Model-free analysis of brain fMRI data by recurrence quantification

Resolving heterogeneity in dynamics of synchronization stability within the salience network in autism spectrum disorder

BACKGROUND

Heterogeneity in resting-state functional connectivity (FC) are one of the characteristics of autism spectrum disorder (ASD). Traditional resting-state FC primarily focuses on linear correlations, ignoring the nonlinear properties involved in synchronization between networks or brain regions.

METHODS

In the present study, the cross-recurrence quantification analysis, a nonlinear method based on dynamical systems, was utilized to quantify the synchronization stability between brain regions within the salience network (SN) of ASD. Using the resting-state functional magnetic resonance imaging data of 207 children (ASD/typically-developing controls (TC): 105/102) in Autism Brain Imaging Data Exchange database, we analyzed the laminarity and trapping time differences of the synchronization stability between the ASD subtype derived by a K-means clustering analysis and the TC group, and examined the relationship between synchronization stability and the severity of clinical symptoms of the ASD subtypes.

RESULTS

Based on the synchronization stability within the SN of ASD, we identified two subtypes that showed opposite changes in synchronization stability relative to the TC group. In addition, the synchronization stability of ASD subtypes 1 and 2 can predict the social interaction and communication impairments, respectively.

CONCLUSIONS

These findings reveal that ASD subgroups with different patterns of synchronization stability within the SN appear distinct clinical symptoms, and highlight the importance of exploring the potential neural mechanism of ASD from a nonlinear perspective.

Corticomuscular cross-recurrence analysis reveals between-limb differences in motor control among individuals with ACL reconstruction

Surgical reconstruction of the anterior cruciate ligament (ACL) and subsequent physical therapy can help athletes return to competition; however, re-injury rates remain disproportionately high due, in part, to lingering biomechanical and neurological factors that are not fully addressed during rehabilitation. Prior reports indicate that individuals exhibit altered electrical activity in both brain and muscle after ACL reconstruction (ACLR). In this investigation, we aimed to extend existing approaches by introducing a novel non-linear analysis of corticomuscular dynamics, which does not assume oscillatory coupling between brain and muscle: Corticomuscular cross-recurrence analysis (CM-cRQA). Our findings indicate that corticomuscular dynamics vary significantly between involved (injured) and uninvolved legs of participants with ACLR during voluntary isometric contractions between the brain and both the vastus medialis and lateralis. This finding points to a potential lingering neural deficit underlying re-injury for athletes after surgical reconstruction, namely the dynamical structure of neuromuscular (brain to quad muscle) coordination, which is significantly asymmetric, between limbs, in those who have ACLR.

Altered hippocampal connectivity dynamics predicts memory performance in neuropsychiatric lupus: a resting-state fMRI study using cross-recurrence quantification analysis

OBJECTIVE

Τo determine whole-brain and regional functional connectivity (FC) characteristics of patients with neuropsychiatric SLE (NPSLE) or without neuropsychiatric manifestations (non-NPSLE) and examine their association with cognitive performance.

METHODS

Cross-recurrence quantification analysis (CRQA) of resting-state functional MRI (rs-fMRI) data was performed in 44 patients with NPSLE, 20 patients without NPSLE and 35 healthy controls (HCs). Volumetric analysis of total brain and specific cortical and subcortical regions, where significant connectivity changes were identified, was performed. Cognitive status of patients with NPSLE was assessed by neuropsychological tests. Group comparisons on nodal FC, global network metrics and regional volumetrics were conducted, and associations with cognitive performance were estimated (at p<0.05 false discovery rate corrected).

RESULTS

FC in patients with NPSLE was characterised by increased modularity (mean (SD)=0.31 (0.06)) as compared with HCs (mean (SD)=0.27 (0.06); p=0.05), hypoconnectivity of the left (mean (SD)=0.06 (0.018)) and right hippocampi (mean (SD)=0.051 (0.0.16)), and of the right amygdala (mean (SD)=0.091 (0.039)), as compared with HCs (mean (SD)=0.075 (0.022), p=0.02; 0.065 (0.019), p=0.01; 0.14 (0.096), p=0.05, respectively). Hyperconnectivity of the left angular gyrus (NPSLE/HCs: mean (SD)=0.29 (0.26) and 0.10 (0.09); p=0.01), left (NPSLE/HCs: mean (SD)=0.16 (0.09) and 0.09 (0.05); p=0.01) and right superior parietal lobule (SPL) (NPSLE/HCs: mean (SD)=0.25 (0.19) and 0.13 (0.13), p=0.01) was noted in NPSLE versus HC groups. Among patients with NPSLE, verbal episodic memory scores were positively associated with connectivity (local efficiency) of the left hippocampus (r²=0.22, p=0.005) and negatively with local efficiency of the left angular gyrus (r²=0.24, p=0.003). Patients without NPSLE displayed hypoconnectivity of the right hippocampus (mean (SD)=0.056 (0.014)) and hyperconnectivity of the left angular gyrus (mean (SD)=0.25 (0.13)) and SPL (mean (SD)=0.17 (0.12)).

CONCLUSION

By using dynamic CRQA of the rs-fMRI data, distorted FC was found globally, as well as in medial temporal and parietal brain regions in patients with SLE, that correlated significantly and adversely with memory capacity in NPSLE. These results highlight the value of dynamic approaches to assessing impaired brain network function in patients with lupus with and without neuropsychiatric symptoms.

Early Warning Signals in Phase Space: Geometric Resilience Loss Indicators From Multiplex Cumulative Recurrence Networks

The detection of Early Warning Signals (EWS) of imminent phase transitions, such as sudden changes in symptom severity could be an important innovation in the treatment or prevention of disease or psychopathology. Recurrence-based analyses are known for their ability to detect differences in behavioral modes and order transitions in extremely noisy data. As a proof of principle, the present paper provides an example of a recurrence network based analysis strategy which can be implemented in a clinical setting in which data from an individual is continuously monitored for the purpose of making decisions about diagnosis and intervention. Specifically, it is demonstrated that measures based on the geometry of the phase space can serve as Early Warning Signals of imminent phase transitions. A publicly available multivariate time series is analyzed using so-called cumulative Recurrence Networks (cRN), which are recurrence networks with edges weighted by recurrence time and directed towards previously observed data points. The results are compared to previous analyses of the same data set, benefits, limitations and future directions of the analysis approach are discussed.

Studying the functional connectivity of the primary motor cortex with the binarized cross recurrence plot: The influence of Parkinson's disease

Two new recurrence plot methods (the binary recurrence plot and binary cross recurrence plot) were introduced here to study the long-term dynamic of the primary motor cortex and its interaction with the primary somatosensory cortex, the anterior motor thalamus of the basal ganglia motor loop and the precuneous nucleus of the default mode network. These recurrence plot methods: 1. identify short-term transient interactions; 2. identify long-lasting delayed interactions that are common in complex systems; 3. work with non-stationary blood oxygen level dependent (BOLD) data; 4. may study the relationship of centers with non-linear functional interactions; 5 may compare different experimental groups performing different tasks. These methods were applied to BOLD time-series obtained in 20 control subjects and 20 Parkinson´s patients during the execution of motor activity and body posture tasks (task-block design). The binary recurrence plot showed the task-block BOLD response normally observed in the primary motor cortex with functional magnetic resonance imaging methods, but also shorter and longer BOLD-fluctuations than the task-block and which provided information about the long-term dynamic of this center. The binary cross recurrence plot showed short-lasting and long-lasting functional interactions between the primary motor cortex and the primary somatosensory cortex, anterior motor thalamus and precuneous nucleus, interactions which changed with the resting and motor tasks. Most of the interactions found in healthy controls were disrupted in Parkinson's patients, and may be at the basis of some of the motor disorders and side-effects of dopaminergic drugs commonly observed in these patients.

Parcellation of the human amygdala using recurrence quantification analysis

Several previous attempts have been made to divide the human amygdala into smaller subregions based on the unique functional properties of the subregions. Although these attempts have provided valuable insight into the functional heterogeneity in this structure, the possibility that spatial patterns of functional characteristics can quickly change over time has rarely been considered in previous studies. In the present study, we explicitly account for the dynamic nature of amygdala activity. Our goal was not only to develop another parcellation method but also to augment existing methods with novel information about amygdala subdivisions. We performed state-specific amygdala parcellation using resting-state fMRI (rsfMRI) data and recurrence quantification analysis (RQA). RsfMRI data from 102 subjects were acquired with a 3T Trio Siemens scanner. We analyzed values of several RQA measures across all voxels in the amygdala and found two amygdala subdivisions, the ventrolateral (VL) and dorsomedial (DM) subdivisions, that differ with respect to one of the RQA measures, Shannon's entropy of diagonal lines. Compared to the DM subdivision, the VL subdivision can be characterized by a higher value of entropy. The results suggest that VL activity is determined and influenced by more brain structures than is DM activity. To assess the biological validity of the obtained subdivisions, we compared them with histological atlases and currently available parcellations based on structural connectivity patterns (Anatomy Probability Maps) and cytoarchitectonic features (SPM Anatomy toolbox). Moreover, we examined their cortical and subcortical functional connectivity. The obtained results are similar to those previously reported on parcellation performed on the basis of structural connectivity patterns. Functional connectivity analysis revealed that the VL subdivision has strong connections to several cortical areas, whereas the DM subdivision is mainly connected to subcortical regions. This finding suggests that the VL subdivision corresponds to the basolateral subdivision of the amygdala (BLA), while the DM subdivision has some characteristics typical of the centromedial amygdala (CMA). The similarity in functional connectivity patterns between the VL subdivision and BLA, as well as between the DM subdivision and CMA, confirm the utility of our parcellation method. Overall, the study shows that parcellation based on BOLD signal dynamics is a powerful tool for identifying distinct functional systems within the amygdala. This tool might be useful for future research on functional brain organization.

Space-time recurrences for functional connectivity evaluation and feature extraction in motor imagery brain-computer interfaces

This work presents a classification performance comparison between different frameworks for functional connectivity evaluation and complex network feature extraction aiming to distinguish motor imagery classes in electroencephalography (EEG)-based brain-computer interfaces (BCIs). The analysis was performed in two online datasets: (1) a classical benchmark-the BCI competition IV dataset 2a-allowing a comparison with a representative set of strategies previously employed in this BCI paradigm and (2) a statistically representative dataset for signal processing technique comparisons over 52 subjects. Besides exploring three classical similarity measures-Pearson correlation, Spearman correlation, and mean phase coherence-this work also proposes a recurrence-based alternative for estimating EEG brain functional connectivity, which takes into account the recurrence density between pairwise electrodes over a time window. These strategies were followed by graph feature evaluation considering clustering coefficient, degree, betweenness centrality, and eigenvector centrality. The features were selected by Fisher's discriminating ratio and classification was performed by a least squares classifier in agreement with classical and online BCI processing strategies. The results revealed that the recurrence-based approach for functional connectivity evaluation was significantly better than the other frameworks, which is probably associated with the use of higher order statistics underlying the electrode joint probability estimation and a higher capability of capturing nonlinear inter-relations. There were no significant differences in performance among the evaluated graph features, but the eigenvector centrality was the best feature regarding processing time. Finally, the best ranked graph-based attributes were found in classical EEG motor cortex positions for the subjects with best performances, relating functional organization and motor activity. Graphical Abstract Evaluating functional connectivity based on Space-Time Recurrence Counting for motor imagery classification in brain-computer interfaces. Recurrences are evaluated between electrodes over a time window, and, after a density threshold, the electrodes adjacency matrix is stablish, leading to a graph. Graph-based topological measures are used for motor imagery classification.

Chaos-chaos transition of left hemisphere EEGs during standard tasks of Waterloo-Stanford Group Scale of hypnotic susceptibility

A recent study, recurrence quantification analysis of EEG signals during standard tasks of Waterloo-Stanford Group Scale of hypnotic susceptibility investigated recurrence quantifiers (RQs) of hypnotic electroencephalograph (EEG) signals recorded after hypnotic induction while subjects were doing standard tasks of Waterloo-Stanford Group Scale (WSGS) of hypnotic susceptibility to distinguish subjects of different hypnotizability levels. Following the same analysis, the current study determines the capability of different RQs to distinguish subjects of low, medium and high hypnotizability level and studies the influence of hypnotizability level on underlying dynamic of tasks. Besides, EEG channels were sorted according to the number of their RQs, which differed significantly among subjects of different hypnotizability levels. Another valuable result was determination of major brain regions in observing significant differences in various task types (ideomotors, hallucination, challenge and memory).

Classifying acoustic signals into phoneme categories: average and dyslexic readers make use of complex dynamical patterns and multifractal scaling properties of the speech signal

Several competing aetiologies of developmental dyslexia suggest that the problems with acquiring literacy skills are causally entailed by low-level auditory and/or speech perception processes. The purpose of this study is to evaluate the diverging claims about the specific deficient peceptual processes under conditions of strong inference. Theoretically relevant acoustic features were extracted from a set of artificial speech stimuli that lie on a /bAk/-/dAk/ continuum. The features were tested on their ability to enable a simple classifier (Quadratic Discriminant Analysis) to reproduce the observed classification performance of average and dyslexic readers in a speech perception experiment. The ‘classical’ features examined were based on component process accounts of developmental dyslexia such as the supposed deficit in Envelope Rise Time detection and the deficit in the detection of rapid changes in the distribution of energy in the frequency spectrum (formant transitions). Studies examining these temporal processing deficit hypotheses do not employ measures that quantify the temporal dynamics of stimuli. It is shown that measures based on quantification of the dynamics of complex, interaction-dominant systems (Recurrence Quantification Analysis and the multifractal spectrum) enable QDA to classify the stimuli almost identically as observed in dyslexic and average reading participants. It seems unlikely that participants used any of the features that are traditionally associated with accounts of (impaired) speech perception. The nature of the variables quantifying the temporal dynamics of the speech stimuli imply that the classification of speech stimuli cannot be regarded as a linear aggregate of component processes that each parse the acoustic signal independent of one another, as is assumed by the ‘classical’ aetiologies of developmental dyslexia. It is suggested that the results imply that the differences in speech perception performance between average and dyslexic readers represent a scaled continuum rather than being caused by a specific deficient component.

Recurrence quantification analysis of electroencephalograph signals during standard tasks of Waterloo-Stanford group scale of hypnotic susceptibility

The purpose of this study was to apply RQA (recurrence quantification analysis) on hypnotic electroencephalograph (EEG) signals recorded after hypnotic induction while subjects were doing standard tasks of the Waterloo-Stanford Group Scale (WSGS) of hypnotic susceptibility. Then recurrence quantifiers were used to analyse the influence of hypnotic depth on EEGs. By the application of this method, the capability of tasks to distinguish subjects of different hypnotizability levels was determined. Besides, medium hypnotizable subjects showed the highest disposition to be inducted by hypnotizer. Similarities between brain governing dynamics during tasks of the same type were also observed. The present study demonstrated two remarkable innovations; investigating the EEGs of the hypnotized as doing mental tasks of Waterloo-Stanford Group Scale (WSGS) and applying RQA on hypnotic EEGs.