fMRI-based Functional Connectivity Research Articles

Resting-State Functional Connectivity of the Primary Visual Cortex in Children with Anisometropia Amblyopia.

This study aimed to explore the functional connectivity of the primary visual cortex (V1) in children with anisometropic amblyopia by using the resting-state functional connectivity analysis method and determine whether anisometropic amblyopia is associated with changes in brain function. Functional magnetic resonance imaging (fMRI) data were obtained from 16 children with anisometropia amblyopia (CAA group) and 12 healthy children (HC group) during the resting state. The Brodmann area 17 (BA17) was used as the region of interest, and the functional connection (FC) of V1 was analyzed in both groups. A two-sample t test was used to analyze the FC value between the two groups. Pearson's correlation was used to analyze the correlation between the mean FC value in the brain function change area of the CAA group and the best corrected visual acuity (BCVA) of amblyopia. p < 0.05 was considered statistically significant. There were no significant differences in age and sex between the CAA and HC groups (p > 0.05). Compared to the HC group, the CAA group showed lower FC values in BA17 and the left medial frontal gyrus, as well as BA17 and the left triangle inferior frontal gyrus. Conversely, the CAA group showed higher FC values in BA17 and the left central posterior gyrus. Notably, BCVA in amblyopia did not correlate with the area of change in mean FC in the brain function of the CAA group. Resting-state fMRI-based functional connectivity analysis indicates a significant alteration in V1 of children with anisometropic amblyopia. These findings contribute additional insights into the neuropathological mechanisms underlying visual impairment in anisometropic amblyopia.

ImageNomer: Description of a functional connectivity and omics analysis tool and case study identifying a race confound

Most packages for the analysis of fMRI-based functional connectivity (FC) and genomic data are used with a programming language interface, lacking an easy-to-navigate GUI frontend. This exacerbates two problems found in these types of data: demographic confounds and quality control in the face of high dimensionality of features. The reason is that it is too slow and cumbersome to use a programming interface to create all the necessary visualizations required to identify all correlations, confounding effects, or quality control problems in a dataset. FC in particular usually contains tens of thousands of features per subject, and can only be summarized and efficiently explored using visualizations. To remedy this situation, we have developed ImageNomer, a data visualization and analysis tool that allows inspection of both subject-level and cohort-level demographic, genomic, and imaging features. The software is Python-based, runs in a self-contained Docker image, and contains a browser-based GUI frontend. We demonstrate the usefulness of ImageNomer by identifying an unexpected race confound when predicting achievement scores in the Philadelphia Neurodevelopmental Cohort (PNC) dataset, which contains multitask fMRI and single nucleotide polymorphism (SNP) data of healthy adolescents. In the past, many studies have attempted to use FC to identify achievement-related features in fMRI. Using ImageNomer to visualize trends in achievement scores between races, we find a clear potential for confounding effects if race can be predicted using FC. Using correlation analysis in the ImageNomer software, we show that FCs correlated with Wide Range Achievement Test (WRAT) score are in fact more highly correlated with race. Investigating further, we find that whereas both FC and SNP (genomic) features can account for 10–15% of WRAT score variation, this predictive ability disappears when controlling for race. We also use ImageNomer to investigate race-FC correlation in the Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP) dataset. In this work, we demonstrate the advantage of our ImageNomer GUI tool in data exploration and confound detection. Additionally, this work identifies race as a strong confound in FC data and casts doubt on the possibility of finding unbiased achievement-related features in fMRI and SNP data of healthy adolescents.

Classification of Alzheimer's Disease Using Maximal Information Coefficient-Based Functional Connectivity with an Extreme Learning Machine.

Alzheimer's disease (AD) is a progressive chronic illness that leads to cognitive decline and dementia. Neuroimaging technologies, such as functional magnetic resonance imaging (fMRI), and deep learning approaches offer promising avenues for AD classification. In this study, we investigate the use of fMRI-based functional connectivity (FC) measures, including the Pearson correlation coefficient (PCC), maximal information coefficient (MIC), and extended maximal information coefficient (eMIC), combined with extreme learning machines (ELM) for AD classification. Our findings demonstrate that employing non-linear techniques, such as MIC and eMIC, as features for classification yields accurate results. Specifically, eMIC-based features achieve a high accuracy of 94% for classifying cognitively normal (CN) and mild cognitive impairment (MCI) individuals, outperforming PCC (81%) and MIC (85%). For MCI and AD classification, MIC achieves higher accuracy (81%) compared to PCC (58%) and eMIC (78%). In CN and AD classification, eMIC exhibits the best accuracy of 95% compared to MIC (90%) and PCC (87%). These results underscore the effectiveness of fMRI-based features derived from non-linear techniques in accurately differentiating AD and MCI individuals from CN individuals, emphasizing the potential of neuroimaging and machine learning methods for improving AD diagnosis and classification.

Model-driven tACS in Alzheimer’s disease with personalized hybrid brain models

Abstract Animal models suggest that 40 Hz induced gamma oscillations reduce Aβ and p-Tau deposition, which is considered central to Alzheimer’s disease (AD) pathophysiology. Transcranial alternating current stimulation (tACS) has been proposed as a feasible option to induce gamma in AD patients and thus ease the cognitive burden of the disease. Here we investigate the potential of personalized whole-brain models to drive the stimulation in AD patients. We build a hybrid brain model that combines the (i) anatomical information, i.e., a parcellated brain, with subcortical parcels and their connections inferred from dMRI, (ii) functional data, i.e. fMRI-based functional connectivity and (iii) physiology based on Laminar Neural Mass Models (NMM). The NMM, personalized further with TMS-EEG data, can represent fast (gamma, 40-80 Hz) and slow (alpha/beta, 4-22 Hz) oscillations. Pathological disruptions have been incorporated in the most affected parcels based on FDG PET SUVR, which result in a decrease of gamma power in said parcels, consistent with findings in EEG and TMS-EEG. We have explored stimulation strategies by targeting small networks of parcels and specific regions, such as the prefrontal cortex (PFC). We show that the interplay of resonance phenomena and network effects can facilitate gamma entrainment and recover part of the gamma-power loss. This study is the first step into building model-driven optimization strategies for non-invasive stimulation in AD. Research Category and Technology and Methods Translational Research: 8. Transcranial Alternating Current Stimulation (tACS) Keywords: tACS, alzheimer's disease, computational neuroscience, resonance phenomena

Modeling the Hemodynamic Response Function Using EEG-fMRI Data During Eyes-Open Resting-State Conditions and Motor Task Execution

Being able to accurately quantify the hemodynamic response function (HRF) that links the blood oxygen level dependent functional magnetic resonance imaging (BOLD-fMRI) signal to the underlying neural activity is important both for elucidating neurovascular coupling mechanisms and improving the accuracy of fMRI-based functional connectivity analyses. In particular, HRF estimation using BOLD-fMRI is challenging particularly in the case of resting-state data, due to the absence of information about the underlying neuronal dynamics. To this end, using simultaneously recorded electroencephalography (EEG) and fMRI data is a promising approach, as EEG provides a more direct measure of neural activations. In the present work, we employ simultaneous EEG-fMRI to investigate the regional characteristics of the HRF using measurements acquired during resting conditions. We propose a novel methodological approach based on combining distributed EEG source space reconstruction, which improves the spatial resolution of HRF estimation and using block-structured linear and nonlinear models, which enables us to simultaneously obtain HRF estimates and the contribution of different EEG frequency bands. Our results suggest that the dynamics of the resting-state BOLD signal can be sufficiently described using linear models and that the contribution of each band is region specific. Specifically, it was found that sensory-motor cortices exhibit positive HRF shapes, whereas the lateral occipital cortex and areas in the parietal cortex, such as the inferior and superior parietal lobule exhibit negative HRF shapes. To validate the proposed method, we repeated the analysis using simultaneous EEG-fMRI measurements acquired during execution of a unimanual hand-grip task. Our results reveal significant associations between BOLD signal variations and electrophysiological power fluctuations in the ipsilateral primary motor cortex, particularly for the EEG beta band, in agreement with previous studies in the literature.

Increased fMRI connectivity upon chemogenetic inhibition of the mouse prefrontal cortex

While shaped and constrained by axonal connections, fMRI-based functional connectivity reorganizes in response to varying interareal input or pathological perturbations. However, the causal contribution of regional brain activity to whole-brain fMRI network organization remains unclear. Here we combine neural manipulations, resting-state fMRI and in vivo electrophysiology to probe how inactivation of a cortical node causally affects brain-wide fMRI coupling in the mouse. We find that chronic inhibition of the medial prefrontal cortex (PFC) via overexpression of a potassium channel increases fMRI connectivity between the inhibited area and its direct thalamo-cortical targets. Acute chemogenetic inhibition of the PFC produces analogous patterns of fMRI overconnectivity. Using in vivo electrophysiology, we find that chemogenetic inhibition of the PFC enhances low frequency (0.1–4 Hz) oscillatory power via suppression of neural firing not phase-locked to slow rhythms, resulting in increased slow and δ band coherence between areas that exhibit fMRI overconnectivity. These results provide causal evidence that cortical inactivation can counterintuitively increase fMRI connectivity via enhanced, less-localized slow oscillatory processes.

Localizing Spectral Interactions in the Resting State Network Using the Hilbert-Huang Transform.

Brain synchronizations are orchestrated from neuronal oscillations through frequency interactions, such as the alpha rhythm during relaxation. Nevertheless, how the intrinsic interaction forges functional integrity across brain segregations remains elusive, thereby motivating recent studies to localize frequency interactions of resting-state fMRI (rs-fMRI). To this point, we aim to unveil the fMRI-based spectral interactions using the time-frequency (TF) analysis; however, Fourier-based TF analyses impose restrictions on revealing frequency interactions given the limited time points in fMRI signals. Instead of using the Fourier-based wavelet analysis to identify the fMRI frequency of interests, we employed the Hilbert–Huang transform (HHT) for probing the specific frequency contribution to the functional integration, called ensemble spectral interaction (ESI). By simulating data with time-variant frequency changes, we demonstrated the Hilbert TF maps with high spectro-temporal resolution and full accessibility in comparison with the wavelet TF maps. By detecting amplitude-to-amplitude frequency couplings (AAC) across brain regions, we elucidated the ESI disparity between the eye-closed (EC) and eye-open (EO) conditions in rs-fMRI. In the visual network, the strength of the spectral interaction within 0.03–0.04 Hz was amplified in EC compared with that in EO condition, whereas a canonical connectivity analysis did not present differences between conditions. Collectively, leveraging from the instantaneous frequency of HHT, we firstly addressed the ESI technique to map the fMRI-based functional connectivity in a brand-new AAC perspective. The ESI possesses potential in elucidating the functional connectivity at specific frequency bins, thereby providing additional diagnostic merits for future clinical neuroscience.

Changes in sensory-related brain networks of patients with moyamoya disease with limb paresthesia: A resting-state fMRI-based functional connectivity analysis

This study’s aim was to investigate functional brain connectivity changes among patients with moyamoya disease (MMD) with limb paresthesia, using functional connectivity analysis based on resting-state functional magnetic resonance imaging (rs-fMRI). A total of 181 patients with MMD were enrolled, including 57 with left limb paresthesia (MLP group), 61 with right limb paresthesia (MRP group), and 63 without paresthesia (MWP group). Encephaloduroarteriosynangiosis (EDAS) was performed in 20 of the 57 patients with left limb paresthesia and 15 of the 61 patients with right limb paresthesia. Twenty-nine age- and sex-matched healthy controls (HC group) were recruited during the same period. All participants underwent rs-fMRI examination, and the patients treated with EDAS were re-examined 3–4 months after the surgery. After data preprocessing, we selected Brodmann area 3 on each side of the brain as the seed region to construct a functional connectivity network of the whole brain, and then we analyzed the differences in functional connectivity between the HC group, MWP group, MLP group, and MRP group. The functional connectivity of Brodmann area 3 (on either side) with the ipsilateral frontal (superior frontal gyrus, middle frontal gyrus, and inferior frontal gyrus) and parietal (supramarginal gyrus, angular gyrus, and superior parietal lobule) cortices was increased among patients with MMD. The functional connectivity enhancement in these brain regions was broader and greater in patients with contralateral limb paresthesia than in patients without paresthesia, and the regions with functional connectivity changes were roughly distributed symmetrically among the MLP group and the MRP group. There were no changes 3–4 months after EDAS in the increased functional connectivity between the frontal and parietal cortices and Brodmann area 3. Limb paresthesia in patients with MMD may be driven by abnormal functional connectivity in the frontal and parietal cortices. Functional changes in associated brain regions may be a target for evaluating the severity of MMD and its response to treatment.

Supraspinal Sensorimotor and Pain-Related Reorganization after a Hemicontusion Rat Cervical Spinal Cord Injury.

Because the presence of pain impedes motor recovery in individuals with spinal cord injury (SCI), it is necessary to understand their supraspinal substrates in translational animal models. Using functional magnetic resonance imaging (fMRI) in a rat model of hemicontusion cervical SCI, supraspinal changes were mapped and correlated with sensorimotor behavioral outcomes. Female adult rats underwent sham or SCI using a 2.5 mm impactor and 150 kdyn force. SCI permanently impaired motor activity in only the ipsilesional forelimb along with thermal hyperalgesia at 5 and 6 weeks. Spinal MRI at 8 weeks after SCI showed ipsilateral T1 and T2 lesions with no discernable lesions across shams. fMRI mapping during electrical forepaw stimulation indicated SCI-induced sensorimotor reorganization with an expansion of the contralesional forelimb representation. Resting state fMRI-based functional connectivity density (FCD), a marker of regional neuronal hubs, increased or decreased across brain regions involved in nociception. FCD increases after SCI were in the primary and secondary somatosensory cortices (S1 and S2), anterior cingulate cortex (ACC), insula, and the pre-frontal cortex (PFC), and decreases were across the hippocampus, thalamus, hypothalamus, and amygdala in SCI. Resting state functional connectivity (RSFC) assessments from the FCD altered regions of interest indicated cortico-cortical RSFC increases and cortico-insular, cortico-thalamic, and cortico-hypothalamic RSFC decreases after SCI. Hippocampus, amygdala, and thalamus showed decreased RSFC with most cortical regions and between themselves except the hippocampus-amygdala network, which showed increased RSFC after SCI. Whereas select nociceptive region's intrinsic activity associated strongly with evoked pain behaviors after SCI (e.g., PFC, ACC, hippocampus, thalamus, hypothalamus, M1, and S1BF) other nociceptive regions had weaker associations (e.g., amygdala, insula, auditory cortex, S1FL, S1HL, S2, and M2), but differed significantly in their intrinsic activities between sham and SCI. The weaker associated nociceptive regions may possibly encode both the evoked and affective components of pain.

Altered Relationship Between Heart Rate Variability and fMRI-Based Functional Connectivity in People With Epilepsy.

Background: Disruptions in central autonomic processes in people with epilepsy have been studied through evaluation of heart rate variability (HRV). Decreased HRV appears in epilepsy compared to healthy controls, suggesting a shift in autonomic balance toward sympathetic dominance; recent studies have associated HRV changes with seizure severity and outcome of interventions. However, the processes underlying these autonomic changes remain unclear. We examined the nature of these changes by assessing alterations in whole-brain functional connectivity, and relating those alterations to HRV.Methods: We examined regional brain activity and functional organization in 28 drug-resistant epilepsy patients and 16 healthy controls using resting-state functional magnetic resonance imaging (fMRI). We employed an HRV state-dependent functional connectivity (FC) framework with low and high HRV states derived from the following four cardiac-related variables: 1. RR interval, 2. root mean square of successive differences (RMSSD), 4. low-frequency HRV (0.04–0.15 Hz; LF-HRV) and high-frequency HRV (0.15–0.40 Hz; HF-HRV). The effect of group (epilepsy vs. controls), HRV state (low vs. high) and the interactions of group and state were assessed using a mixed analysis of variance (ANOVA). We assessed FC within and between 7 large-scale functional networks consisting of cortical regions and 4 subcortical networks, the amygdala, hippocampus, basal ganglia and thalamus networks.Results: Consistent with previous studies, decreased RR interval (increased heart rate) and decreased HF-HRV appeared in people with epilepsy compared to healthy controls. For both groups, fluctuations in heart rate were positively correlated with BOLD activity in bilateral thalamus and regions of the cerebellum, and negatively correlated with BOLD activity in the insula, putamen, superior temporal gyrus and inferior frontal gyrus. Connectivity strength in patients between right thalamus and ventral attention network (mainly insula) increased in the high LF-HRV state compared to low LF-HRV; the opposite trend appeared in healthy controls. A similar pattern emerged for connectivity between the thalamus and basal ganglia.Conclusion: The findings suggest that resting connectivity patterns between the thalamus and other structures underlying HRV expression are modified in people with drug-resistant epilepsy compared to healthy controls.

Functional Connectivity-Based Prediction of Autism on Site Harmonized ABIDE Dataset.

The larger sample sizes available from multi-site publicly available neuroimaging data repositories makes machine-learning based diagnostic classification of mental disorders more feasible by alleviating the curse of dimensionality. However, since multi-site data are aggregated post-hoc, i.e. they were acquired from different scanners with different acquisition parameters, non-neural inter-site variability may mask inter-group differences that are at least in part neural in origin. Hence, the advantages gained by the larger sample size in the context of machine-learning based diagnostic classification may not be realized. We address this issue using harmonization of multi-site neuroimaging data using the ComBat technique, which is based on an empirical Bayes formulation to remove inter-site differences in data distributions, to improve diagnostic classification accuracy. Specifically, we demonstrate this using ABIDE (Autism Brain Imaging Data Exchange) multi-site data for classifying individuals with Autism from healthy controls using resting state fMRI-based functional connectivity data. Our results show that higher classification accuracies across multiple classification models can be obtained (especially for models based on artificial neural networks) from multi-site data post harmonization with the ComBat technique as compared to without harmonization, outperforming earlier results from existing studies using ABIDE. Furthermore, our network ablation analysis facilitated important insights into autism spectrum disorder pathology and the connectivity in networks shown to be important for classification covaried with verbal communication impairments in Autism. Multi-site data harmonization using ComBat improves neuroimaging-based diagnostic classification of mental disorders. ComBat has the potential to make AI-based clinical decision-support systems more feasible in psychiatry.

Resting-State Functional Connectivity in Mathematical Expertise.

To what extent are different levels of expertise reflected in the functional connectivity of the brain? We addressed this question by using resting-state functional magnetic resonance imaging (fMRI) in mathematicians versus non-mathematicians. To this end, we investigated how the two groups of participants differ in the correlation of their spontaneous blood oxygen level-dependent fluctuations across the whole brain regions during resting state. Moreover, by using the classification algorithm in machine learning, we investigated whether the resting-state fMRI networks between mathematicians and non-mathematicians were distinguished depending on features of functional connectivity. We showed diverging involvement of the frontal–thalamic–temporal connections for mathematicians and the medial–frontal areas to precuneus and the lateral orbital gyrus to thalamus connections for non-mathematicians. Moreover, mathematicians who had higher scores in mathematical knowledge showed a weaker connection strength between the left and right caudate nucleus, demonstrating the connections’ characteristics related to mathematical expertise. Separate functional networks between the two groups were validated with a maximum classification accuracy of 91.19% using the distinct resting-state fMRI-based functional connectivity features. We suggest the advantageous role of preconfigured resting-state functional connectivity, as well as the neural efficiency for experts’ successful performance.

Investigating the effects of healthy cognitive aging on brain functional connectivity using 4.7T resting-state functional magnetic resonance imaging.

Functional changes in the aging human brain have been previously reported using functional magnetic resonance imaging (fMRI). Earlier resting-state fMRI studies revealed an age-associated weakening of intra-system functional connectivity (FC) and age-associated strengthening of inter-system FC. However, the majority of such FC studies did not investigate the relationship between age and network amplitude, without which correlation-based measures of FC can be challenging to interpret. Consequently, the main aim of this study was to investigate how three primary measures of resting-state fMRI signal-network amplitude, network topography, and inter-network FC-are affected by healthy cognitive aging. We acquired resting-state fMRI data on a 4.7T scanner for 105 healthy participants representing the entire adult lifespan (18-85years of age). To study age differences in network structure, we combined ICA-based network decomposition with sparse graphical models. Older adults displayed lower blood-oxygen-level-dependent (BOLD) signal amplitude in all functional systems, with sensorimotor networks showing the largest age differences. Our age comparisons of network topography and inter-network FC demonstrated a substantial amount of age invariance in the brain's functional architecture. Despite architecture similarities, old adults displayed a loss of communication efficiency in our inter-network FC comparisons, driven primarily by theFC reduction in frontal and parietal association cortices. Together, our results provide a comprehensive overview of age effects on fMRI-based FC.

The IEEE Brain Data Bank Challenge 2020

The 2020 Brain Data Bank (BDB) Challenge reached its closure on December 5, 2020, in a virtual conference format, due to COVID-19. Having 88 registrants (roughly 20% medical, non-IEEE, and the rest primarily IEEE engineering professionals) from 10 countries, the BDBC-Finale program consisted of presentations from 5 selected teams resulting from 3 preliminary runs earlier in 2020. The program was further enriched with a National Institute of Aging (NIA) Keynote on US funding sources and a Special Panel on Codesigning with an End-User, Prof. Justin Yerbury, who has been suffering from motor neuron disease since 2016. The theme for 2020 was the Aging Brain, making use of large brain records, (1) Alzheimer’'s Disease NeuroImaging (ADNI) containing magnetic resonance imaging (MRI), positron emission tomography, CerebroSpinal Fluid images, and clinical data (~3 TB), and (2) ElectroEncephaloGraphy (EEG) corpus (48–350 GB) to examine brain degeneration ending in Alzheimer's Disease (AD). Individual teams specified selected brain datasets to apply deep learning/machine learning techniques for the detection of elderly brain impairment. Other approaches to understand AD were also presented in terms of fMRI-based functional connectivity alteration, and experiments in rehabilitation using turmeric administered rats after bulbectomy. The author discuses the gains from these BDB Challenge presentations.

Cerebellar transcranial alternating current stimulation in the gamma range applied during the acquisition of a novel motor skill

The development of novel strategies to augment motor training success is of great interest for healthy persons and neurological patients. A promising approach is the combination of training with transcranial electric stimulation. However, limited reproducibility and varying effect sizes make further protocol optimization necessary. We tested the effects of a novel cerebellar transcranial alternating current stimulation protocol (tACS) on motor skill learning. Furthermore, we studied underlying mechanisms by means of transcranial magnetic stimulation and analysis of fMRI-based resting-state connectivity. N = 15 young, healthy participants were recruited. 50 Hz tACS was applied to the left cerebellum in a double-blind, sham-controlled, cross-over design concurrently to the acquisition of a novel motor skill. Potential underlying mechanisms were assessed by studying short intracortical inhibition at rest (SICIrest) and in the premovement phase (SICImove), intracortical facilitation at rest (ICFrest), and seed-based resting-state fMRI-based functional connectivity (FC) in a hypothesis-driven motor learning network. Active stimulation did not enhance skill acquisition or retention. Minor effects on striato-parietal FC were present. Linear mixed effects modelling identified SICImove modulation and baseline task performance as the most influential determining factors for predicting training success. Accounting for the identified factors may allow to stratify participants for future training-based interventions.

Resting-state “physiological networks”

Slow changes in systemic brain physiology can elicit large fluctuations in fMRI time series, which manifest as structured spatial patterns of temporal correlations between distant brain regions. Here, we investigated whether such “physiological networks”—sets of segregated brain regions that exhibit similar responses following slow changes in systemic physiology—resemble patterns associated with large-scale networks typically attributed to remotely synchronized neuronal activity. By analyzing a large group of subjects from the 3T Human Connectome Project (HCP) database, we demonstrate brain-wide and noticeably heterogenous dynamics tightly coupled to either respiratory variation or heart rate changes. We show, using synthesized data generated from physiological recordings across subjects, that these physiologically-coupled fluctuations alone can produce networks that strongly resemble previously reported resting-state networks, suggesting that, in some cases, the “physiological networks” seem to mimic the neuronal networks. Further, we show that such physiologically-relevant connectivity estimates appear to dominate the overall connectivity observations in multiple HCP subjects, and that this apparent “physiological connectivity” cannot be removed by the use of a single nuisance regressor for the entire brain (such as global signal regression) due to the clear regional heterogeneity of the physiologically-coupled responses. Our results challenge previous notions that physiological confounds are either localized to large veins or globally coherent across the cortex, therefore emphasizing the necessity to consider potential physiological contributions in fMRI-based functional connectivity studies. The rich spatiotemporal patterns carried by such “physiological” dynamics also suggest great potential for clinical biomarkers that are complementary to large-scale neuronal networks.

Distinct structure-function relationships across cortical regions and connectivity scales in the rat brain

An improved understanding of the structure-function relationship in the brain is necessary to know to what degree structural connectivity underpins abnormal functional connectivity seen in disorders. We integrated high-field resting-state fMRI-based functional connectivity with high-resolution macro-scale diffusion-based and meso-scale neuronal tracer-based structural connectivity, to obtain an accurate depiction of the structure-function relationship in the rat brain. Our main goal was to identify to what extent structural and functional connectivity strengths are correlated, macro- and meso-scopically, across the cortex. Correlation analyses revealed a positive correspondence between functional and macro-scale diffusion-based structural connectivity, but no significant correlation between functional connectivity and meso-scale neuronal tracer-based structural connectivity. Zooming in on individual connections, we found strong functional connectivity in two well-known resting-state networks: the sensorimotor and default mode network. Strong functional connectivity within these networks coincided with strong short-range intrahemispheric structural connectivity, but with weak heterotopic interhemispheric and long-range intrahemispheric structural connectivity. Our study indicates the importance of combining measures of connectivity at distinct hierarchical levels to accurately determine connectivity across networks in the healthy and diseased brain. Although characteristics of the applied techniques may affect where structural and functional networks (dis)agree, distinct structure-function relationships across the brain could also have a biological basis.

A decade of test-retest reliability of functional connectivity: A systematic review and meta-analysis

BackgroundOnce considered mere noise, fMRI-based functional connectivity has become a major neuroscience tool in part due to early studies demonstrating its reliability. These fundamental studies revealed only the tip of the iceberg; over the past decade, many test-retest reliability studies have continued to add nuance to our understanding of this complex topic. A summary of these diverse and at times contradictory perspectives is needed. ObjectivesWe aimed to summarize the existing knowledge regarding test-retest reliability of functional connectivity at the most basic unit of analysis: the individual edge level. This entailed (1) a meta-analytic estimate of reliability and (2) a review of factors influencing reliability. MethodsA search of Scopus was conducted to identify studies that estimated edge-level test-retest reliability. To facilitate comparisons across studies, eligibility was restricted to studies measuring reliability via the intraclass correlation coefficient (ICC). The meta-analysis included a random effects pooled estimate of mean edge-level ICC, with studies nested within datasets. The review included a narrative summary of factors influencing edge-level ICC. ResultsFrom an initial pool of 212 studies, 44 studies were identified for the qualitative review and 25 studies for quantitative meta-analysis. On average, individual edges exhibited a “poor” ICC of 0.29 (95% CI = 0.23 to 0.36). The most reliable measurements tended to involve: (1) stronger, within-network, cortical edges, (2) eyes open, awake, and active recordings, (3) more within-subject data, (4) shorter test-retest intervals, (5) no artifact correction (likely due in part to reliable artifact), and (6) full correlation-based connectivity with shrinkage. ConclusionThis study represents the first meta-analysis and systematic review investigating test-retest reliability of edge-level functional connectivity. Key findings suggest there is room for improvement, but care should be taken to avoid promoting reliability at the expense of validity. By pooling existing knowledge regarding this key facet of accuracy, this study supports broader efforts to improve inferences in the field.

Topological Properties of Resting-State fMRI Functional Networks Improve Machine Learning-Based Autism Classification.

Automatic algorithms for disease diagnosis are being thoroughly researched for use in clinical settings. They usually rely on pre-identified biomarkers to highlight the existence of certain problems. However, finding such biomarkers for neurodevelopmental disorders such as Autism Spectrum Disorder (ASD) has challenged researchers for many years. With enough data and computational power, machine learning (ML) algorithms can be used to interpret the data and extract the best biomarkers from thousands of candidates. In this study, we used the fMRI data of 816 individuals enrolled in the Autism Brain Imaging Data Exchange (ABIDE) to introduce a new biomarker extraction pipeline for ASD that relies on the use of graph theoretical metrics of fMRI-based functional connectivity to inform a support vector machine (SVM). Furthermore, we split the dataset into 5 age groups to account for the effect of aging on functional connectivity. Our methodology achieved better results than most state-of-the-art investigations on this dataset with the best model for the >30 years age group achieving an accuracy, sensitivity, and specificity of 95, 97, and 95%, respectively. Our results suggest that measures of centrality provide the highest contribution to the classification power of the models.

Degrees of functional connectome abnormality in disorders of consciousness.

Understanding the neuronal basis of disorders of consciousness can help improve the accuracy of their diagnosis, indicate potential targets for therapeutic interventions, and provide insights into the organization of normal conscious information processing. Measurements of brain activity have been used to find associations of the levels of consciousness with brain complexity, topological features of functional connectomes, and disruption of resting-state networks. However, obtainment of a detailed picture of activity patterns underlying the vegetative state/unresponsive wakefulness syndrome and the minimally conscious state remains a work in progress. We here aimed at finding the aspects of fMRI-based functional connectivity that differentiate these states from each other and from the normal condition. A group of 22 patients was studied (9 minimally conscious state and 13 vegetative state/unresponsive wakefulness syndrome). Patients were shown to have reduced connectivity in most resting-state networks and disrupted patterns of relative connection strengths as compared to healthy subjects. Differences between the unresponsive wakefulness syndrome and the minimally conscious state were found in the patterns formed by a relatively small number of strongest positive correlations selected by thresholding. These differences were captured by measures of functional connectivity disruption that integrate area-specific abnormalities over the whole brain. The results suggest that the strong positive correlations between the functional activities of specific brain areas observed in healthy individuals may be critical for consciousness and be an important target of disruption in disorders of consciousness.