GraphVar 2.0: A user-friendly toolbox for machine learning on functional connectivity measures

Brain age prediction based on functional magnetic resonance imaging (fMRI) data has the potential to serve as a biomarker for quantifying brain health. To predict the brain age based on fMRI data robustly and accurately, we curated a large dataset (n = 4259) of fMRI scans from seven different data acquisition sites and computed personalized functional connectivity measures at multiple scales from each subject's fMRI scan. Particularly, we computed personalized large-scale functional networks and generated functional connectivity measures at multiple scales to characterize each fMRI scan. To account for inter-site effects on the functional connectivity measures, we harmonized the functional connectivity measures in their tangent space and then built brain age prediction models on the harmonized functional connectivity measures. We compared the brain age prediction models with alternatives that were built on the functional connectivity measures computed at a single scale and harmonized using different strategies. Comparison results have demonstrated that the best brain age prediction performance was achieved by the prediction model built on the multi-scale functional connectivity measures that were harmonized in tangent space, indicating that multi-scale functional connectivity measures provided richer information than those computed at any single scales and the harmonization of functional connectivity measures in tangent space improved the brain age prediction.

In the current study we focus on the modeling of functional processes of brain tissue using functional Magnetic Resonance Imaging (fMRI) data. A brain connectivity analysis of Restless Legs Syndrome (RLS) is presented. Thirteen un-medicated patients with late-onset RLS and six healthy subjects are studied using structural and functional brain images. We compare functional connectivity analysis methods, according to their dependency on models or data, as well as to model effective connectivity. An Independent Component Analysis (ICA) method is implemented and all spontaneously activated areas in resting-state condition in both patients and healthy subjects are recorded and be compared with previous studies. Functional connectivity correlation matrices of both RLS and control subjects are extracted and these functional connectivity measures were compared using a seed-based analysis method. We model the brain tissue, based on the influence that one region exerts over another, using a spectral Dynamic Causal Model (DCM) analysis, which has not yet been implemented for RLS data. Finally, a Bayesian Model Selection is chosen in order to compare the winning model that effectively describes the data. The benefits of each methodology are presented.

The relationship of anxious and depressive symptoms in Parkinson's disease with voxel-based neuroanatomical and functional connectivity measures

Brain Connectivity: A Journal of Clinical Neurology, Neuroscience, and Neuroimaging Advancing the Field of Neurology.

Neurological and neuropsychiatric disorders are major causes of morbidity worldwide. A systems level analysis including functional and structural neuroimaging is particularly useful when the pathology leads to disorders of higher order cognitive functions in human patients. However, an analysis that is restricted to regional effects is impoverished and insensitive, compared to the analysis of distributed brain networks. We discuss the issues to consider when choosing an appropriate connectivity method, and compare the results from several different methods that are relevant to fMRI and PET data. These include psychophysiological interactions in general linear models, structural equation modeling, dynamic causal modeling, and independent components analysis. The advantages of connectivity analysis are illustrated with a range of structural and neurodegenerative brain disorders. We illustrate the sensitivity of these methods to the presence or severity of disease and/or treatment, even where analyses of voxel-wise activations are insensitive. However, functional and structural connectivity methods should be seen as complementary to, not a substitute for, other imaging and behavioral approaches. The functional relevance of changes in connectivity, to motor or cognitive performance, are considered alongside the complex relationship between structural and functional changes and neuropathology. Finally some of the problems associated with connectivity analysis are discussed. We suggest that the analysis of brain connectivity is an essential complement to the analysis of regionally specific dysfunction, in order to understand neurological and neuropsychiatric disease, and to evaluate the mechanisms of effective therapies.

Acquiring resting-state functional magnetic resonance imaging (fMRI) datasets at multiple MRI scanners and clinical sites can improve statistical power and generalizability of results. However, multi-site neuroimaging studies have reported considerable non-biological variability in fMRI measurements due to different scanner manufacturers and acquisition protocols. These undesirable sources of variability may limit power to detect effects of interest and may even result in erroneous findings. Until now, there has not been an approach that removes unwanted site effects. In this study, using a relatively large multi-site (4 sites) fMRI dataset, we investigated the impact of site effects on functional connectivity and network measures estimated by widely used connectivity metrics and brain parcellations. The protocols and image acquisition of the dataset used in this study had been homogenized using identical MRI phantom acquisitions from each of the neuroimaging sites, however inter-site acquisition effects were not completely eliminated. Indeed, in the current study we found that the magnitude of site effects depended on the choice of connectivity metric and brain atlas. Therefore, to further remove site effects, we applied ComBat, a harmonization technique previously shown to eliminate site effects in multi-site diffusion tensor imaging (DTI) and cortical thickness studies. In the current work, ComBat successfully removed site effects identified in connectivity and network measures and increased the power to detect age associations when using optimal combinations of connectivity metrics and brain atlases. Our proposed ComBat harmonization approach for fMRI-derived connectivity measures facilitates reliable and efficient analysis of retrospective and prospective multi-site fMRI neuroimaging studies.

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Granger causality analysis is becoming central for the analysis of interactions between neural populations and oscillatory networks. However, it is currently unclear whether single-trial estimates of Granger causality spectra can be used reliably to assess directional influence. We addressed this issue by combining single-trial Granger causality spectra with statistical inference based on general linear models. The approach was assessed on synthetic and neurophysiological data. Synthetic bivariate data was generated using two autoregressive processes with unidirectional coupling. We simulated two hypothetical experimental conditions: the first mimicked a constant and unidirectional coupling, whereas the second modelled a linear increase in coupling across trials. The statistical analysis of single-trial Granger causality spectra, based on t-tests and linear regression, successfully recovered the underlying pattern of directional influence. In addition, we characterised the minimum number of trials and coupling strengths required for significant detection of directionality. Finally, we demonstrated the relevance for neurophysiology by analysing two local field potentials (LFPs) simultaneously recorded from the prefrontal and premotor cortices of a macaque monkey performing a conditional visuomotor task. Our results suggest that the combination of single-trial Granger causality spectra and statistical inference provides a valuable tool for the analysis of large-scale cortical networks and brain connectivity.

Measures of functional connectivity have played a central role in advancing our understanding of how information is transmitted and processed within the brain. Traditionally, these studies have focused on identifying redundant functional connectivity, which involves determining when activity is similar across different sites or neurons. However, recent research has highlighted the importance of also identifying synergistic connectivity—that is, connectivity that gives rise to information not contained in either site or neuron alone. Here, we measured redundant and synergistic functional connectivity between neurons in the mouse primary auditory cortex during a sound discrimination task. Specifically, we measured directed functional connectivity between neurons simultaneously recorded with calcium imaging. We used Granger Causality as a functional connectivity measure. We then used Partial Information Decomposition to quantify the amount of redundant and synergistic information about the presented sound that is carried by functionally connected or functionally unconnected pairs of neurons. We found that functionally connected pairs present proportionally more redundant information and proportionally less synergistic information about sound than unconnected pairs, suggesting that their functional connectivity is primarily redundant. Further, synergy and redundancy coexisted both when mice made correct or incorrect perceptual discriminations. However, redundancy was much higher (both in absolute terms and in proportion to the total information available in neuron pairs) in correct behavioural choices compared to incorrect ones, whereas synergy was higher in absolute terms but lower in relative terms in correct than in incorrect behavioural choices. Moreover, the proportion of redundancy reliably predicted perceptual discriminations, with the proportion of synergy adding no extra predictive power. These results suggest a crucial contribution of redundancy to correct perceptual discriminations, possibly due to the advantage it offers for information propagation, and also suggest a role of synergy in enhancing information level during correct discriminations.

SUMMARYNeuronal oscillations are suggested to play an important role in auditory working memory (WM), but their contribution to content-specific representations has remained unclear. Here, we measure magnetoencephalography during a retro-cueing task with parametric ripple-sound stimuli, which are spectrotemporally similar to speech but resist non-auditory memory strategies. Using machine learning analyses, with rigorous between-subject cross-validation and non-parametric permutation testing, we show that memorized sound content is strongly represented in phase-synchronization patterns between subregions of auditory and frontoparietal cortices. These phase-synchronization patterns predict the memorized sound content steadily across the studied maintenance period. In addition to connectivity-based representations, there are indices of more local, “activity silent” representations in auditory cortices, where the decoding accuracy of WM content significantly increases after task-irrelevant “impulse stimuli.” Our results demonstrate that synchronization patterns across auditory sensory and association areas orchestrate neuronal coding of auditory WM content. This connectivity-based coding scheme could also extend beyond the auditory domain.

Purpose:The estimation of functional connectivity (FC) measures using resting state functional MRI (fMRI) is often affected by head motion during functional imaging scans. Head motion is more common in the elderly than in young participants and could therefore affect the evaluation of age-related changes in brain networks. Thus, this study aimed to investigate the influence of head motion in FC estimation when evaluating age-related changes in brain networks.Methods:This study involved 132 healthy volunteers divided into 3 groups: elderly participants with high motion (OldHM, mean age (±SD) = 69.6 (±5.31), N = 44), elderly participants with low motion (OldLM, mean age (±SD) = 68.7 (±4.59), N = 43), and young adult participants with low motion (YugLM, mean age (±SD) = 27.6 (±5.26), N = 45). Head motion was quantified using the mean of the framewise displacement of resting state fMRI data. After preprocessing all resting state fMRI datasets, several resting state networks (RSNs) were extracted using independent component analysis (ICA). In addition, several network metrics were also calculated using network analysis. These FC measures were then compared among the 3 groups.Results:In ICA, the number of voxels with significant differences in RSNs was higher in YugLM vs. OldLM comparison than in YugLM vs. OldHM. In network analysis, all network metrics showed significant (P < 0.05) differences in comparisons involving low vs. high motion groups (OldHM vs. OldLM and OldHM vs. YugLM). However, there was no significant (P > 0.05) difference in the comparison involving the low motion groups (OldLM vs. YugLM).Conclusion:Our findings showed that head motion during functional imaging could significantly affect the evaluation of age-related brain network changes using resting state fMRI data.

Parcellation of the human cortex has important implications in neuroscience. Parcellation is often a crucial requirement before meaningful regional analysis can occur. The human cortex can be parcellated into distinct regions based on structural features, such as gyri and sulci. Brain network patterns in a given region with respect to its neighbors, known as connectional fingerprints, can be used to parcellate the cortex. Distinct imaging modalities might provide complementary information for brain parcellation. Here, we established functional connectivity with time series data from functional MRI (fMRI) combined with a correlation map of cortical thickness obtained from T1-weighted MRI. We aimed to extend the previous study, which parcellated the medial frontal cortex (MFC) using functional connectivity, and to test the value of additional information regarding cortical thickness. Two types of network information were used to parcellate the MFC into two sub-regions with spectral and Ward’s clustering approaches. The MFC region was defined using manual delineation based on in-house data (n = 12). Parcellation was applied to independent large-scale data obtained from the Human Connectome Project (HCP, n = 248). Agreement between parcellation using fMRI- and thickness-driven connectivity yielded dice coefficient overlaps of 0.74 (Ward’s clustering) and 0.54 (spectral clustering). We also explored whole brain connectivity using the MFC sub-regions as seed regions based on these two types of information. The results of whole brain connectivity analyses were also consistent for both types of information. We observed that an inter-regional correlation map derived from cortical thickness strongly reflected the underlying functional connectivity of MFC region.

Assessment of flourishing levels of individuals by using resting-state fNIRS with different functional connectivity measures

ObjectiveAlzheimer’s disease (AD) is a neurodegenerative disease characterized by progressive deterioration of memory and cognition. Mild cognitive impairment (MCI) has been implicated as a prodromal phase of AD. Although abnormal functional connectivity (FC) has been demonstrated in AD and MCI, the clinical differentiation of AD, MCI, and normal aging remains difficult, and the distinction between MCI and normal aging is especially problematic. We hypothesized that FC between the hippocampus and other brain structures is altered in AD and MCI, and that measurement of abnormal FC could have diagnostic utility for the classification of different AD stages.MethodsElderly adults aged 60–85 years were assigned to AD, MCI, or normal control (NC) groups based on clinical criteria. Functional magnetic resonance scanning was completed by 119 subjects. Five dimension reduction/classification methods were applied, using hippocampus-derived FC strengths as input features. Classification performance of the five dimensionality reduction methods was compared between AD, MCI, and NC groups.ResultsFCs between the hippocampus and left insula, left thalamus, cerebellum, right lingual gyrus, posterior cingulate cortex, and precuneus were significantly reduced in AD and MCI. Support vector machine learning coupled with sparse principal component analysis demonstrated the best discriminative performance, yielding classification accuracies of 82.02% (AD vs. NC), 81.33% (MCI vs. NC), and 81.08% (AD vs. MCI).ConclusionHippocampus-seed-based FCs were significantly different between AD, MCI, and NC groups. FC assessment combined with widely used machine learning methods can improve AD differential diagnosis, and may be especially useful to distinguish MCI from normal aging.

Ageing is associated with functional reorganization that is mainly characterized by declining functional connectivity due to general neurodegeneration and increasing incidence of disease. Functional connectivity has been studied across the lifespan; however, there is a paucity of research within the older groups (≥75 years) where neurodegeneration and disease prevalence are at its highest. In this cross-sectional study, we investigated associations between age and functional connectivity and the influence of cerebral small vessel disease (CSVD)-a common age-related morbidity-in 167 community-dwelling older adults aged 75-91 years (mean = 80.3 ± 3.8). Resting-state functional MRI was used to determine functional connectivity within ten standard networks and calculate the whole-brain graph theoretical measures global efficiency and clustering coefficient. CSVD features included white matter hyperintensities, lacunar infarcts, cerebral microbleeds, and atrophy that were assessed in each individual and a composite score was calculated. Both main and interaction effects (age*CSVD features) on functional connectivity were studied. We found stable levels of functional connectivity across the age range. CSVD was not associated with functional connectivity measures. To conclude, our data show that the functional architecture of the brain is relatively unchanged after 75 years of age and not differentially affected by individual levels of vascular pathology.