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There has been an increasing interest in examining organisational principles of the cerebral cortex (and subcortical regions) using different MRI features such as structural or functional connectivity. Despite the widespread interest, introductory tutorials on the underlying technique targeted for the novice neuroimager are sparse in the literature. Articles that investigate various "neural gradients" (for example based on region studied "cortical gradients," "cerebellar gradients," "hippocampal gradients" etc … or feature of interest "functional gradients," "cytoarchitectural gradients," "myeloarchitectural gradients" etc …) have increased in popularity. Thus, we believe that it is opportune to discuss what is generally meant by "gradient analysis". We introduce basics concepts in graph theory, such as graphs themselves, the degree matrix, and the adjacency matrix. We discuss how one can think about gradients of feature similarity (the similarity between timeseries in fMRI, or streamline in tractography) using graph theory and we extend this to explore such gradients across the whole MRI scale; from the voxel level to the whole brain level. We proceed to introduce a measure for quantifying the level of similarity in regions of interest. We propose the term "the Vogt-Bailey index" for such quantification to pay homage to our history as a brain mapping community. We run through the techniques on sample datasets including a brain MRI as an example of the application of the techniques on real data and we provide several appendices that expand upon details. To maximise intuition, the appendices contain a didactic example describing how one could use these techniques to solve a particularly pernicious problem that one may encounter at a wedding. Accompanying the article is a tool, available in both MATLAB and Python, that enables readers to perform the analysis described in this article on their own data. We refer readers to the graphical abstract as an overview of the analysis pipeline presented in this work., Competing Interests: Declaration of competing interest GJMP is a shareholder and director of Bioxydyn, a company with an interest in imaging services and products., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: There is amassing evidence that risky decision-making in bipolar disorder is related to reward-based differences in frontostriatal regions. However, the roles of early attentional and later cognitive processes remain unclear, limiting theoretical understanding and development of targeted interventions., Methods: Twenty euthymic bipolar disorder and 19 matched control participants played a Roulette task in which they won and lost money. Event-related potentials and source analysis were used to quantify predominantly sensory-attentional (N1), motivational salience (feedback-related negativities [FRN]), and cognitive appraisal (P300) stages of processing. We predicted that the bipolar disorder group would show increased N1, consistent with increased attentional orienting, and reduced FRN, consistent with a bias to perceive outcomes more favorably., Results: As predicted, the bipolar disorder group showed increased N1 and reduced FRN but no differences in P300. N1 amplitude was additionally associated with real-life risk taking, and N1 source activity was reduced in visual cortex but increased activity in precuneus, frontopolar, and premotor cortex, compared to those of controls., Conclusions: These findings demonstrate an early attentional bias to reward that potentially drives risk taking by priming approach behavior and elevating reward salience in the frontostriatal pathway. Although later cognitive appraisals of these inputs may be relatively intact in remission, interventions targeting attention orienting may also be effective in long-term reduction of relapse., (Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.)

We analyze the functional significance of different event-related potentials (ERPs) as electrophysiological indices of face perception and face recognition, according to cognitive and neurofunctional models of face processing. Initially, the processing of faces seems to be supported by early extrastriate occipital cortices and revealed by modulations of the occipital P1. This early response is thought to reflect the detection of certain primary structural aspects indicating the presence grosso modo of a face within the visual field. The posterior-temporal N170 is more sensitive to the detection of faces as complex-structured stimuli and, therefore, to the presence of its distinctive organizational characteristics prior to within-category identification. In turn, the relatively late and probably more rostrally generated N250r and N400-like responses might respectively indicate processes of access and retrieval of face-related information, which is stored in long-term memory (LTM). New methods of analysis of electrophysiological and neuroanatomical data, namely, dynamic causal modeling, single-trial and time-frequency analyses, are highly recommended to advance in the knowledge of those brain mechanisms concerning face processing.

We introduce a new generative model of the Encephalography (EEG/MEG) data, the inversion of which allows for inferring the locations and temporal evolution of the underlying sources as well as their dynamical interactions. The proposed Switching Mesostate Space Model (SMSM) builds on the multi-scale generative model for EEG/MEG by Daunizeau and Friston (2007). SMSM inherits the assumptions that (1) bioelectromagnetic activity is generated by a set of distributed sources, (2) the dynamics of these sources can be modelled as random fluctuations about a small number of mesostates, and (3) the number of mesostates engaged by a cognitive task is small. Additionally, four generalising assumptions are now included: (4) the mesostates interact according to a full Dynamical Causal Network (DCN) that can be estimated; (5) the dynamics of the mesostates can switch between multiple approximately linear operating regimes; (6) each operating regime remains stable over finite periods of time (temporal clusters); and (7) the total number of times the mesostates' dynamics can switch is small. The proposed model adds, therefore, a level of flexibility by accommodating complex brain processes that cannot be characterised by purely linear and stationary Gaussian dynamics. Importantly, the SMSM furnishes a new interpretation of the EEG/MEG data in which the source activity may have multiple discrete modes of behaviour, each with approximately linear dynamics. This is modelled by assuming that the connection strengths of the underlying mesoscopic DCN are time-dependent but piecewise constant, i.e. they can undergo discrete changes over time. A Variational Bayes inversion scheme is derived to estimate all the parameters of the model by maximising a (Negative Free Energy) lower bound on the model evidence. This bound is used to select among different model choices that are defined by the number of mesostates as well as by the number of stationary linear regimes. The full model is compared to a simplified version that uses no dynamical assumptions as well as to a standard EEG inversion technique. The comparison is carried out using an extensive set of simulations, and the application of SMSM to a real data set is also demonstrated. Our results show that for experimental situations in which we have some a priori belief that there are multiple approximately linear dynamical regimes, the proposed SMSM provides a natural modelling tool., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Electrophysiological (EEG/MEG) imaging challenges statistics by providing two views of the same underlying spatio-temporal brain activity: a topographic view (EEG/MEG) and tomographic view (EEG/MEG source reconstructions). It is a common practice that statistical parametric mapping (SPM) for these two situations is developed separately. In particular, assessing statistical significance of functional connectivity is a major challenge in these types of studies. This work introduces statistical tests for assessing simultaneously the significance of spatio-temporal correlation structure between ERP/ERF components as well as that of their generating sources. We introduce a greatest root statistic as the multivariate test statistic for detecting functional connectivity between two sets of EEG/MEG measurements at a given time instant. We use some new results in random field theory to solve the multiple comparisons problem resulting from the correlated test statistics at each time instant. In general, our approach using the union-intersection (UI) principle provides a framework for hypothesis testing about any linear combination of sensor data, which allows the analysis of the correlation structure of both topographic and tomographic views. The performance of the proposed method is illustrated with real ERP data obtained from a face recognition experiment., ((c) 2009 Wiley-Liss, Inc.)

This paper extends a previously formulated deterministic metabolic/hemodynamic model for the generation of blood oxygenated level dependent (BOLD) responses to include both physiological and observation stochastic components (sMHM). This adds a degree of flexibility when fitting the model to actual data by accounting for un-modelled activity. We then show how the innovation method can be used to estimate unobserved metabolic/hemodynamic as well as vascular variables of the sMHM, from simulated and actual BOLD data. The proposed estimation method allowed for doing model comparison by calculating the model's AIC and BIC. This methodology was then used to select between different neurovascular coupling assumptions underlying sMHM. The proposed framework was first validated on simulations and then applied to BOLD data from a motor task experiment. The models under comparison in the analysis of the actual data considered that vascular response was coupled to: (I) inhibition, (II) excitation, (III) both excitation and inhibition. Data was best described by model II, although model III was also supported.

When something appears, how soon is the first neural correlate of awareness of it, and where is that activity in the brain? To answer these questions, we measured the electroencephalogram under conditions in which visual stimuli changed identically but in which awareness differed. We manipulated awareness by using binocular rivalry between orthogonal gratings viewed one to each eye. Then we changed the orientation of the grating to one eye to be the same as that to the other eye. Because of the rivalry, sometimes this happened to the visible grating, producing a clear change in perceived orientation, and other times it happened to the invisible grating, producing no change in perceived orientation. This procedure allowed us to analyze time-locked topographic scalp and tomographic primary current densities of the event-related potentials to physically identical events differing in their perceptual consequences. When the change in orientation reached awareness, neural responses began at about 100 ms, spreading mainly from dorsal occipital areas. When the change in orientation did not reach awareness, neural responses also began at about 100 ms, but they were attenuated, particularly in the right fusiform gyrus. We place the earliest correlate of visual awareness following binocular rivalry in the ventrolateral occipitotemporal cortex.

Our goal is to model the coupling between neuronal activity, cerebral metabolic rates of glucose and oxygen consumption, cerebral blood flow (CBF), electroencephalography (EEG) and blood oxygenation level-dependent (BOLD) responses. In order to accomplish this, two previous models are coupled: a metabolic/hemodynamic model (MHM) for a voxel, linking BOLD signals and neuronal activity, and a neural mass model describing the neuronal dynamics within a voxel and its interactions with voxels of the same area (short-range interactions) and other areas (long-range interactions). For coupling both models, we take as the input to the BOLD model, the number of active synapses within the voxel, that is, the average number of synapses that will receive an action potential within the time unit. This is obtained by considering the action potentials transmitted between neuronal populations within the voxel, as well as those arriving from other voxels. Simulations are carried out for testing the integrated model. Results show that realistic evoked potentials (EP) at electrodes on the scalp surface and the corresponding BOLD signals for each voxel are produced by the model. In another simulation, the alpha rhythm was reproduced and reasonable similarities with experimental data were obtained when calculating correlations between BOLD signals and the alpha power curve. The origin of negative BOLD responses and the characteristics of EEG, PET and BOLD signals in Alzheimer's disease were also studied.

The formation of cortical object representations requires the activation of cell assemblies, correlated by induced oscillatory bursts of activity > 20 Hz (induced gamma band responses; iGBRs). One marker of the functional dynamics within such cell assemblies is the suppression of iGBRs elicited by repeated stimuli. This effect is commonly interpreted as a signature of 'sharpening' processes within cell-assemblies, which are behaviourally mirrored in repetition priming effects. The present study investigates whether the sharpening of primed objects is an automatic consequence of repeated stimulus processing, or whether it depends on task demands. Participants performed either a 'living/non-living' or a 'bigger/smaller than a shoebox' classification on repeated pictures of everyday objects. We contrasted repetition-related iGBR effects after the same task was used for initial and repeated presentations (no-switch condition) with repetitions after a task-switch occurred (switch condition). Furthermore, we complemented iGBR analysis by examining other brain responses known to be modulated by repetition-related memory processes (evoked gamma oscillations and event-related potentials; ERPs). The results obtained for the 'no-switch' condition replicated previous findings of repetition suppression of iGBRs at 200-300 ms after stimulus onset. Source modelling showed that this effect was distributed over widespread cortical areas. By contrast, after a task-switch no iGBR suppression was found. We concluded that iGBRs reflect the sharpening of a cell assembly only within the same task. After a task switch the complete object representation is reactivated. The ERP (220-380 ms) revealed suppression effects independent of task demands in bilateral posterior areas and might indicate correlates of repetition priming in perceptual structures.

In order to keep track of potentially relevant information in the acoustic environment, the human brain processes sounds to a high extent even when they are not attended: it extracts basic features, encodes regularities, and detects deviances. Here, we deliver evidence that the initial 300 ms of a sound contribute more to this preattentive processing than the sound's later parts. We directly compared the influence of the temporal distance relative to sound onset on the processing of the sound's duration and frequency information. The mismatch negativity (MMN), an event-related potential indicator for preattentive feature encoding and deviance detection, was measured for infrequent duration deviants and frequency modulation deviants. The onset of either deviancy was at 100, 200, 300, or 400 ms relative to sound onset. MMN was only elicited for deviations occurring within the first 300 ms after sound onset for both types of deviants. Its neural sources were localized in supra-temporal cortices with source current density analyses (SCD) and variable resolution electromagnetic tomography (VARETA), revealing a right-hemispheric preponderance for frequency modulations but not for duration shortenings. This suggests that preattentive deviance detection is based upon partly diverging functional memory registers for temporal and dynamic spectral information. The influence of temporal distance on MMN in both conditions supports the view that temporal and spectral sound properties are integrated into an auditory object representation prior to preattentive deviance detection. Importantly, the decline of MMN to unattended sounds with larger temporal distance suggests that parts beyond 300 ms are less important for preattentive auditory object representation.

The formation of cortical object representations requires the activation of cell assemblies, correlated by induced oscillatory bursts above 20 Hz (gamma band), which are characterized by trial-by-trial latency fluctuations around a mean of approximately 300 ms after stimulus onset. The present electroencephalogram (EEG) study was intended to uncover to the generators of induced gamma band responses (GBRs) and to analyze phase-synchronization between these sources. A standard object recognition task was used to elicit gamma activity. At the scalp surface (electrode space), we found an augmentation of induced GBRs after the presentation of meaningful (familiar) as opposed to meaningless (unfamiliar) stimuli, which was accompanied by a dense pattern of significant phase-locking values between distant recording sites. Subsequently, intracranial current density distributions compatible with the observed scalp voltage topographies were estimated by means of VARETA (Variable Resolution Electromagnetic Tomography). In source space brain electrical tomographies (BETs) revealed widespread generators of induced GBRs at temporal, parietal, posterior, and frontal areas. Phase-locking analysis was calculated between re-constructed electrode signals based on separate forward solutions of the observed generators, thereby eliminating the possibly confounding influence of activity from areas not under observation. The results support the view that induced GBRs signify synchronous neuronal activity in a broadly distributed network during object recognition. The localization of the generators of event-related potentials (ERPs), evoked gamma activity, and induced alpha activity revealed different sources as compared to the induced GBR and, thus, seem to mirror complementary functions during the present task as compared to induced high-frequency brain dynamics.

We describe a Bayesian estimation and inference procedure for fMRI time series based on the use of General Linear Models (GLMs). Importantly, we use a spatial prior on regression coefficients which embodies our prior knowledge that evoked responses are spatially contiguous and locally homogeneous. Further, using a computationally efficient Variational Bayes framework, we are able to let the data determine the optimal amount of smoothing. We assume an arbitrary order Auto-Regressive (AR) model for the errors. Our model generalizes earlier work on voxel-wise estimation of GLM-AR models and inference in GLMs using Posterior Probability Maps (PPMs). Results are shown on simulated data and on data from an event-related fMRI experiment.

In this paper, the Bayesian Theory is used to formulate the Inverse Problem (IP) of the EEG/MEG. This formulation offers a comparison framework for the wide range of inverse methods available and allows us to address the problem of model uncertainty that arises when dealing with different solutions for a single data. In this case, each model is defined by the set of assumptions of the inverse method used, as well as by the functional dependence between the data and the Primary Current Density (PCD) inside the brain. The key point is that the Bayesian Theory not only provides for posterior estimates of the parameters of interest (the PCD) for a given model, but also gives the possibility of finding posterior expected utilities unconditional on the models assumed. In the present work, this is achieved by considering a third level of inference that has been systematically omitted by previous Bayesian formulations of the IP. This level is known as Bayesian model averaging (BMA). The new approach is illustrated in the case of considering different anatomical constraints for solving the IP of the EEG in the frequency domain. This methodology allows us to address two of the main problems that affect linear inverse solutions (LIS): (a) the existence of ghost sources and (b) the tendency to underestimate deep activity. Both simulated and real experimental data are used to demonstrate the capabilities of the BMA approach, and some of the results are compared with the solutions obtained using the popular low-resolution electromagnetic tomography (LORETA) and its anatomically constraint version (cLORETA).

Neural oscillations occur within a wide frequency range with different brain regions exhibiting resonance-like characteristics at specific points in the spectrum. At the microscopic scale, single neurons possess intrinsic oscillatory properties, such that is not yet known whether cortical resonance is consequential to neural oscillations or an emergent property of the networks that interconnect them. Using a network model of loosely-coupled Wilson-Cowan oscillators to simulate a patch of cortical sheet, we demonstrate that the size of the activated network is inversely related to its resonance frequency. Further analysis of the parameter space indicated that the number of excitatory and inhibitory connections, as well as the average transmission delay between units, determined the resonance frequency. The model predicted that if an activated network within the visual cortex increased in size, the resonance frequency of the network would decrease. We tested this prediction experimentally using the steady-state visual evoked potential where we stimulated the visual cortex with different size stimuli at a range of driving frequencies. We demonstrate that the frequency corresponding to peak steady-state response inversely correlated with the size of the network. We conclude that although individual neurons possess resonance properties, oscillatory activity at the macroscopic level is strongly influenced by network interactions, and that the steady-state response can be used to investigate functional networks. [ABSTRACT FROM AUTHOR]

We study the generation of EEG rhythms by means of realistically coupled neural mass models. Previous neural mass models were used to model cortical voxels and the thalamus. Interactions between voxels of the same and other cortical areas and with the thalamus were taken into account. Voxels within the same cortical area were coupled (short-range connections) with both excitatory and inhibitory connections, while coupling between areas (long-range connections) was considered to be excitatory only. Short-range connection strengths were modeled by using a connectivity function depending on the distance between voxels. Coupling strength parameters between areas were defined from empirical anatomical data employing the information obtained from probabilistic paths, which were tracked by water diffusion imaging techniques and used to quantify white matter tracts in the brain. Each cortical voxel was then described by a set of 16 random differential equations, while the thalamus was described by a set of 12 random differential equations. Thus, for analyzing the neuronal dynamics emerging from the interaction of several areas, a large system of differential equations needs to be solved. The sparseness of the estimated anatomical connectivity matrix reduces the number of connection parameters substantially, making the solution of this system faster. Simulations of human brain rhythms were carried out in order to test the model. Physiologically plausible results were obtained based on this anatomically constrained neural mass model. [ABSTRACT FROM AUTHOR]