estimation: A comparison between minimum-norm solution and beamforming.

Despite numerous important contributions, the investigation of brain connectivity with magnetoencephalography (MEG) still faces multiple challenges. One critical aspect of source-level connectivity, largely overlooked in the literature, is the putative effect of the choice of the inverse method on the subsequent cortico-cortical coupling analysis. We set out to investigate the impact of three inverse methods on source coherence detection using simulated MEG data. To this end, thousands of randomly located pairs of sources were created. Several parameters were manipulated, including inter- and intra-source correlation strength, source size and spatial configuration. The simulated pairs of sources were then used to generate sensor-level MEG measurements at varying signal-to-noise ratios (SNR). Next, the source level power and coherence maps were calculated using three methods (a) L2-Minimum-Norm Estimate (MNE), (b) Linearly Constrained Minimum Variance (LCMV) beamforming, and (c) Dynamic Imaging of Coherent Sources (DICS) beamforming. The performances of the methods were evaluated using Receiver Operating Characteristic (ROC) curves. The results indicate that beamformers perform better than MNE for coherence reconstructions if the interacting cortical sources consist of point-like sources. On the other hand, MNE provides better connectivity estimation than beamformers, if the interacting sources are simulated as extended cortical patches, where each patch consists of dipoles with identical time series (high intra-patch coherence). However, the performance of the beamformers for interacting patches improves substantially if each patch of active cortex is simulated with only partly coherent time series (partial intra-patch coherence). These results demonstrate that the choice of the inverse method impacts the results of MEG source-space coherence analysis, and that the optimal choice of the inverse solution depends on the spatial and synchronization profile of the interacting cortical sources. The insights revealed here can guide method selection and help improve data interpretation regarding MEG connectivity estimation

Data?driven model optimization for optically pumped magnetometer sensor arrays

© 2019 The Authors. Human Brain Mapping published by Wiley Periodicals, Inc. Optically pumped magnetometers (OPMs) have reached sensitivity levels that make them viable portable alternatives to traditional superconducting technology for magnetoencephalography (MEG). OPMs do not require cryogenic cooling and can therefore be placed directly on the scalp surface. Unlike cryogenic systems, based on a well-characterised fixed arrays essentially linear in applied flux, OPM devices, based on different physical principles, present new modelling challenges. Here, we outline an empirical Bayesian framework that can be used to compare between and optimise sensor arrays. We perturb the sensor geometry (via simulation) and with analytic model comparison methods estimate the true sensor geometry. The width of these perturbation curves allows us to compare different MEG systems. We test this technique using simulated and real data from SQUID and OPM recordings using head-casts and scanner-casts. Finally, we show that given knowledge of underlying brain anatomy, it is possible to estimate the true sensor geometry from the OPM data themselves using a model comparison framework. This implies that the requirement for accurate knowledge of the sensor positions and orientations a priori may be relaxed. As this procedure uses the cortical manifold as spatial support there is no co-registration procedure or reliance on scalp landmarks

A unified view on beamformers for M/EEG source reconstruction

Beamforming is a popular method for functional source reconstruction using magnetoencephalography (MEG) and electroencephalography (EEG) data. Beamformers, which were first proposed for MEG more than two decades ago, have since been applied in hundreds of studies, demonstrating that they are a versatile and robust tool for neuroscience. However, certain characteristics of beamformers remain somewhat elusive and there currently does not exist a unified documentation of the mathematical underpinnings and computational subtleties of beamformers as implemented in the most widely used academic open source software packages for MEG analysis (Brainstorm, FieldTrip, MNE, and SPM). Here, we provide such documentation that aims at providing the mathematical background of beamforming and unifying the terminology. Beamformer implementations are compared across toolboxes and pitfalls of beamforming analyses are discussed. Specifically, we provide details on handling rank deficient covariance matrices, prewhitening, the rank reduction of forward fields, and on the combination of heterogeneous sensor types, such as magnetometers and gradiometers. The overall aim of this paper is to contribute to contemporary efforts towards higher levels of computational transparency in functional neuroimaging

Sedation Modulates Frontotemporal Predictive Coding Circuits and the Double Surprise Acceleration Effect.

Two important theories in cognitive neuroscience are predictive coding (PC) and the global workspace (GW) theory. A key research task is to understand how these two theories relate to one another, and particularly, how the brain transitions from a predictive early state to the eventual engagement of a brain-scale state (the GW). To address this question, we present a source-localization of EEG responses evoked by the local-global task-an experimental paradigm that engages a predictive hierarchy, which encompasses the GW. The results of our source reconstruction suggest three phases of processing. The first phase involves the sensory (here auditory) regions of the superior temporal lobe and predicts sensory regularities over a short timeframe (as per the local effect). The third phase is brain-scale, involving inferior frontal, as well as inferior and superior parietal regions, consistent with a global neuronal workspace (GNW; as per the global effect). Crucially, our analysis suggests that there is an intermediate (second) phase, involving modulatory interactions between inferior frontal and superior temporal regions. Furthermore, sedation with propofol reduces modulatory interactions in the second phase. This selective effect is consistent with a PC explanation of sedation, with propofol acting on descending predictions of the precision of prediction errors; thereby constraining access to the GNW.University if Kent Internal Funds to Dr. Bowma

Updating dynamic noise models with moving magnetoencephalographic (MEG) systems

Optically pumped magnetometers have opened many possibilities for the study of human brain function using wearable moveable technology. In order to fully exploit this capability, a stable low-field environment at the sensors is required. One way to achieve this is to predict (and compensate for) changes in the ambient magnetic field as the subject moves through the room. The ultimate aim is to account for dynamically changing noise environments by updating a model based on measurements from a moving sensor array. We begin by demonstrating how an appropriate environmental spatial noise model can be developed through Free-energy based model selection. We then develop a Kalman-filter based strategy to account for dynamically changing interference. We demonstrate how such a method could not only provide realistic estimates of interfering signals when the sensors are moving, but also provide powerful predictive performance (at a fixed point within the room) when both sensors and sources of interference are in motion

Predictive decoding of neural data

In the last five decades the number of techniques available for non-invasive functional imaging has increased dramatically. Researchers today can choose from a variety of imaging modalities that include EEG, MEG, PET, SPECT, MRI, and fMRI. This doctoral dissertation offers a methodology for the reliable analysis of neural data at different levels of investigation. By using statistical learning algorithms the proposed approach allows single-trial analysis of various neural data by decoding them into variables of interest. Unbiased testing of the decoder on new samples of the data provides a generalization assessment of decoding performance reliability. Through consecutive analysis of the constructed decoder\u27s sensitivity it is possible to identify neural signal components relevant to the task of interest. The proposed methodology accounts for covariance and causality structures present in the signal. This feature makes it more powerful than conventional univariate methods which currently dominate the neuroscience field. Chapter 2 describes the generic approach toward the analysis of neural data using statistical learning algorithms. Chapter 3 presents an analysis of results from four neural data modalities: extracellular recordings, EEG, MEG, and fMRI. These examples demonstrate the ability of the approach to reveal neural data components which cannot be uncovered with conventional methods. A further extension of the methodology, Chapter 4 is used to analyze data from multiple neural data modalities: EEG and fMRI. The reliable mapping of data from one modality into the other provides a better understanding of the underlying neural processes. By allowing the spatial-temporal exploration of neural signals under loose modeling assumptions, it removes potential bias in the analysis of neural data due to otherwise possible forward model misspecification. The proposed methodology has been formalized into a free and open source Python framework for statistical learning based data analysis. This framework, PyMVPA, is described in Chapter 5

Brain Activity Mapping from MEG Data via a Hierarchical Bayesian Algorithm with Automatic Depth Weighting

A recently proposed iterated alternating sequential (IAS) MEG inverse solver algorithm, based on the coupling of a hierarchical Bayesian model with computationally efficient Krylov subspace linear solver, has been shown to perform well for both superficial and deep brain sources. However, a systematic study of its ability to correctly identify active brain regions is still missing. We propose novel statistical protocols to quantify the performance of MEG inverse solvers, focusing in particular on how their accuracy and precision at identifying active brain regions. We use these protocols for a systematic study of the performance of the IAS MEG inverse solver, comparing it with three standard inversion methods, wMNE, dSPM, and sLORETA. To avoid the bias of anecdotal tests towards a particular algorithm, the proposed protocols are Monte Carlo sampling based, generating an ensemble of activity patches in each brain region identified in a given atlas. The performance in correctly identifying the active areas is measured by how much, on average, the reconstructed activity is concentrated in the brain region of the simulated active patch. The analysis is based on Bayes factors, interpreting the estimated current activity as data for testing the hypothesis that the active brain region is correctly identified, versus the hypothesis of any erroneous attribution. The methodology allows the presence of a single or several simultaneous activity regions, without assuming that the number of active regions is known. The testing protocols suggest that the IAS solver performs well with both with cortical and subcortical activity estimation