Robyn. L. Miller

The cortical hierarchy is a central organizing feature of brain structure and function, yet whether it is continuously expressed in spontaneous neural activity remains unresolved. Here, we show that resting-state brain dynamics are organized along a directional coordination axis that recapitulates hierarchical information flow. Focusing on the directional dynamics of interregional coordination, we identify three recurrent coordination regimes: a feedback-dominated mode in which transmodal cortex leads sensory systems, a feedforward-dominated mode reflecting the reverse, and an integrative mode of balanced bidirectional exchange. These modes define a low-dimensional coordination landscape that replicates across four independent cohorts, establishing directional structure as a stable property of the adult brain. In schizophrenia, this landscape is selectively reorganized: feedback-dominated coordination becomes less persistent, integrative coordination becomes more persistent, and global dynamics shift toward faster convergence and reduced entropy, reflecting a loss of directional constraint and dynamical flexibility. These alterations track symptom severity, cognitive performance, and medication exposure. Mediation analyses suggest that medication-related reductions in integrative coordination are statistically routed through feedforward dynamics, consistent with dopaminergic modulation of recurrent cortical loops as a candidate mechanism. Together, these findings identify directional functional dynamics as a fundamental and clinically informative axis of large-scale brain organization.

High dimensionality of dynamic functional connectivity (dFNC) data representation complicates clinical interpretation and biomarker discovery. We propose a new complementary analytical framework based on dynamic inter-network connectivity entropy (DICE) and its potential use as a biomarker of mental illness. Our framework shows that DICE features extend beyond patient-control discrimination, revealing distinct pathophysiological signatures and differential associations with symptom dimensions. Using resting-state fMRI data from 311 participants, 160 controls, 151 schizophrenia (SZ) patients, we identified 53 intrinsic networks, computed DICE and derived three families of DICE-based metrics: (i) entropy level and range, (ii) distributional shape and temporal organization, (iii) entropy-state repertoire and occupancy. These measures revealed a multidimensional signature of altered entropy dynamics in SZ: (1) elevated baseline entropy with reduced fluctuation magnitude and reduced entropy acceleration; (2) reduced temporal persistence of entropy excursions and entropy distributions closer to Gaussian; and (3) a narrowed repertoire of entropy states, prolonged time in near-baseline entropy configurations. The DICE-based metrics within the SZ group show different associations with symptom dimensions. Reduced fluctuation magnitude and acceleration were associated with greater PANSS general symptom severity (disturbance of volition and preoccupation). Reduced deviation from Gaussianity was associated with higher PANSS positive severity (delusions and hallucinations). Reduced temporal persistence was associated with multiple PANSS positive, negative, and general symptoms. Reduced entropy-state diversity and prolonged dwell time in near-baseline states were associated with depression and PANSS positive/general severity, respectively. The multidimensional pathophysiology revealed through the different entropy patterns may potentially guide biomarker development and personalized treatments.

The estimation of brain networks is instrumental in quantifying and evaluating brain function. Nevertheless, achieving precise estimations of subject‐level networks has proven to be a formidable task. In response to this challenge, researchers have developed group‐inference frameworks that leverage robust group‐level estimations as a common reference point to infer corresponding subject‐level networks. Generally, existing approaches either leverage the common reference as a strict, voxel‐wise spatial constraint (i.e., strong constraints at the voxel level) or impose no constraints. Here, we propose a targeted approach that harnesses the topological information of group‐level networks to encode a high‐level representation of spatial properties to be used as constraints, which we refer to as Topologically Optimized Intrinsic Brain Networks (TOIBN). Consequently, our method inherits the significant advantages of constraint‐based approaches, such as enhancing estimation efficacy in noisy data or small sample sizes. On the other hand, our method provides a softer constraint than voxel‐wise penalties, which can result in the loss of individual variation, increased susceptibility to model biases, and potentially missing important subject‐specific information. Our analyses show that the subject maps from our method are less noisy and true to the group networks while promoting subject variability that can be lost from strict constraints. We also find that the topological properties resulting from the TOIBN maps are more expressive of differences between individuals with schizophrenia and controls in the default mode, subcortical, and visual networks.

Gaining insight into the spectral and temporal alterations in brain connectivity associated with Alzheimer’s disease (AD) may offer pathways toward more informative biomarkers and a deeper understanding of disease mechanisms. We propose FINE (Frequency-aware Interpretable Neural Encoder), a novel deep learning model designed to capture multi-scale temporal and frequency-specific patterns in dynamic functional network connectivity (dFNC) derived from resting-state fMRI. FINE integrates multiple expert branches, including convolutional layers, learnable wavelet layers, transformers, and static encoders, enabling the joint modeling of temporal evolution and spectral content of brain networks in an end-to-end framework. Beyond classification, FINE supports frequency-wise interpretability by aligning gradient-based saliency maps with statistical group differences, revealing potential robust, biologically meaningful biomarkers of AD. Evaluated on the large OASIS-3 dataset (856 subjects), FINE achieves AD classification performance (ROC-AUC 0.769) and provides insights into frequency-specific connectivity disruptions, particularly within subcortical, sensorimotor, and cerebellar networks. Our results demonstrate that incorporating frequency-aware modeling and interpretable architectures can advance both disease classification and underlying functional disruption of AD-related brain dynamics.

Schizophrenia has long been linked to impaired coordination of brain activity, yet most frameworks overlook two key dimensions: the amplitude of brain signals and the differing timescales on which regions operate. These factors are critical in disorders where neural activity is exaggerated and slowed. In healthy adults, networks compensate for mismatched processing speeds to maintain proportionate activity, but this process is poorly understood in schizophrenia. We developed a timescale-aligned, time-resolved framework that separates temporal distortions from genuine amplitude differences, enabling measurement of amplitude balance between networks across timescales. This approach was applied to large-scale fMRI datasets, including the Human Connectome Project and a multi-site schizophrenia cohort. Patients with schizophrenia showed greater amplitude imbalance, especially during fast fluctuations, along with more frequent re-entry into unbalanced states and slower recovery to stable coordination. We further identified a flexible intermediate state that patients occupied more often, and that predicted better working-memory performance. Across cohorts, amplitude imbalance was associated with greater symptom severity and poorer reasoning ability. These findings provide a new mechanistic view of dyscoordination in schizophrenia grounded in timescale-normalized amplitude dynamics, highlight aberrant recovery of amplitude balance as a core feature of the illness, and suggest that timescale-aligned amplitude imbalance may serve as a promising target for biomarker development.

The estimation of brain networks is instrumental in quantifying and evaluating brain function. Nevertheless, achieving precise estimations of subject-level networks has proven to be a formidable task. In response to this challenge, researchers have developed group-inference frameworks that leverage robust group-level estimations as a common reference point to infer corresponding subject-level networks. Generally, existing approaches either leverage the common reference as a strict, voxel-wise spatial constraint (i.e., strong constraints at the voxel level) or impose no constraints. Here, we propose a targeted approach that harnesses the topological information of group-level networks to encode a high-level representation of spatial properties to be used as constraints, which we refer to as Topologically Optimized Intrinsic Brain Networks (TOIBN). Consequently, our method inherits the significant advantages of constraint-based approaches, such as enhancing estimation efficacy in noisy data or small sample sizes. On the other hand, our method provides a softer constraint than voxel-wise penalties, which can result in the loss of individual variation, increased susceptibility to model biases, and potentially missing important subject-specific information. Our analyses show that the subject maps from our method are less noisy and true to the group networks while promoting subject variability that can be lost from strict constraints. We also find that the topological properties resulting from the TOIBN maps are more expressive of differences between individuals with schizophrenia and controls in the default mode, subcortical, and visual networks.

Schizophrenia (SZ) patients exhibit abnormal static and dynamic functional connectivity across various brain domains. We present a novel approach based on static and dynamic inter‐network connectivity entropy (ICE), which represents the entropy of a given network's connectivity to all the other brain networks. This novel approach enables the investigation of how connectivity strength is heterogeneously distributed across available targets in both SZ patients and healthy controls. We analyzed fMRI data from 151 SZ patients and 160 demographically matched healthy controls (HC). Our assessment encompassed both static and dynamic ICE, revealing significant differences in the heterogeneity of connectivity levels across available functional brain networks between SZ patients and HC. These networks are associated with subcortical (SC), auditory (AUD), sensorimotor (SM), visual (VIS), cognitive control (CC), default mode network (DMN), and cerebellar (CB) functional brain domains. Elevated ICE observed in individuals with SZ suggests that patients exhibit significantly higher randomness in the distribution of time‐varying connectivity strength across functional regions from each source network, compared to HC. C‐means fuzzy clustering analysis of functional ICE correlation matrices revealed that SZ patients exhibit significantly higher occupancy weights in clusters with weak, low‐scale functional entropy correlation, while the control group shows greater occupancy weights in clusters with strong, large‐scale functional entropy correlation. K‐means clustering analysis on time‐indexed ICE vectors revealed that cluster with highest ICE have higher occupancy rates in SZ patients whereas clusters characterized by lowest ICE have larger occupancy rates for control group. Furthermore, our dynamic ICE approach revealed that in HC, the brain primarily communicates through complex, less structured connectivity patterns, with occasional transitions into more focused patterns. Individuals with SZ are significantly less likely to attain these more focused and structured transient connectivity patterns. The proposed ICE measure presents a novel framework for gaining deeper insight into mechanisms of healthy and diseased brain states and represents a useful step forward in developing advanced methods to help diagnose mental health conditions.

Our study advances the application of dynamic time warping (DTW) as a functional connectivity measure by introducing a normalization technique which enhances the detection of schizophrenia effects in comparison to both standard DTW and traditional correlation methods. By rigorously examining the statistical validity of DTW and our proposed normalized DTW measure, we show that it effectively captures interdependencies between fMRI signals beyond linear correlation, offering a more robust, complementary and informative approach to functional connectivity analysis. Through comprehensive evaluations, we demonstrate that normalized DTW is more sensitive to differences in functional brain network connections between schizophrenia and controls, highlighting its potential to provide deeper insight into clinical research. Clinical Relevance: This study enhances our understanding of the functional specificity of schizophrenia by emphasizing the importance of nonlinear relationships through the introduction of a normalization technique for the DTW metric.

Despite increasing interest in the dynamics of functional brain networks, most studies focus on the changing relationships over time between spatially static networks or regions. Here we propose an approach to study dynamic spatial brain networks in human resting state functional magnetic resonance imaging (rsfMRI) data and evaluate the temporal changes in the volumes of these 4D networks. Our results show significant volumetric coupling (i.e., synchronized shrinkage and growth) between networks during the scan, that we refer to as dynamic spatial network connectivity (dSNC). We find that several features of such dynamic spatial brain networks are associated with cognition, with higher dynamic variability in these networks and higher volumetric coupling between network pairs positively associated with cognitive performance. We show that these networks are modulated differently in individuals with schizophrenia versus typical controls, resulting in network growth or shrinkage, as well as altered focus of activity within a network. Schizophrenia also shows lower spatial dynamical variability in several networks, and lower volumetric coupling between pairs of networks, thus upholding the role of dynamic spatial brain networks in cognitive impairment seen in schizophrenia. Our data show evidence for the importance of studying the typically overlooked voxel‐wise changes within and between brain networks.