Functional Connectivity Matrix Research Articles

Diminished functional segregation and resilience are associated with symptomatic severity and cognitive impairments in schizophrenia: a large-scale study

BackgroundThe research findings on the topological properties of functional connectomes (TP-FCs) in patients with schizophrenia (SZPs) exhibit inconsistencies and contradictions, which can be attributed to limitations such as small sample...

MDD brain network analysis based on EEG functional connectivity and graph theory

BackgroundExisting studies have shown that the brain network of major depression disorder (MDD) has abnormal topologies. However, constructing reliable MDD brain networks is still an open problem. New methodThis paper proposed a reliable MDD brain network construction method. First, seven connectivity methods are used to calculate the correlation between channels and obtain the functional connectivity matrix. Then, the matrix is binarized using four binarization methods to obtain the EEG brain network. Besides, we proposed an improved binarization method based on the criterion of maximizing differences between groups: the adaptive threshold (AT) method. The AT can automatically set the optimal binarization threshold and overcome the artificial influence of traditional methods. After that, several network metrics are extracted from the brain network to analyze inter-group differences. Finally, we used statistical analysis and Fscore values to compare the performance of different methods and establish the most reliable method for brain network construction. ResultsIn theta, alpha, and total frequency bands, the clustering coefficient, global efficiency, local efficiency, and degree of the MDD brain network decrease, and the path length of the MDD brain network increases. Comparison with existing methodsThe results show that AT outperforms the existing binarization methods. Compared with other methods, the brain network construction method based on phase-locked value (PLV) and AT has better reliability. ConclusionsMDD has brain dysfunction, particularly in the frontal and temporal lobes.

Neuroanatomical evidence and a mouse calcitonin gene-related peptide model in line with human functional magnetic resonance imaging data support the involvement of peptidergic Edinger-Westphal nucleus in migraine.

The urocortin 1 (UCN1)-expressing centrally projecting Edinger-Westphal (EWcp) nucleus is influenced by circadian rhythms, hormones, stress, and pain, all known migraine triggers. Our study investigated EWcp's potential involvement in migraine. Using RNAscope in situ hybridization and immunostaining, we examined the expression of calcitonin gene-related peptide (CGRP) receptor components in both mouse and human EWcp and dorsal raphe nucleus (DRN). Tracing study examined connection between EWcp and the spinal trigeminal nucleus (STN). The intraperitoneal CGRP injection model of migraine was applied and validated by light-dark box, and von Frey assays in mice, in situ hybridization combined with immunostaining, were used to assess the functional-morphological changes. The functional connectivity matrix of EW was examined using functional magnetic resonance imaging in control humans and interictal migraineurs. We proved the expression of CGRP receptor components in both murine and human DRN and EWcp. We identified a direct urocortinergic projection from EWcp to the STN. Photophobic behavior, periorbital hyperalgesia, increased c-fos gene-encoded protein immunoreactivity in the lateral periaqueductal gray matter and trigeminal ganglia, and phosphorylated c-AMP-responsive element binding protein in the STN supported the efficacy of CGRP-induced migraine-like state. Calcitonin gene-related peptide administration also increased c-fos gene-encoded protein expression, Ucn1 mRNA, and peptide content in EWcp/UCN1 neurons while reducing serotonin and tryptophan hydroxylase-2 levels in the DRN. Targeted ablation of EWcp/UCN1 neurons induced hyperalgesia. A positive functional connectivity between EW and STN as well as DRN has been identified by functional magnetic resonance imaging. The presented data strongly suggest the regulatory role of EWcp/UCN1 neurons in migraine through the STN and DRN with high translational value.

Multimodal Predictive Modeling: Scalable Imaging Informed Approaches to Predict Future Brain Health.

Predicting future brain health is a complex endeavor that often requires integrating diverse data sources. The neural patterns and interactions identified through neuroimaging serve as the fundamental basis and early indicators that precede the manifestation of observable behaviors or psychological states. In this work, we introduce a multimodal predictive modeling approach that leverages an imaging-informed methodology to gain insights into future behavioral outcomes. We employed three methodologies for evaluation: an assessment-only approach using support vector regression (SVR), a neuroimaging-only approach using random forest (RF), and an image-assisted method integrating the static functional network connectivity (sFNC) matrix from resting-state functional magnetic resonance imaging (rs-fMRI) alongside assessments. The image-assisted approach utilized a partially conditional variational autoencoder (PCVAE) to predict brain health constructs in future visits from the behavioral data alone. Our performance evaluation indicates that the image-assisted method excels in handling conditional information to predict brain health constructs in subsequent visits and their longitudinal changes. These results suggest that during the training stage, the PCVAE model effectively captures relevant information from neuroimaging data, thereby potentially improving accuracy in making future predictions using only assessment data. The proposed image-assisted method outperforms traditional assessment-only and neuroimaging-only approaches by effectively integrating neuroimaging data with assessment factors. This study underscores the potential of neuroimaging-informed predictive modeling to advance our comprehension of the complex relationships between cognitive performance and neural connectivity.

DeepGCN based on variable multi‐graph and multimodal data for ASD diagnosis

AbstractDiagnosing individuals with autism spectrum disorder (ASD) accurately faces great challenges in clinical practice, primarily due to the data's high heterogeneity and limited sample size. To tackle this issue, the authors constructed a deep graph convolutional network (GCN) based on variable multi‐graph and multimodal data (VMM‐DGCN) for ASD diagnosis. Firstly, the functional connectivity matrix was constructed to extract primary features. Then, the authors constructed a variable multi‐graph construction strategy to capture the multi‐scale feature representations of each subject by utilising convolutional filters with varying kernel sizes. Furthermore, the authors brought the non‐imaging information into the feature representation at each scale and constructed multiple population graphs based on multimodal data by fully considering the correlation between subjects. After extracting the deeper features of population graphs using the deep GCN(DeepGCN), the authors fused the node features of multiple subgraphs to perform node classification tasks for typical control and ASD patients. The proposed algorithm was evaluated on the Autism Brain Imaging Data Exchange I (ABIDE I) dataset, achieving an accuracy of 91.62% and an area under the curve value of 95.74%. These results demonstrated its outstanding performance compared to other ASD diagnostic algorithms.

Diagnosis-Guided Deep Subspace Clustering Association Study for Pathogenetic Markers Identification of Alzheimer's Disease Based on Comparative Atlases.

The roles of brain region activities and genotypic functions in the pathogenesis of Alzheimer's disease (AD) remain unclear. Meanwhile, current imaging genetics methods are difficult to identify potential pathogenetic markers by correlation analysis between brain network and genetic variation. To discover disease-related brain connectome from the specific brain structure and the fine-grained level, based on the Automated Anatomical Labeling (AAL) and human Brainnetome atlases, the functional brain network is first constructed for each subject. Specifically, the upper triangle elements of the functional connectivity matrix are extracted as connectivity features. The clustering coefficient and the average weighted node degree are developed to assess the significance of every brain area. Since the constructed brain network and genetic data are characterized by non-linearity, high-dimensionality, and few subjects, the deep subspace clustering algorithm is proposed to reconstruct the original data. Our multilayer neural network helps capture the non-linear manifolds, and subspace clustering learns pairwise affinities between samples. Moreover, most approaches in neuroimaging genetics are unsupervised learning, neglecting the diagnostic information related to diseases. We presented a label constraint with diagnostic status to instruct the imaging genetics correlation analysis. To this end, a diagnosis-guided deep subspace clustering association (DDSCA) method is developed to discover brain connectome and risk genetic factors by integrating genotypes with functional network phenotypes. Extensive experiments prove that DDSCA achieves superior performance to most association methods and effectively selects disease-relevant genetic markers and brain connectome at the coarse-grained and fine-grained levels.

A novel approach for ASD recognition based on graph attention networks.

Early detection and diagnosis of Autism Spectrum Disorder (ASD) can significantly improve the quality of life for affected individuals. Identifying ASD based on brain functional connectivity (FC) poses a challenge due to the high heterogeneity of subjects' fMRI data in different sites. Meanwhile, deep learning algorithms show efficacy in ASD identification but lack interpretability. In this paper, a novel approach for ASD recognition is proposed based on graph attention networks. Specifically, we treat the region of interest (ROI) of the subjects as node, conduct wavelet decomposition of the BOLD signal in each ROI, extract wavelet features, and utilize them along with the mean and variance of the BOLD signal as node features, and the optimized FC matrix as the adjacency matrix, respectively. We then employ the self-attention mechanism to capture long-range dependencies among features. To enhance interpretability, the node-selection pooling layers are designed to determine the importance of ROI for prediction. The proposed framework are applied to fMRI data of children (younger than 12 years old) from the Autism Brain Imaging Data Exchange datasets. Promising results demonstrate superior performance compared to recent similar studies. The obtained ROI detection results exhibit high correspondence with previous studies and offer good interpretability.

Spectral dynamic causal modeling: A didactic introduction and its relationship with functional connectivity.

We present a didactic introduction to spectral dynamic causal modeling (DCM), a Bayesian state-space modeling approach used to infer effective connectivity from noninvasive neuroimaging data. Spectral DCM is currently the most widely applied DCM variant for resting-state functional MRI analysis. Our aim is to explain its technical foundations to an audience with limited expertise in state-space modeling and spectral data analysis. Particular attention will be paid to cross-spectral density, which is the most distinctive feature of spectral DCM and is closely related to functional connectivity, as measured by (zero-lag) Pearson correlations. In fact, the model parameters estimated by spectral DCM are those that best reproduce the cross-correlations between all measurements-at all time lags-including the zero-lag correlations that are usually interpreted as functional connectivity. We derive the functional connectivity matrix from the model equations and show how changing a single effective connectivity parameter can affect all pairwise correlations. To complicate matters, the pairs of brain regions showing the largest changes in functional connectivity do not necessarily coincide with those presenting the largest changes in effective connectivity. We discuss the implications and conclude with a comprehensive summary of the assumptions and limitations of spectral DCM.

Diffusion time-related structure-function coupling reveals differential association with inter-individual variations in body mass index

Body mass index (BMI) is an indicator of obesity, and recent neuroimaging studies have demonstrated that inter-individual variations in BMI are associated with altered brain structure and function. However, the mechanism underlying the alteration of structure-function correspondence according to BMI is under-investigated. In this study, we studied structural and functional connectivity derived from diffusion MRI tractography and inter-regional correlations of functional MRI time series, respectively. We combined the structural and functional connectivity information using the Riemannian optimization approach. First, the low-dimensional principal eigenvectors (i.e., gradients) of the structural connectivity were generated by applying diffusion map embedding with varying diffusion times. A transformation was identified so that the structural and functional embeddings share the same coordinate system, and subsequently, the functional connectivity matrix was simulated. Then, we generated gradients from the simulated functional connectivity matrix. We found the most apparent cortical hierarchical organization differentiating between low-level sensory and higher-order transmodal regions in the middle of the diffusion time, indicating that the hierarchical organization of the brain may reflect the intermediate mechanisms of mono- and polysynaptic communications. Associations between the functional gradients and BMI were strongest when the hierarchical structure was the most evident. Moreover, the gradient-BMI association map was related to the microstructural features, and the findings indicated that the BMI-related structure-function coupling was significantly associated with brain microstructure, particularly in higher-order transmodal areas. Finally, transcriptomic association analysis revealed the potential biological underpinnings specifying gene enrichment in the striatum, hypothalamus, and cortical cells. Our findings provide evidence that structure-function correspondence is strongly coupled with BMI when hierarchical organization is the most apparent and that the associations are related to the multiscale properties of the brain, leading to an advanced understanding of the neural mechanisms related to BMI.

Increased Thalamic Connectivity in Juvenile Myoclonic Epilepsy Based on Electroencephalography Source-Level Analysis.

Background: This study investigated alterations in the intrinsic thalamic network of patients with juvenile myoclonic epilepsy (JME) based on an electroencephalography (EEG) source-level analysis. Materials and Methods: We enrolled patients newly diagnosed with JME as well as healthy controls. The assessments were conducted in the resting state. We computed sources based on the scalp electrical potentials using a minimum-norm imaging method and a standardized, low-resolution, brain electromagnetic tomography approach. To create a functional connectivity matrix, we used the Talairach atlas to define thalamic nodes and applied the coherence method to measure brain synchronization as edges. We then calculated the intrinsic thalamic network using graph theory. We compared the intrinsic thalamic network of patients with JME with those of healthy controls. Results: This study included 67 patients with JME and 66 healthy controls. EEG source-level analysis revealed significant differences in the intrinsic thalamic networks between patients with JME and healthy controls. The measures of functional connectivity (radius, diameter, and characteristic path length) were significantly lower in patients with JME than in healthy controls (radius: 2.769 vs. 3.544, p = 0.015; diameter: 4.464 vs. 5.443, p = 0.024; and characteristic path length: 2.248 vs. 2.616, p = 0.046). Conclusions: We demonstrated alterations in the intrinsic thalamic network in patients with JME compared with those in healthy controls based on the EEG source-level analysis. These findings indicated increased thalamic connectivity in the JME group. These intrinsic thalamic network changes may be related to the pathophysiology of JME.

Sex differences in fetal brain functional network topology.

The fetal period is a critical stage in brain development, and understanding the characteristics of the fetal brain is crucial. Although some studies have explored aspects of fetal brain functional networks, few have specifically focused on sex differences in brain network characteristics. We adopted the graph theory method to calculate brain network functional connectivity and topology properties (including global and nodal properties), and further compared the differences in these parameters between male and female fetuses. We found that male fetuses showed an increased clustering coefficient and local efficiency than female fetuses, but no significant group differences concerning other graph parameters and the functional connectivity matrix. Our study suggests the existence of sex-related distinctions in the topological properties of the brain network at the fetal stage of development and demonstrates an increase in brain network separation in male fetuses compared with female fetuses.

Construction and Analysis of a New Resting-State Whole-Brain Network Model.

Mathematical modeling and computer simulation are important methods for understanding complex neural systems. The whole-brain network model can help people understand the neurophysiological mechanisms of brain cognition and functional diseases of the brain. In this study, we constructed a resting-state whole-brain network model (WBNM) by using the Wendling neural mass model as the node and a real structural connectivity matrix as the edge of the network. By analyzing the correlation between the simulated functional connectivity matrix in the resting state and the empirical functional connectivity matrix, an optimal global coupling coefficient was obtained. Then, the waveforms and spectra of simulated EEG signals and four commonly used measures from graph theory and small-world network properties of simulated brain networks under different thresholds were analyzed. The results showed that the correlation coefficient of the functional connectivity matrix of the simulated WBNM and empirical brain networks could reach a maximum value of 0.676 when the global coupling coefficient was set to 20.3. The simulated EEG signals showed rich waveform and frequency-band characteristics. The commonly used graph-theoretical measures and small-world properties of the constructed WBNM were similar to those of empirical brain networks. When the threshold was set to 0.22, the maximum correlation between the simulated WBNM and empirical brain networks was 0.709. The constructed resting-state WBNM is similar to a real brain network to a certain extent and can be used to study the neurophysiological mechanisms of complex brain networks.

Distinct functional subnetworks of cognitive domains in older adults with minor cognitive deficits.

Although past research has established a relationship between functional connectivity and cognitive function, less is known about which cognitive domains are associated with which specific functional networks. This study investigated associations between functional connectivity and global cognitive function and performance in the domains of memory, executive function and psychomotor speed in 166 older adults aged 75-91 years (mean = 80.3 ± 3.8) with minor cognitive deficits (Mini-Mental State Examination scores between 21 and 27). Functional connectivity was assessed within 10 standard large-scale resting-state networks and on a finer spatial resolution between 300 nodes in a functional connectivity matrix. No domain-specific associations with mean functional connectivity within large-scale resting-state networks were found. Node-level analysis revealed that associations between functional connectivity and cognitive performance differed across cognitive functions in strength, location and direction. Specific subnetworks of functional connections were found for each cognitive domain in which higher connectivity between some nodes but lower connectivity between other nodes were related to better cognitive performance. Our findings add to a growing body of literature showing differential sensitivity of functional connections to specific cognitive functions and may be a valuable resource for hypothesis generation of future studies aiming to investigate specific cognitive dysfunction with resting-state functional connectivity in people with beginning cognitive deficits.

Response solutions for a kind of quasi-periodic forced neuron system

Based on the transcranial magnetic stimulation (TMS) therapy for major depression disorder and anxiety disorder, an abstract form of neuron differential equation with quasi-periodic coefficients is established. Considering the interactions among neurons, electrical effect induced by TMS therapy, and random effect, the probability density function with respect to the firing rates of neurons of the above equation is constructed, which satisfies a static Fokker–Planck equation with quasi-periodic coefficients. Hence, different clinical TMS therapies are discussed numerically by setting different parameters, such as the coupling strengths, the intensity, frequency, initial phase, phase difference of the electric field. In addition, a functional connectivity matrix related to the adjacency matrix with variable coupling strengths based on data from a real brain network is constructed. It is shown that the proper coupling strengths and the electric field parameters are crucial for TMS therapy. The methods include Kolmogorov–Arnold–Moser (KAM) theory, numerical analysis, and data analysis, having interdisciplinary characteristics. The result is original, which may be applied to TMS combined with drug therapy and the cognitive process of the brain.

Fusing multi-scale fMRI features using a brain-inspired multi-channel graph neural network for major depressive disorder diagnosis

Depression stands as one of the most pernicious mental disorders in contemporary society, characterized by a highly intricate pathological mechanism. Specifically, individuals suffering from Major Depressive Disorder (MDD) exhibit heightened vulnerability to suicidal tendencies. Currently, healthcare practitioners often encounter challenges related to the misdiagnosis and underdiagnosis of depression during clinical assessments. Consequently, it is of paramount importance to develop highly accurate auxiliary diagnostic tools for depression. Unfortunately, traditional machine learning and deep learning methodologies frequently neglect the integration of multi-source data and disregard the intricate topological structure and high-order attributes of brain networks. In this study, a multi-scale feature fusion classification framework is proposed to distinguish between MDD patients and healthy controls. Within the proposed model, a novel method, the Cross-Level High-Order Interaction (CLHOI), is introduced and implemented on a low-order functional connectivity (LOFC) matrix to derive two distinct high-order functional connectivity (HOFC) matrices. Subsequently, a Multi-Channel Fusion Graph Convolutional Network (MFGCN) is trained by integrating high-order and low-order brain graph features along with phenotypic information. The results of 10-fold cross-validation experiments conducted on the publicly available REST-meta-MDD dataset indicate that the fusion of multi-scale features improves the average accuracy by approximately 3%, resulting in an accuracy rate of 77.6%. Simultaneously, the hypothesis asserting the existence of intricate information interactions at various levels within brain connectivity networks is validated. Moreover, our model exhibits strong explanatory capabilities, effectively identifying brain regions closely associated with MDD, including the Precentral gyrus, Superior frontal gyrus, Cuneus, Lingual gyrus, and Fusiform gyrus. In comparison to numerous advanced studies within the same domain, our approach has produced competitive results. Furthermore, our proposed method can be readily extended to facilitate the diagnosis of various neurological diseases.

TSP-GNN: a novel neuropsychiatric disorder classification framework based on task-specific prior knowledge and graph neural network.

Neuropsychiatric disorder (ND) is often accompanied by abnormal functional connectivity (FC) patterns in specific task contexts. The distinctive task-specific FC patterns can provide valuable features for ND classification models using deep learning. However, most previous studies rely solely on the whole-brain FC matrix without considering the prior knowledge of task-specific FC patterns. Insight by the decoding studies on brain-behavior relationship, we develop TSP-GNN, which extracts task-specific prior (TSP) connectome patterns and employs graph neural network (GNN) for disease classification. TSP-GNN was validated using publicly available datasets. Our results demonstrate that different ND types show distinct task-specific connectivity patterns. Compared with the whole-brain node characteristics, utilizing task-specific nodes enhances the accuracy of ND classification. TSP-GNN comprises the first attempt to incorporate prior task-specific connectome patterns and the power of deep learning. This study elucidates the association between brain dysfunction and specific cognitive processes, offering valuable insights into the cognitive mechanism of neuropsychiatric disease.

Structural and functional multilayer network analysis in restless legs syndrome patients.

The combination of brain structural and functional connectivity offers complementary insights into its organisation. Multilayer network analysis explores various relationships across different layers within a single system. We aimed to investigate changes in the structural and functional multilayer network in 69 patients with primary restless legs syndrome (RLS) compared with 50 healthy controls. Participants underwent diffusion tensor imaging (DTI) and resting state-functional magnetic resonance imaging (rs-fMRI) using a three-tesla MRI scanner. We constructed a structural connectivity matrix derived from DTI using a DSI program and made a functional connectivity matrix based on rs-fMRI using an SPM program and CONN toolbox. A multilayer network analysis, using BRAPH program, was then conducted to assess the connectivity patterns in both groups. At the global level, significant differences there were between the patients with RLS and healthy controls. The average multiplex participation was lower in patients with RLS than in healthy controls (0.804 vs. 0.821, p = 0.042). Additionally, several regions showed significant differences in the nodal level in multiplex participation between patients with RLS and healthy controls, particularly the frontal and temporal lobes. The regions affected included the inferior frontal gyrus, medial orbital gyrus, precentral gyrus, rectus gyrus, insula, superior and inferior temporal gyrus, medial and lateral occipitotemporal gyrus, and temporal pole. These results represent evidence of diversity in interactions between structural and functional connectivity in patients with RLS, providing a more comprehensive understanding of the brain network in RLS. This may contribute to a precise diagnosis of RLS, and aid the development of a biomarker to track treatment effectiveness.

Effects of visual-electrotactile stimulation feedback on brain functional connectivity during motor imagery practice

The use of neurofeedback is an important aspect of effective motor rehabilitation as it offers real-time sensory information to promote neuroplasticity. However, there is still limited knowledge about how the brain’s functional networks reorganize in response to such feedback. To address this gap, this study investigates the reorganization of the brain network during motor imagery tasks when subject to visual stimulation or visual-electrotactile stimulation feedback. This study can provide healthcare professionals with a deeper understanding of the changes in the brain network and help develop successful treatment approaches for brain–computer interface-based motor rehabilitation applications. We examine individual edges, nodes, and the entire network, and use the minimum spanning tree algorithm to construct a brain network representation using a functional connectivity matrix. Furthermore, graph analysis is used to detect significant features in the brain network that might arise in response to the feedback. Additionally, we investigate the power distribution of brain activation patterns using power spectral analysis and evaluate the motor imagery performance based on the classification accuracy. The results showed that the visual and visual-electrotactile stimulation feedback induced subject-specific changes in brain activation patterns and network reorganization in the alpha band. Thus, the visual-electrotactile stimulation feedback significantly improved the integration of information flow between brain regions associated with motor-related commands and higher-level cognitive functions, while reducing cognitive workload in the sensory areas of the brain and promoting positive emotions. Despite these promising results, neither neurofeedback modality resulted in a significant improvement in classification accuracy, compared with the absence of feedback. These findings indicate that multimodal neurofeedback can modulate imagery-mediated rehabilitation by enhancing motor-cognitive communication and reducing cognitive effort. In future interventions, incorporating this technique to ease cognitive demands for participants could be crucial for maintaining their motivation to engage in rehabilitation.

Capturing functional connectomics using Riemannian partial least squares

For neurological disorders and diseases, functional and anatomical connectomes of the human brain can be used to better inform targeted interventions and treatment strategies. Functional magnetic resonance imaging (fMRI) is a non-invasive neuroimaging technique that captures spatio-temporal brain function through change in blood-oxygen-level-dependent (BOLD) signals over time. FMRI can be used to study the functional connectome through the functional connectivity matrix; that is, Pearson’s correlation matrix between time series from the regions of interest of an fMRI image. One approach to analysing functional connectivity is using partial least squares (PLS), a multivariate regression technique designed for high-dimensional predictor data. However, analysing functional connectivity with PLS ignores a key property of the functional connectivity matrix; namely, these matrices are positive definite. To account for this, we introduce a generalisation of PLS to Riemannian manifolds, called R-PLS, and apply it to symmetric positive definite matrices with the affine invariant geometry. We apply R-PLS to two functional imaging datasets: COBRE, which investigates functional differences between schizophrenic patients and healthy controls, and; ABIDE, which compares people with autism spectrum disorder and neurotypical controls. Using the variable importance in the projection statistic on the results of R-PLS, we identify key functional connections in each dataset that are well represented in the literature. Given the generality of R-PLS, this method has the potential to investigate new functional connectomes in the brain, and with future application to structural data can open up further avenues of research in multi-modal imaging analysis.

Spectral representation of EEG data using learned graphs with application to motor imagery decoding

Electroencephalography (EEG) data entail a complex spatiotemporal structure that reflects ongoing organization of brain activity. Characterization of the spatial patterns is an indispensable step in numerous EEG processing pipelines. We present a novel method for transforming EEG data into a spectral representation. First, we learn subject-specific graphs from each subject’s EEG data. Second, by eigendecomposition of the normalized Laplacian matrix of each subject’s graph, an orthonormal basis is obtained using which any given EEG map of the subject can be decomposed, providing a spectral representation of the data. We show that energy of EEG maps is strongly associated with low frequency components of the learned basis, reflecting the smooth topography of EEG maps. As a proof-of-concept for this alternative view of EEG data, we consider the task of decoding two-class motor imagery (MI) data. To this aim, the spectral representations are first mapped into a discriminative subspace for differentiating two-class data using a projection matrix obtained by the Fukunaga–Koontz transform (FKT). An SVM classifier is then trained and tested on the resulting features to differentiate MI classes. The method is benchmarked against features extracted from a subject-specific functional connectivity matrix as well as four alternative MI-decoding methods on Dataset IVa of BCI Competition III. Experimental results show the superiority of the proposed method over alternative approaches in differentiating MI classes, reflecting the added benefit of (i) decomposing EEG data using data-driven, subject-specific harmonic bases, and (ii) accounting for class-specific temporal variations in spectral profiles.