Reliability correction for functional connectivity: Theory and implementation

Longitudinal stability of individual brain plasticity patterns in blindness

The primary visual cortex (V1) in blindness is engaged in a wide spectrum of tasks and sensory modalities, including audition, touch, language, and memory. This widespread involvement raises questions regarding the constancy of its role and whether it might exhibit flexibility in its function over time, connecting to diverse network functions specific to task demands. This would suggest that reorganized V1 assumes a role like multiple-demand system regions. Alternatively, varying patterns of plasticity in blind V1 may be attributed to individual factors, with different blind individuals recruiting V1 preferentially for different functions. In support of this, we recently showed that V1 functional connectivity (FC) varies greatly across blind individuals. But do these represent stable individual patterns of plasticity, or are they driven more by instantaneous changes, like a multiple-demand system now inhabiting V1? Here, we tested whether individual FC patterns from the V1 of blind individuals are stable over time. We show that over two years, FC from the V1 is unique and highly stable in a small sample of repeatedly sampled congenitally blind individuals. Further, using multivoxel pattern analysis, we demonstrate that the unique reorganization patterns of these individuals allow decoding of participant identity. Together with recent evidence for substantial individual differences in V1 connectivity, this indicates that there may be a consistent role for V1 in blindness, which may differ for each individual. Further, it suggests that the variability in visual reorganization in blindness across individuals could be used to seek stable neuromarkers for sight rehabilitation and assistive approaches.

Connectome caricatures: removing large-amplitude co-activation patterns in resting-state fMRI emphasizes individual differences

High-amplitude co-activation patterns are sparsely present during resting-state fMRI but drive functional connectivity1-5. Further, they resemble task activation patterns and are well-studied3,5-10. However, little research has characterized the remaining majority of the resting-state signal. In this work, we introduced caricaturing-a method to project resting-state data to a subspace orthogonal to a manifold of co-activation patterns estimated from the task fMRI data. Projecting to this subspace removes linear combinations of these co-activation patterns from the resting-state data to create Caricatured connectomes. We used rich task data from the Human Connectome Project (HCP)11 and the UCLA Consortium for Neuropsychiatric Phenomics12 to construct a manifold of task co-activation patterns. Caricatured connectomes were created by projecting resting-state data from the HCP and the Yale Test-Retest13 datasets away from this manifold. Like caricatures, these connectomes emphasized individual differences by reducing between-individual similarity and increasing individual identification14. They also improved predictive modeling of brain-phenotype associations. As caricaturing removes group-relevant task variance, it is an initial attempt to remove task-like co-activations from rest. Therefore, our results suggest that there is a useful signal beyond the dominating co-activations that drive resting-state functional connectivity, which may better characterize the brain's intrinsic functional architecture.

How do tasks impact the reliability of fMRI functional connectivity?

While there is growing interest in the use of functional magnetic resonance imaging-functional connectivity (fMRI-FC) for biomarker research, low measurement reliability of conventional acquisitions may limit applications. Factors known to impact FC reliability include scan length, head motion, signal properties, such as temporal signal-to-noise ratio (tSNR), and the acquisition state or task. As tasks impact signal in a region-wise fashion, they likely impact FC reliability differently across the brain, making task an important decision in study design. Here, we use the densely sampled Midnight Scan Club (MSC) dataset, comprising 5 h of rest and 6 h of task fMRI data in 10 healthy adults, to investigate regional effects of tasks on FC reliability. We further considered how BOLD signal properties contributing to tSNR, that is, temporal mean signal (tMean) and temporal standard deviation (tSD), vary across the brain, associate with FC reliability, and are modulated by tasks. We found that, relative to rest, tasks enhanced FC reliability and increased tSD for specific task-engaged regions. However, FC signal variability and reliability is broadly dampened during tasks outside task-engaged regions. From our analyses, we observed signal variability was the strongest driver of FC reliability. Overall, our findings suggest that the choice of task can have an important impact on reliability and should be considered in relation to maximizing reliability in networks of interest as part of study design.

Personalized connectivity-based network targeting model of transcranial magnetic stimulation for treatment of psychiatric disorders: computational feasibility and reproducibility

Repetitive transcranial magnetic stimulation (rTMS) holds promise for treating psychiatric disorders; however, the variability in treatment efficacy among individuals underscores the need for further improvement. Growing evidence has shown that TMS induces a broad network modulatory effect, and its effectiveness may rely on accurate modulation of the pathological network specific to each disorder. Therefore, determining the optimal TMS coil setting that will engage the functional pathway delivering the stimulation is crucial. Compared to group-averaged functional connectivity (FC), individual FC provides specific information about a person's brain functional architecture, offering the potential for more accurate network targeting for personalized TMS. However, the low signal-to-noise ratio (SNR) of FC poses a challenge when utilizing individual resting-state FC. To overcome this challenge, the proposed solutions include increasing the scan duration and employing the cluster method to enhance the stability of FC. This study aimed to evaluate the stability of a personalized FC-based network targeting model in individuals with major depressive disorder or schizophrenia with auditory verbal hallucinations. Using resting-state functional magnetic resonance imaging data from the Human Connectome Project, we assessed the model's stability. We employed longer scan durations and cluster methodologies to improve the precision in identifying optimal individual sites. Our findings demonstrate that a scan duration of 28 minutes and the utilization of the cluster method achieved stable identification of individual sites, as evidenced by the intraindividual distance falling below the ~1cm spatial resolution of TMS. The current model provides a feasible approach to obtaining stable personalized TMS targets from the scalp, offering a more accurate method of TMS targeting in clinical applications.

Personalized brain MRI revealed distinct functional and anatomical disruptions in Creutzfeldt-Jakob disease and Alzheimer's disease

AIMS

Creutzfeldt-Jakob disease (CJD) is a lethal neurodegenerative disorder, which leads to a rapidly progressive dementia. This study aimed to examine the cortical alterations in CJD, changes in these brain characteristics over time, and the differences between CJD and Alzheimer's disease (AD) that show similar clinical manifestations.

METHODS

To obtain reliable, subject-specific functional measures, we acquired 24 min of resting-state fMRI data from each subject. We applied an individual-based approach to characterize the functional brain organization of 10 patients with CJD, 8 matched patients with AD, and 8 normal controls. We measured cortical atrophy as well as disruption in resting-state functional connectivity (rsFC) and then investigated longitudinal brain changes in a subset of CJD patients.

RESULTS

CJD was associated with widespread cortical thinning and weakened rsFC. Compared with AD, CJD showed distinct atrophy patterns and greater disruptions in rsFC. Moreover, the longitudinal data demonstrated that the progressive cortical thinning and disruption in rsFC mainly affected the association rather than the primary cortex in CJD.

CONCLUSIONS

CJD shows unique anatomical and functional disruptions in the cerebral cortex, distinct from AD. Rapid progression of CJD affects both the cortical thickness and rsFC in the association cortex.

Altered stability of dynamic brain functional architecture in primary open-angle glaucoma: a surface-based resting-state fMRI study

Delineating the neuropathological characteristics of primary open-angle glaucoma (POAG) is critical for understanding its pathophysiology. While temporal stability represents a crucial aspect of the brain's functional architecture, the specific patterns underlying its contribution to POAG remain unclear. This study aims to analyze the brain functional abnormalities in POAG using functional stability, a dynamic functional connectivity (DFC) approach based on resting-state functional magnetic resonance imaging (rs-fMRI). Seventy patients with POAG and forty-five healthy controls underwent rs-fMRI and ophthalmological examinations. The stability of DFC was calculated as the concordance of DFC over time using a sliding-window approach, and the differences in stability between the two groups were compared. Subsequently, Spearman's correlation analyses were conducted to examine the relationship between functional stability and clinical indicators. Compared with healthy controls, patients with POAG exhibited significantly decreased functional stability in the visual network, including the early visual center, ventral and dorsal stream visual cortex in both hemispheres. Conversely, stability values increased in the bilateral inferior parietal gyrus and right inferior frontal cortex. In POAG patients, the dynamic stability of the left early visual cortex and ventral stream visual cortex correlated with the mean deviation of visual field defects (r = 0.251, p = 0.037). The evidence from this study suggests that functional stability may provide a new understanding of brain alterations in the progression of POAG.

Longitudinal stability of individual brain plasticity patterns in blindness

The primary visual cortex (V1) in individuals born blind is engaged in a wide spectrum of tasks and sensory modalities, including audition, touch, language, and memory. This widespread involvement raises questions regarding the constancy of its role and whether it might exhibit flexibility in its function over time, connecting to diverse network functions in response to task-specific demands. This would suggest that reorganized V1 takes on a role similar to cognitive multiple-demand system regions. Alternatively, it is possible that the varying patterns of plasticity observed in the blind V1 can be attributed to individual factors, whereby different blind individuals recruit V1 for different functions, highlighting the immense idiosyncrasy of plasticity. In support of this second account, we have recently shown that V1 functional connectivity varies greatly across blind individuals. But do these represent stable individual patterns of plasticity or merely instantaneous changes, for a multiple-demand system now inhabiting V1? Here we tested if individual connectivity patterns from the visual cortex of blind individuals are stable over time. We show that over two years, fMRI functional connectivity from the primary visual cortex is unique and highly stable in a small sample of repeatedly sampled congenitally blind individuals. Further, using multivoxel pattern analysis, we demonstrate that the unique reorganization patterns of these individuals allow decoding of participant identity. Together with recent evidence for substantial individual differences in visual cortex connectivity, this indicates there may be a consistent role for the visual cortex in blindness, which may differ for each individual. Further, it suggests that the variability in visual reorganization in blindness across individuals could be used to seek stable neuromarkers for sight rehabilitation and assistive approaches.

Reliability and clinical utility of spatially constrained estimates of intrinsic functional networks from very short fMRI scans

Resting-state functional network connectivity (rsFNC) has shown utility for identifying characteristic functional brain patterns in individuals with psychiatric and mood disorders, providing a promising avenue for biomarker development. However, several factors have precluded widespread clinical adoption of rsFNC diagnostics, namely a lack of standardized approaches for capturing comparable and reproducible imaging markers across individuals, as well as the disagreement on the amount of data required to robustly detect intrinsic connectivity networks (ICNs) and diagnostically relevant patterns of rsFNC at the individual subject level. Recently, spatially constrained independent component analysis (scICA) has been proposed as an automated method for extracting ICNs standardized to a chosen network template while still preserving individual variation. Leveraging the scICA methodology, which solves the former challenge of standardized neuroimaging markers, we investigate the latter challenge of identifying a minimally sufficient data length for clinical applications of resting-state fMRI (rsfMRI). Using a dataset containing rsfMRI scans of individuals with schizophrenia and controls (M = 310) as well as simulated rsfMRI, we evaluated the robustness of ICN and rsFNC estimates at both the subject- and group-level, as well as the performance of diagnostic classification, with respect to the length of the rsfMRI time course. We found individual estimates of ICNs and rsFNC from the full-length (5 min) reference time course were sufficiently approximated with just 3-3.5 min of data (r = 0.85, 0.88, respectively), and significant differences in group-average rsFNC could be sufficiently approximated with even less data, just 2 min (r = 0.86). These results from the shorter clinical data were largely consistent with the results from validation experiments using longer time series from both simulated (30 min) and real-world (14 min) datasets, in which estimates of subject-level FNC were reliably estimated with 3-5 min of data. Moreover, in the real-world data we found rsFNC and ICN estimates generated across the full range of data lengths (0.5-14 min) more reliably matched those generated from the first 5 min of scan time than those generated from the last 5 min, suggesting increased influence of "late scan" noise factors such as fatigue or drowsiness may limit the reliability of FNC from data collected after 10+ min of scan time, further supporting the notion of shorter scans. Lastly, a diagnostic classification model trained on just 2 min of data retained 97%-98% classification accuracy relative to that of the full-length reference model. Our results suggest that, when decomposed with scICA, rsfMRI scans of just 2-5 min show good clinical utility without significant loss of individual FNC information of longer scan lengths.

Individualized precision targeting of dorsal attention and default mode networks with rTMS in traumatic brain injury-associated depression

At the group level, antidepressant efficacy of rTMS targets is inversely related to their normative connectivity with subgenual anterior cingulate cortex (sgACC). Individualized connectivity may yield better targets, particularly in patients with neuropsychiatric disorders who may have aberrant connectivity. However, sgACC connectivity shows poor test-retest reliability at the individual level. Individualized resting-state network mapping (RSNM) can reliably map inter-individual variability in brain network organization. Thus, we sought to identify individualized RSNM-based rTMS targets that reliably target the sgACC connectivity profile. We used RSNM to identify network-based rTMS targets in 10 healthy controls and 13 individuals with traumatic brain injury-associated depression (TBI-D). These "RSNM targets" were compared with consensus structural targets and targets based on individualized anti-correlation with a group-mean-derived sgACC region ("sgACC-derived targets"). The TBI-D cohort was also randomized to receive active (n = 9) or sham (n = 4) rTMS to RSNM targets with 20 daily sessions of sequential high-frequency left-sided stimulation and low-frequency right-sided stimulation. We found that the group-mean sgACC connectivity profile was reliably estimated by individualized correlation with default mode network (DMN) and anti-correlation with dorsal attention network (DAN). Individualized RSNM targets were thus identified based on DAN anti-correlation and DMN correlation. These RSNM targets showed greater test-retest reliability than sgACC-derived targets. Counterintuitively, anti-correlation with the group-mean sgACC connectivity profile was also stronger and more reliable for RSNM-derived targets than for sgACC-derived targets. Improvement in depression after RSNM-targeted rTMS was predicted by target anti-correlation with the portions of sgACC. Active treatment also led to increased connectivity within and between the stimulation sites, the sgACC, and the DMN. Overall, these results suggest that RSNM may enable reliable individualized rTMS targeting, although further research is needed to determine whether this personalized approach can improve clinical outcomes.

Connectional Hierarchy in Human Brain Revealed by Individual Variability of Functional Network Edges

The human cerebral cortex is connected by intricate inter-areal wiring at the macroscale. The cortical hierarchy from primary sensorimotor to higher-order association areas is a unifying organizational principle across various neurobiological properties; however, previous studies have not clarified whether the connections between cortical regions exhibit a similar hierarchical pattern. Here, we identify a connectional hierarchy indexed by inter-individual variability of functional connectivity edges, which continuously progresses along a hierarchical gradient from within-network connections to between-network edges connecting sensorimotor and association networks. We found that this connectional hierarchy of variability aligns with both hemodynamic and electromagnetic connectivity strength and is constrained by structural connectivity strength. Moreover, the patterning of connectional hierarchy is related to inter-regional similarity in transcriptional and neurotransmitter receptor profiles. Using the Neurosynth cognitive atlas and cortical vulnerability maps in 13 brain disorders, we found that the connectional hierarchy of variability is associated with similarity networks of cognitive relevance and that of disorder vulnerability. Finally, we found that the prominence of this hierarchical gradient of connectivity variability declines during youth. Together, our results reveal a novel hierarchal organizational principle at the connectional level that links multimodal and multiscale human connectomes to individual variability in functional connectivity.

Robust dynamic brain coactivation states estimated in individuals

A confluence of evidence indicates that brain functional connectivity is not static but rather dynamic. Capturing transient network interactions in the individual brain requires a technology that offers sufficient within-subject reliability. Here, we introduce an individualized network-based dynamic analysis technique and demonstrate that it is reliable in detecting subject-specific brain states during both resting state and a cognitively challenging language task. We evaluate the extent to which brain states show hemispheric asymmetries and how various phenotypic factors such as handedness and gender might influence network dynamics, discovering a right-lateralized brain state that occurred more frequently in men than in women and more frequently in right-handed versus left-handed individuals. Longitudinal brain state changes were also shown in 42 patients with subcortical stroke over 6 months. Our approach could quantify subject-specific dynamic brain states and has potential for use in both basic and clinical neuroscience research.

Test-retest reliability of modular-relevant analysis in brain functional network

Introduction

The human brain could be modeled as a complex network via functional magnetic resonance imaging (fMRI), and the architecture of these brain functional networks can be studied from multiple spatial scales with different graph theory tools. Detecting modules is an important mesoscale network measuring approach that has provided crucial insights for uncovering how brain organizes itself among different functional subsystems. Despite its successful application in a wide range of brain network studies, the lack of comprehensive reliability assessment prevents its potential extension to clinical trials.

Methods

To fill this gap, this paper, using resting-state test-retest fMRI data, systematically explored the reliabilities of five popular network metrics derived from modular structure. Considering the repeatability of network partition depends heavily on network size and module detection algorithm, we constructed three types of brain functional networks for each subject by using a set of coarse-to-fine brain atlases and adopted four methods for single-subject module detection and twelve methods for group-level module detection.

Results

The results reported moderate-to-good reliability in modularity, intra- and inter-modular functional connectivities, within-modular degree and participation coefficient at both individual and group levels, indicating modular-relevant network metrics can provide robust evaluation results. Further analysis identified the significant influence of module detection algorithm and node definition approach on reliabilities of network partitions and its derived network analysis results.

Discussion

This paper provides important guidance for choosing reliable modular-relevant network metrics and analysis strategies in future studies.

Cross-cohort replicability and generalizability of connectivity-based psychometric prediction patterns

An increasing number of studies have investigated the relationships between inter-individual variability in brain regions' connectivity and behavioral phenotypes, making use of large population neuroimaging datasets. However, the replicability of brain-behavior associations identified by these approaches remains an open question. In this study, we examined the cross-dataset replicability of brain-behavior association patterns for fluid cognition and openness predictions using a previously developed region-wise approach, as well as using a standard whole-brain approach. Overall, we found moderate similarity in patterns for fluid cognition predictions across cohorts, especially in the Human Connectome Project Young Adult, Human Connectome Project Aging, and Enhanced Nathan Kline Institute Rockland Sample cohorts, but low similarity in patterns for openness predictions. In addition, we assessed the generalizability of prediction models in cross-dataset predictions, by training the model in one dataset and testing in another. Making use of the region-wise prediction approach, we showed that first, a moderate extent of generalizability could be achieved with fluid cognition prediction, and that, second, a set of common brain regions related to fluid cognition across cohorts could be identified. Nevertheless, the moderate replicability and generalizability could only be achieved in specific contexts. Thus, we argue that replicability and generalizability in connectivity-based prediction remain limited and deserve greater attention in future studies.

Alterations in whole-brain dynamic functional stability during memory tasks under dexmedetomidine sedation

Purpose

This study aimed to explore the neurological effects of dexmedetomidine-induced sedation on memory using functional stability, a whole-brain voxel-wise dynamic functional connectivity approach.

Methods

A total of 16 participants (10 men) underwent auditory memory task-related fMRI in the awake state and under dexmedetomidine sedation. Explicit and implicit memory tests were conducted 4 h after ceasing dexmedetomidine administration. One-sample Wilcoxon signed rank test was applied to determine the formation of explicit and implicit memory in the two states. Functional stability was calculated and compared voxel-wise between the awake and sedated states. The association between functional stability and memory performance was also assessed.

Results

In the awake baseline tests, explicit and implicit memory scores were significantly different from zero (p < 0.05). In the tests under sedation, explicit and implicit memory scores were not significantly different from zero. Compared to that at wakeful baseline, functional stability during light sedation was reduced in the medial prefrontal cortex, left angular gyrus, and right hippocampus (all clusters, p < 0.05, GRF-corrected), whereas the left superior temporal gyrus exhibited higher functional stability (cluster p < 0.05, GRF-corrected). No significant associations were observed between functional stability and memory test scores.

Conclusions

The distribution and patterns of alterations in functional stability during sedation illustrate the modulation of functional architecture by dexmedetomidine from a dynamic perspective. Our findings provide novel insight into the dynamic brain functional networks underlying consciousness and memory in humans.

Test-retest reliability of peak location in the sensorimotor network of resting state fMRI for potential rTMS targets

Most stroke repetitive transcranial magnetic stimulation (rTMS) studies have used hand motor hotspots as rTMS stimulation targets; in addition, recent studies demonstrated that functional magnetic resonance imaging (fMRI) task activation could be used to determine suitable targets due to its ability to reveal individualized precise and stronger functional connectivity with motor-related brain regions. However, rTMS is unlikely to elicit motor evoked potentials in the affected hemisphere, nor would activity be detected when stroke patients with severe hemiplegia perform an fMRI motor task using the affected limbs. The current study proposed that the peak voxel in the resting-state fMRI (RS-fMRI) motor network determined by independent component analysis (ICA) could be a potential stimulation target. Twenty-one healthy young subjects underwent RS-fMRI at three visits (V1 and V2 on a GE MR750 scanner and V3 on a Siemens Prisma) under eyes-open (EO) and eyes-closed (EC) conditions. Single-subject ICA with different total number of components (20, 30, and 40) were evaluated, and then the locations of peak voxels on the left and right sides of the sensorimotor network (SMN) were identified. While most ICA RS-fMRI studies have been carried out on the group level, that is, Group-ICA, the current study performed individual ICA because only the individual analysis could guide the individual target of rTMS. The intra- (test-retest) and inter-scanner reliabilities of the peak location were calculated. The use of 40 components resulted in the highest test-retest reliability of the peak location in both the left and right SMN compared with that determined when 20 and 30 components were used for both EC and EO conditions. ICA with 40 components might be another way to define a potential target in the SMN for poststroke rTMS treatment.

Aberrant stability of brain functional architecture in cirrhotic patients with minimal hepatic encephalopathy

To investigate the stability changes of brain functional architecture and the relationship between stability change and cognitive impairment in cirrhotic patients. Fifty-one cirrhotic patients (21 with minimal hepatic encephalopathy (MHE) and 30 without MHE (NHE)) and 29 healthy controls (HCs) underwent resting-state functional magnetic resonance imaging and neurocognitive assessment using the Psychometric Hepatic Encephalopathy Score (PHES). Voxel-wise functional connectivity density (FCD) was calculated as the sum of connectivity strength between one voxel and others within the entire brain. The sliding window correlation approach was subsequently utilized to calculate the FCD dynamics over time. Functional stability (FS) is measured as the concordance of dynamic FCD. From HCs to the NHE and MHE groups, a stepwise reduction of FS was found in the right supramarginal gyrus (RSMG), right middle cingulate cortex, left superior frontal gyrus, and bilateral posterior cingulate cortex (BPCC), whereas a progressive increment of FS was observed in the left middle occipital gyrus (LMOG) and right temporal pole (RTP). The mean FS values in RSMG/LMOG/RTP (r = 0.470 and P = 0.001; r = -0.458 and P = 0.001; and r = -0.384 and P = 0.005, respectively) showed a correlation with PHES in cirrhotic patients. The FS index in RSMG/LMOG/BPCC/RTP showed moderate discrimination potential between the NHE and MHE groups. Changes in FS may be linked to neuropathological bias of cognitive impairment in cirrhotic patients and could serve as potential biomarkers for MHE diagnosis and monitoring the progression of hepatic encephalopathy.

Resting-State fMRI Functional Connectivity Strength Predicts Local Activity Change in the Dorsal Cingulate Cortex: A Multi-Target Focused rTMS Study

Previous resting state functional magnetic resonance imaging (RS-fMRI) studies suggested that repetitive transcranial magnetic stimulation (rTMS) can modulate local activity in distant areas via functional connectivity (FC). A brain region has more than one connection with the superficial cortical areas. The current study proposed a multi-target focused rTMS protocol for indirectly stimulating a deep region, and to investigate 1) whether FC strength between stimulation targets (right middle frontal gyrus [rMFG] and right inferior parietal lobule [rIPL]) and effective region (dorsal anterior cingulate cortex [dACC]) can predict local activity changes of dACC and 2) whether multiple stimulation targets can focus on the dACC via FC. A total of 24 healthy participants received rTMS with two stimulation targets, both showing strong FC with the dACC. There were four rTMS conditions (>1 week apart, 10 Hz, 1800 pulses for each): rMFG-target, rIPL-target, Double-targets (900 pulses for each target), and Sham. The results failed to validate the multi-target focused rTMS hypothesis. But rMFG-target significantly decreased the local activity in the dACC. In addition, stronger dACC-rMFG FC was associated with a greater local activity change in the dACC. Future studies should use stronger FC to focus stimulation effects on the deep region.

A longitudinal resource for studying connectome development and its psychiatric associations during childhood

Most psychiatric disorders are chronic, associated with high levels of disability and distress, and present during pediatric development. Scientific innovation increasingly allows researchers to probe brain-behavior relationships in the developing human. As a result, ambitions to (1) establish normative pediatric brain development trajectories akin to growth curves, (2) characterize reliable metrics for distinguishing illness, and (3) develop clinically useful tools to assist in the diagnosis and management of mental health and learning disorders have gained significant momentum. To this end, the NKI-Rockland Sample initiative was created to probe lifespan development as a large-scale multimodal dataset. The NKI-Rockland Sample Longitudinal Discovery of Brain Development Trajectories substudy (N = 369) is a 24- to 30-month multi-cohort longitudinal pediatric investigation (ages 6.0-17.0 at enrollment) carried out in a community-ascertained sample. Data include psychiatric diagnostic, medical, behavioral, and cognitive phenotyping, as well as multimodal brain imaging (resting fMRI, diffusion MRI, morphometric MRI, arterial spin labeling), genetics, and actigraphy. Herein, we present the rationale, design, and implementation of the Longitudinal Discovery of Brain Development Trajectories protocol.

The effect of acquisition duration on cerebral blood flow-based resting-state functional connectivity

Resting-state functional connectivity (rs-FC) is widely used to examine the functional architecture of the brain, and the blood-oxygenation-level-dependent (BOLD) signal is often utilized for determining rs-FC. However, the BOLD signal is susceptible to various factors that have less influence on the cerebral blood flow (CBF). Therefore, CBF could comprise an alternative for determining rs-FC. Since acquisition duration is one of the essential parameters for obtaining reliable rs-FC, we investigated the effect of acquisition duration on CBF-based rs-FC to examine the reliability of CBF-based rs-FC. Nineteen participants underwent CBF scanning for a total duration of 50 min. Variance of CBF-based rs-FC within the whole brain and 13 large-scale brain networks at various acquisition durations was compared to that with a 50-min duration using the Levene's test. Variance of CBF-based rs-FC at any durations did not differ from that at a 50-min duration (p > .05). Regarding variance of rs-FC within each large-scale brain network, the acquisition duration required to obtain reliable estimates of CBF-based rs-FC was shorter than 10 min and varied across large-scale brain networks. Altogether, an acquisition duration of at least 10 min is required to obtain reliable CBF-based rs-FC. These results indicate that CBF-based resting-state functional magnetic resonance imaging (rs-fMRI) with more than 10 min of total acquisition duration could be an alternative method to BOLD-based rs-fMRI to obtain reliable rs-FC.

Personality network neuroscience: Promises and challenges on the way toward a unifying framework of individual variability

We propose that the application of network theory to established psychological personality conceptions has great potential to advance a biologically plausible model of human personality. Stable behavioral tendencies are conceived as personality “traits.” Such traits demonstrate considerable variability between individuals, and extreme expressions represent risk factors for psychological disorders. Although the psychometric assessment of personality has more than hundred years tradition, it is not yet clear whether traits indeed represent “biophysical entities” with specific and dissociable neural substrates. For instance, it is an open question whether there exists a correspondence between the multilayer structure of psychometrically derived personality factors and the organizational properties of traitlike brain systems. After a short introduction into fundamental personality conceptions, this article will point out how network neuroscience can enhance our understanding about human personality. We will examine the importance of intrinsic (task-independent) brain connectivity networks and show means to link brain features to stable behavioral tendencies. Questions and challenges arising from each discipline itself and their combination are discussed and potential solutions are developed. We close by outlining future trends and by discussing how further developments of network neuroscience can be applied to personality research.

Abnormal Stability of Dynamic Functional Architecture in Amyotrophic Lateral Sclerosis: A Preliminary Resting-State fMRI Study

Purpose: Static and dynamic analyses for identifying functional connectivity (FC) have demonstrated brain dysfunctions in amyotrophic lateral sclerosis (ALS). However, few studies on the stability of dynamic FC have been conducted among ALS patients. This study explored the change of functional stability in ALS and how it correlates with disease severity.

Methods: We gathered resting-state functional magnetic resonance data from 20 patients with ALS and 22 healthy controls (HCs). The disease severity was assessed with the Revised ALS Functional Rating Scale (ALSFRS-R). We used a sliding window correlation approach to identify dynamic FC and measured the concordance of dynamic FC over time to obtain the functional stability of each voxel. We assessed the between-group difference in functional stability by voxel-wise two-sample t-test. The correlation between the functional stability index and ALSFRS-R in ALS patients was evaluated using Spearman's correlation analysis.

Results: Compared with the HC group, the ALS group had significantly increased functional stability in the left pre-central and post-central gyrus and right temporal pole while decreased functional stability in the right middle and inferior frontal gyrus. The results revealed a significant correlation between ALSFRS-R and the mean functional stability in the right temporal pole (r = −0.452 and P = 0.046) in the ALS patients.

Conclusions: ALS patients have abnormal stability of brain functional architecture, which is associated with the severity of the disease.

Recent developments in representations of the connectome

Research into the human connectome (i.e., all connections in the human brain) with the use of resting state functional MRI has rapidly increased in popularity in recent years, especially with the growing availability of large-scale neuroimaging datasets. The goal of this review article is to describe innovations in functional connectome representations that have come about in the past 8 years, since the 2013 NeuroImage special issue on 'Mapping the Connectome'. In the period, research has shifted from group-level brain parcellations towards the characterization of the individualized connectome and of relationships between individual connectomic differences and behavioral/clinical variation. Achieving subject-specific accuracy in parcel boundaries while retaining cross-subject correspondence is challenging, and a variety of different approaches are being developed to meet this challenge, including improved alignment, improved noise reduction, and robust group-to-subject mapping approaches. Beyond the interest in the individualized connectome, new representations of the data are being studied to complement the traditional parcellated connectome representation (i.e., pairwise connections between distinct brain regions), such as methods that capture overlapping and smoothly varying patterns of connectivity ('gradients'). These different connectome representations offer complimentary insights into the inherent functional organization of the brain, but challenges for functional connectome research remain. Interpretability will be improved by future research towards gaining insights into the neural mechanisms underlying connectome observations obtained from functional MRI. Validation studies comparing different connectome representations are also needed to build consensus and confidence to proceed with clinical trials that may produce meaningful clinical translation of connectome insights.

A guide to the measurement and interpretation of fMRI test-retest reliability

The test-retest reliability of functional neuroimaging data has recently been a topic of much discussion. Despite early conflicting reports, converging reports now suggest that test-retest reliability is poor for standard univariate measures-namely, voxel- and region-level task-based activation and edge-level functional connectivity. To better understand the implications of these recent studies requires understanding the nuances of test-retest reliability as commonly measured by the intraclass correlation coefficient (ICC). Here we provide a guide to the measurement and interpretation of test-retest reliability in functional neuroimaging and review major findings in the literature. We highlight the importance of making choices that improve reliability so long as they do not diminish validity, pointing to the potential of multivariate approaches that improve both. Finally, we discuss the implications of recent reports of low test-retest reliability in the context of ongoing work in the field.

Importance of test-retest reliability for promoting fMRI based screening and interventions in major depressive disorder

Proponents of personalized medicine have promoted neuroimaging in three areas of clinical application for major depression: clinical prediction, outcome evaluation, and treatment, via neurofeedback. Whereas psychometric considerations such as test-retest reliability are basic precursors to clinical adoption for most clinical instruments, we show, in this article, that basic psychometrics have not been regularly attended to in fMRI of depression. For instance, no fMRI neurofeedback study has included measures of test-retest reliability, despite the implicit assumption that brain signals are stable enough to train. We consider several factors that could be useful to aid clinical translation, including (1) attending to how the BOLD response is parameterized, (2) identifying and promoting regions or voxels with stronger psychometric properties, (3) accounting for within-individual changes (e.g., in symptomatology) across time, and (4) focusing on tasks and clinical populations that are relevant for the intended clinical application. We apply these principles to published prognostic and neurofeedback data sets. The broad implication of this work is that attention to psychometrics is important for clinical adoption of mechanistic assessment, is feasible, and may improve the underlying science.

"Impact of ICA Dimensionality on the Test-Retest Reliability of Resting-State Functional Connectivity

As resting-state functional connectivity (rsFC) research moves toward the study of individual differences, test-retest reliability is increasingly important to understand. Previous literature supports the test-retest reliability of rsFC derived with independent component analysis (ICA) and dual regression, yet the impact of dimensionality (i.e., the number of components to extract from group-ICA) remained obscure in the current context of large-scale datasets. To provide principled guidelines on this issue, ICA at dimensionalities varying from 25 to 350 was applied to the cortical surface with resting-state functional magnetic resonance imaging data from 1003 participants in the Human Connectome Project. The reliability of two rsFC measures: (within-component) coherence and (between-component) connectivity was estimated. Reliability and its change with dimensionality varied by network: the cognitive (frontoparietal, cingulo-opercular, dorsal attention, and default) networks were measured with the highest reliability which improved with increased dimensionality until at least 150; the visual and somatomotor networks were measured with lower reliability which benefited mildly from increased dimensionality; the temporal pole/orbitofrontal cortex (TP/OFC) network was measured with the lowest reliability. Overall, ICA reliability was optimized at dimensionalities of 150 or above. Compared with two popular binary, non-overlapping cortical atlases, ICA and dual regression resulted in higher reliability for the cognitive networks, lower reliability for the somatomotor network, and similar reliability for the visual and TP/OFC networks. These findings highlight analytical decisions that maximize the reliability of rsFC measures and how they depend on one's networks of interest.

Resting-state fMRI detects alterations in whole brain connectivity related to tumor biology in glioma patients

BACKGROUND

Systemic infiltration of the brain by tumor cells is a hallmark of glioma pathogenesis which may cause disturbances in functional connectivity. We hypothesized that aggressive high-grade tumors cause more damage to functional connectivity than low-grade tumors.

METHODS

We designed an imaging tool based on resting-state functional (f)MRI to individually quantify abnormality of functional connectivity and tested it in a prospective cohort of patients with newly diagnosed glioma.

RESULTS

Thirty-four patients were analyzed (World Health Organization [WHO] grade II, n = 13; grade III, n = 6; grade IV, n = 15; mean age, 48.7 y). Connectivity abnormality could be observed not only in the lesioned brain area but also in the contralateral hemisphere with a close correlation between connectivity abnormality and aggressiveness of the tumor as indicated by WHO grade. Isocitrate dehydrogenase 1 (IDH1) mutation status was also associated with abnormal connectivity, with more alterations in IDH1 wildtype tumors independent of tumor size. Finally, deficits in neuropsychological performance were correlated with connectivity abnormality.

CONCLUSION

Here, we suggested an individually applicable resting-state fMRI marker in glioma patients. Analysis of the functional connectome using this marker revealed that abnormalities of functional connectivity could be detected not only adjacent to the visible lesion but also in distant brain tissue, even in the contralesional hemisphere. These changes were associated with tumor biology and cognitive function. The ability of our novel method to capture tumor effects in nonlesional brain suggests a potential clinical value for both individualizing and monitoring glioma therapy.

Reliability modelling of resting-state functional connectivity

Resting-state functional magnetic resonance imaging (rs-fMRI) has an inherently low signal-to-noise ratio largely due to thermal and physiological noise that attenuates the functional connectivity (FC) estimates. Such attenuation limits the reliability of FC and may bias its association with other traits. Low reliability also limits heritability estimates. Classical test theory can be used to obtain a true correlation estimate free of random measurement error from parallel tests, such as split-half sessions of a rs-fMRI scan. We applied a measurement model to split-half FC estimates from the resting-state fMRI data of 1003 participants from the Human Connectome Project (HCP) to examine the benefit of reliability modelling of FC in association with traits from various domains. We evaluated the efficiency of the measurement model on extracting a stable and reliable component of FC and its association with several traits for various sample sizes and scan durations. In addition, we aimed to replicate our previous findings of increased heritability estimates when using a measurement model in a longitudinal adolescent twin cohort. The split-half measurement model improved test-retest reliability of FC on average with +0.33 points (from +0.49 to +0.82), improved strength of associations between FC and various traits on average 1.2-fold (range 1.09-1.35), and increased heritability estimates on average with +20% points (from 39% to 59%) for the full HCP dataset. On average, about half of the variance in split-session FC estimates was attributed to the stable and reliable component of FC. Shorter scan durations showed greater benefit of reliability modelling (up to 1.6-fold improvement), with an additional gain for smaller sample sizes (up to 1.8-fold improvement). Reliability modelling of FC based on a split-half using a measurement model can benefit genetic and behavioral studies by extracting a stable and reliable component of FC that is free from random measurement error and improves genetic and behavioral associations.

Low-motion fMRI data can be obtained in pediatric participants undergoing a 60-minute scan protocol

Performing functional magnetic resonance imaging (fMRI) scans of children can be a difficult task, as participants tend to move while being scanned. Head motion represents a significant confound in fMRI connectivity analyses. One approach to limit motion has been to use shorter MRI protocols, though this reduces the reliability of results. Hence, there is a need to implement methods to achieve high-quality, low-motion data while not sacrificing data quantity. Here we show that by using a mock scan protocol prior to a scan, in conjunction with other in-scan steps (weighted blanket and incentive system), it is possible to achieve low-motion fMRI data in pediatric participants (age range: 7-17 years old) undergoing a 60 min MRI session. We also observe that motion is low during the MRI protocol in a separate replication group of participants, including some with autism spectrum disorder. Collectively, the results indicate it is possible to conduct long scan protocols in difficult-to-scan populations and still achieve high-quality data, thus potentially allowing more reliable fMRI findings.

Development and Emergence of Individual Variability in the Functional Connectivity Architecture of the Preterm Human Brain

Individual variability in human brain networks underlies individual differences in cognition and behaviors. However, researchers have not conclusively determined when individual variability patterns of the brain networks emerge and how they develop in the early phase. Here, we employed resting-state functional MRI data and whole-brain functional connectivity analyses in 40 neonates aged around 31-42 postmenstrual weeks to characterize the spatial distribution and development modes of individual variability in the functional network architecture. We observed lower individual variability in primary sensorimotor and visual areas and higher variability in association regions at the third trimester, and these patterns are generally similar to those of adult brains. Different functional systems showed dramatic differences in the development of individual variability, with significant decreases in the sensorimotor network; decreasing trends in the visual, subcortical, and dorsal and ventral attention networks, and limited change in the default mode, frontoparietal and limbic networks. The patterns of individual variability were negatively correlated with the short- to middle-range connection strength/number and this distance constraint was significantly strengthened throughout development. Our findings highlight the development and emergence of individual variability in the functional architecture of the prenatal brain, which may lay network foundations for individual behavioral differences later in life.

Common and distinct functional stability abnormalities across three major psychiatric disorders

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Functional stability is a recently developed dynamic functional connectivity approach.

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Schizophrenia individuals had a distributed pattern of higher and lower stability.

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Individuals with bipolar disorder only manifested local higher stability.

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Individuals with attention deficit/hyperactivity disorder exhibited no stability differences.

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Psychiatric disorders show common and distinct functional stability abnormalities.

Delineating the neuropathological characteristics across psychiatric disorders is critical for understanding their pathophysiology. The purpose of this study was to investigate common and distinct brain functional abnormalities across psychiatric disorders by using functional stability, a recently developed dynamic functional connectivity approach. Resting-state functional magnetic resonance imaging data were collected from a transdisease sample of healthy controls (n = 115) and individuals with schizophrenia (SZ) (n = 47), bipolar disorder (BD) (n = 44), and attention deficit/hyperactivity disorder (ADHD) (n = 40). Functional stability of each voxel was calculated by measuring the concordance of dynamic functional connectivity over time. Differences in functional stability among the four groups were assessed voxel-wisely. Compared to healthy controls, individuals with SZ demonstrated a distributed pattern of higher functional stability in the bilateral inferior temporal gyrus yet lower stability in the bilateral calcarine sulcus and left insula; individuals with BD only manifested local higher stability in the left inferior temporal gyrus; no differences were found between ADHD and healthy individuals. Notably, individuals with SZ and BD had common higher functional stability in the left inferior temporal gyrus, whereas higher functional stability in the right inferior temporal gyrus and lower stability in the bilateral calcarine sulcus and left insula were unique abnormalities in individuals with SZ. Additionally, direct comparisons between disorders revealed that individuals with SZ showed lower functional stability in the right calcarine sulcus compared to those with BD and higher stability in the left inferior temporal gyrus compared to those with ADHD. However, no significant associations between functional stability and clinical symptoms were observed. Our findings suggest that the functional stability approach has the potential to be extended to the domain of psychiatry and encourage further investigations of shared and unique neuropathology of psychiatric disorders.

Brain network topology predicts participant adherence to mental training programs

Adherence determines the success and benefits of mental training (e.g., meditation) programs. It is unclear why some participants engage more actively in programs for mental training than others. Understanding neurobiological factors that predict adherence is necessary for understanding elements of learning and to inform better designs for new learning regimens. Clustering patterns in brain networks have been suggested to predict learning performance, but it is unclear whether these patterns contribute to motivational aspects of learning such as adherence. This study tests whether configurations of brain connections in resting-state fMRI scans can be used to predict adherence to two programs: meditation and creative writing. Results indicate that greater system segregation and clustering predict the number of practice sessions and class participation in both programs at a wide range of network thresholds (corrected p value < 0.05). At a local level, regions in subcortical circuitry such as striatum and accumbens predicted adherence in all subjects. Furthermore, there were also some important distinctions between groups: Adherence to meditation was predicted by connectivity within local network of the anterior insula and default mode network; and in the writing program, adherence was predicted by network neighborhood of frontal and temporal regions. Four machine learning methods were applied to test the robustness of the brain metric for classifying individual capacity for adherence and yielded reasonable accuracy. Overall, these findings underscore the fact that adherence and the ability to perform prescribed exercises is associated with organizational patterns of brain connectivity.

Bootstrapping promotes the RSFC-behavior associations: An application of individual cognitive traits prediction

Resting‐state functional connectivity (RSFC) records enormous functional interaction information between any pair of brain nodes, which enriches the individual‐phenotypic prediction. To reduce high‐dimensional features, correlation analysis is a common way for feature selection. However, resting state fMRI signal exhibits typically low signal‐to‐noise ratio and the correlation analysis is sensitive to outliers and data distribution, which may bring unstable features to prediction. To alleviate this problem, a bootstrapping‐based feature selection framework was proposed and applied to connectome‐based predictive modeling, support vector regression, least absolute shrinkage and selection operator, and Ridge regression to predict a series of cognitive traits based on Human Connectome Project data. To systematically investigate the influences of different parameter settings on the bootstrapping‐based framework, 216 parameter combinations were evaluated and the best performance among them was identified as the final prediction result for each cognitive trait. By using the bootstrapping methods, the best prediction performances outperformed the baseline method in all four prediction models. Furthermore, the proposed framework could effectively reduce the feature dimension by retaining the more stable features. The results demonstrate that the proposed framework is an easy‐to‐use and effective method to improve RSFC prediction of cognitive traits and is highly recommended in future RSFC‐prediction studies.

Variable functional connectivity architecture of the preterm human brain: Impact of developmental cortical expansion and maturation

Functional connectivity (FC) is known to be individually unique and to reflect cognitive variability. Although FC can serve as a valuable correlate and potential predictor of (patho-) physiological nervous function in high-risk constellations, such as preterm birth, templates for individualized FC analysis are lacking, and knowledge about the capacity of the premature brain to develop FC variability is limited. In a cohort of prospectively recruited, preterm-born infants undergoing magnetic resonance imaging close to term-equivalent age, we show that the overall pattern could be reliably detected with a broad range of interindividual FC variability in regions of higher-order cognitive functions (e.g., association cortices) and less interindividual variability in unimodal regions (e.g., visual and motor cortices). However, when comparing the preterm and adult brains, some brain regions showed a marked shift in variability toward adulthood. This shift toward greater variability was strongest in cognitive networks like the attention and frontoparietal networks and could be partially predicted by developmental cortical expansion. Furthermore, FC variability was reflected by brain tissue characteristics indicating cortical maturation. Brain regions with high functional variability (e.g., the inferior frontal gyrus and temporoparietal junction) displayed lower cortical maturation at birth compared with somatosensory cortices. In conclusion, the overall pattern of interindividual variability in FC is already present preterm; however, some brain regions show increased variability toward adulthood, identifying characteristic patterns, such as in cognitive networks. These changes are related to postnatal cortical expansion and maturation, allowing for environmental and developmental factors to translate into marked individual differences in FC.

Development of Network Topology and Functional Connectivity of the Prefrontal Cortex

The prefrontal cortex (PFC) comprises distinct regions and networks that vary in their trajectories across development. Further understanding these diverging trajectories may elucidate the neural mechanisms by which distinct PFC regions contribute to cognitive maturity. In particular, it remains unclear whether PFC regions of distinct network affiliations differ in topology and their relationship to cognition. We examined 615 individuals (8–21 years) to characterize age-related effects in participation coefficient of 28 PFC regions of distinct networks, evaluating connectivity profiles of each region to understand patterns influencing topological maturity. Findings revealed that PFC regions of attention, frontoparietal, and default mode networks (DMN) displayed varying rates of decline in participation coefficient with age, characterized by stronger connectivity with each PFC’s respective network; suggesting that PFC regions largely aid network segregation. Conversely, PFC regions of the cinguloopercular/salience network increased in participation coefficient with age, marked by stronger between-network connections, suggesting that some PFC regions feature a distinctive ability to facilitate network integration. PFC topology of the DMN, in particular, predicted improvements in global cognition, including motor speed and higher order abilities. Together, these findings elucidate systematic differences in topology across PFC regions of different network affiliation, representing important neural signatures of typical brain development.

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

BACKGROUND

Once 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.

OBJECTIVES

We 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.

METHODS

A 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.

RESULTS

From 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.

CONCLUSION

This 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.

Single-subject manual independent component analysis and resting state fMRI connectivity outcomes in patients with juvenile absence epilepsy

The quality of fMRI data impacts functional connectivity measures and consequently, the decisions that clinicians and researchers make regarding functional connectivity interpretation. The present study used resting state fMRI to investigate resting state network connectivity in a sample of patients with Juvenile Absence Epilepsy. Single-subject manual independent component analysis was used in two levels, whereby all noise components were removed, and cerebrospinal fluid pulsation components only were isolated and removed. Improved temporal signal to noise ratios and functional connectivity metrics were observed in each of the cleaning levels for both epilepsy and control cohorts. Results showed full, single-subject manual independent component analysis reduced the number of functional connectivity correlations and increased the strength of these correlations. Similar effects were also observed for the cerebrospinal fluid pulsation only cleaned data relative to the uncleaned, and fully cleaned data. Single-subject manual independent component analysis coupled with short TR multiband acquisition can significantly improve the validity of findings derived from fMRI data sets.

Addressing the reliability fallacy in fMRI: Similar group effects may arise from unreliable individual effects

To cast valid predictions of future behavior or diagnose disorders, the reliable measurement of a "biomarker" such as the brain activation to prospective reward is a prerequisite. Surprisingly, only a small fraction of functional magnetic resonance imaging (fMRI) studies report or cite the reliability of brain activation maps involved in group analyses. Here, using simulations and exemplary longitudinal data of 126 healthy adolescents performing an intertemporal choice task, we demonstrate that reproducing a group activation map over time is not a sufficient indication of reliable measurements at the individual level. Instead, selecting regions based on significant main effects at the group level may yield estimates that fail to reliably capture individual variance in the subjective evaluation of an offer. Collectively, our results call for more attention on the reliability of supposed biomarkers at the level of the individual. Thus, caution is warranted in employing brain activation patterns prematurely for clinical applications such as diagnosis or tailored interventions before their reliability has been conclusively established by large-scale studies. To facilitate assessing and reporting of the reliability of fMRI contrasts in future studies, we provide a toolbox that incorporates common measures of global and local reliability.

Performing group-level functional image analyses based on homologous functional regions mapped in individuals

Functional MRI (fMRI) studies have traditionally relied on intersubject normalization based on global brain morphology, which cannot establish proper functional correspondence between subjects due to substantial intersubject variability in functional organization. Here, we reliably identified a set of discrete, homologous functional regions in individuals to improve intersubject alignment of fMRI data. These functional regions demonstrated marked intersubject variability in size, position, and connectivity. We found that previously reported intersubject variability in functional connectivity maps could be partially explained by variability in size and position of the functional regions. Importantly, individual differences in network topography are associated with individual differences in task-evoked activations, suggesting that these individually specified regions may serve as the "localizer" to improve the alignment of task-fMRI data. We demonstrated that aligning task-fMRI data using the regions derived from resting state fMRI may lead to increased statistical power of task-fMRI analyses. In addition, resting state functional connectivity among these homologous regions is able to capture the idiosyncrasies of subjects and better predict fluid intelligence (gF) than connectivity measures derived from group-level brain atlases. Critically, we showed that not only the connectivity but also the size and position of functional regions are related to human behavior. Collectively, these findings suggest that identifying homologous functional regions across individuals can benefit a wide range of studies in the investigation of connectivity, task activation, and brain-behavior associations.

Disrupted prefrontal functional connectivity during post-stress adaption in high ruminators

Rumination is a perseverative thinking style that is associated with adverse mental and physical health. Stressful situations have been considered as a trigger for this kind of thinking. Until today, there are mixed findings with respect to the relations of functional connectivity (FC) and rumination. The study at hand aimed to investigate, in how far high and low ruminators would show elevated levels of state rumination after a stress induction and if these changes would show corresponding changes in FC in the cognitive control network (CCN) and dorsal attention network (DAN). 23 high and 22 low trait ruminators underwent resting-state measurements before and after a stress induction with the Trier Social Stress Test (TSST). Changes in rsFC through the TSST were measured with functional near-infrared spectroscopy within and between regions of the CCN. Stress successfully induced state rumination in both groups but stronger in the high trait ruminators. High trait ruminators showed elevated FC within the CCN at baseline, but attenuated increase in FC following the TSST. Increases in FC correlated negatively with state rumination. A lack of FC reactivity within the CCN in high ruminators might reflect reduced network integration between brain regions necessary for emotion regulation and cognitive control.

Resting-state brain network features associated with short-term skill learning ability in humans and the influence of N-methyl-d-aspartate receptor antagonism

Graph theoretical functional magnetic resonance imaging (fMRI) studies have demonstrated that brain networks reorganize significantly during motor skill acquisition, yet the associations between motor learning ability, brain network features, and the underlying biological mechanisms remain unclear. In the current study, we applied a visually guided sequential pinch force learning task and graph theoretical analyses to investigate the associations between short-term motor learning ability and resting-state brain network metrics in 60 healthy subjects. We further probed the test-retest reliability (n = 26) and potential effects of the N-methyl-d-aspartate (NMDA) antagonist ketamine (n = 19) in independent healthy volunteers. Our results show that the improvement of motor performance after short-term training was positively correlated with small-worldness (p = 0.032) and global efficiency (p = 0.025), whereas negatively correlated with characteristic path length (p = 0.014) and transitivity (p = 0.025). In addition, using network-based statistics (NBS), we identified a learning ability–associated (p = 0.037) and ketamine-susceptible (p = 0.027) cerebellar-cortical network with fair to good reliability (intraclass correlation coefficient [ICC] > 0.7) and higher functional connectivity in better learners. Our results provide new evidence for the association of intrinsic brain network features with motor learning and suggest a role of NMDA-related glutamatergic processes in learning-associated subnetworks.

Learning a new motor skill prompts immediate reconfigurations of distributed brain networks followed by adaptive changes in intrinsic brain circuits related to synaptic plasticity. Here, we identify global brain network properties and a cerebellar-cortical functional subnetwork that are both significantly associated with motor learning ability in a previously trained visuomotor task in humans. We further show that the associated functional subnetwork connectivity but not the global brain network properties are susceptible to ketamine. Our findings suggest a distinct functional role for learning-related global versus local network metrics and support the idea of a preferential susceptibility of learning-associated subnetworks to N-methyl-d-aspartate antagonist and plasticity-related consolidation effects.

Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI

A central goal in systems neuroscience is the parcellation of the cerebral cortex into discrete neurobiological "atoms". Resting-state functional magnetic resonance imaging (rs-fMRI) offers the possibility of in vivo human cortical parcellation. Almost all previous parcellations relied on 1 of 2 approaches. The local gradient approach detects abrupt transitions in functional connectivity patterns. These transitions potentially reflect cortical areal boundaries defined by histology or visuotopic fMRI. By contrast, the global similarity approach clusters similar functional connectivity patterns regardless of spatial proximity, resulting in parcels with homogeneous (similar) rs-fMRI signals. Here, we propose a gradient-weighted Markov Random Field (gwMRF) model integrating local gradient and global similarity approaches. Using task-fMRI and rs-fMRI across diverse acquisition protocols, we found gwMRF parcellations to be more homogeneous than 4 previously published parcellations. Furthermore, gwMRF parcellations agreed with the boundaries of certain cortical areas defined using histology and visuotopic fMRI. Some parcels captured subareal (somatotopic and visuotopic) features that likely reflect distinct computational units within known cortical areas. These results suggest that gwMRF parcellations reveal neurobiologically meaningful features of brain organization and are potentially useful for future applications requiring dimensionality reduction of voxel-wise fMRI data. Multiresolution parcellations generated from 1489 participants are publicly available (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).

Within-subject test-retest reliability of the atlas-based cortical volume measurement in the rat brain: A voxel-based morphometry study

BACKGROUND

Various neurological and psychological disorders are related to cortical volume changes in specific brain regions, which can be measured in vivo using structural magnetic resonance imaging (sMRI). There is an increasing interest in MRI studies using rat models, especially in longitudinal studies of brain disorders and pharmacologic interventions. However, morphometric changes observed in sMRI are only meaningful if the measurements are reliable. To date, a systematic evaluation of the test-retest reliability of the morphometric measures in the rat brain is still lacking.

NEW METHOD

We rigorously evaluated the test-retest reliability of morphometric measures derived from the voxel-based morphometry (VBM) analysis. 37 Sprague-Dawley rats were scanned twice at an interval of six hours and the gray matter volume was estimated using the VBM-DARTEL method. The intraclass coefficient, percent volume change and Pearson correlation coefficient were used to evaluate the reliability in 96 subregions of the rat brain.

RESULTS

Most subregions showed excellent test-retest reliabilities within an interval of 6 h while a few regions demonstrated lower reliability, especially in the retrosplenial granular cortex. The results were consistent between different methods of reliability assessment.

COMPARISON WITH EXISTING METHOD

To the best of our knowledge, this is the first study to quantify the test-retest reliability of the VBM measurements of the rat brain.

CONCLUSION

Atlas-based cortical volume of the rat brain can be reliably estimated using the VBM-DARTEL method in most subregions. However, findings in subregions with lower reliability must be interpreted with caution.

Fluid intelligence relates to the resting state amplitude of low-frequency fluctuation and functional connectivity: a multivariate pattern analysis

The goal of this study was to investigate the relationship between fluid intelligence (gF) and the pattern of the functional characteristics in the resting state in adults using multivariate pattern analysis. Resting-state functional images from 100 participants in the Human Connectome Project data set were analyzed. The amplitude of low-frequency fluctuation (ALFF) was first calculated, and a support vector regression approach was used to identify the association with gF. To discover whether the connectivity of the gF-associated areas was also related to gF, we further checked the seed-based functional connectivity using the seeds from the ALFF. The ALFF showed that gF was correlated with the left anterior cingulate cortex, which is involved in high cognitive control processes. The functional connectivity showed that the connection between the right prefrontal cortex (Brodmann area 8) and the left anterior cingulate cortex could predict gF. The multivariate pattern analysis result indicated that the brain functional activity and functional integrity that we identified have the potential to become an objective biomarker for evaluating individual differences in gF.

Influences on the Test-Retest Reliability of Functional Connectivity MRI and its Relationship with Behavioral Utility

Best practices are currently being developed for the acquisition and processing of resting-state magnetic resonance imaging data used to estimate brain functional organization—or “functional connectivity.” Standards have been proposed based on test–retest reliability, but open questions remain. These include how amount of data per subject influences whole-brain reliability, the influence of increasing runs versus sessions, the spatial distribution of reliability, the reliability of multivariate methods, and, crucially, how reliability maps onto prediction of behavior. We collected a dataset of 12 extensively sampled individuals (144 min data each across 2 identically configured scanners) to assess test–retest reliability of whole-brain connectivity within the generalizability theory framework. We used Human Connectome Project data to replicate these analyses and relate reliability to behavioral prediction. Overall, the historical 5-min scan produced poor reliability averaged across connections. Increasing the number of sessions was more beneficial than increasing runs. Reliability was lowest for subcortical connections and highest for within-network cortical connections. Multivariate reliability was greater than univariate. Finally, reliability could not be used to improve prediction; these findings are among the first to underscore this distinction for functional connectivity. A comprehensive understanding of test–retest reliability, including its limitations, supports the development of best practices in the field.

Extracting orthogonal subject- and condition-specific signatures from fMRI data using whole-brain effective connectivity

The study of brain communication based on fMRI data is often limited because such measurements are a mixture of session-to-session variability with subject- and condition-related information. Disentangling these contributions is crucial for real-life applications, in particular when only a few recording sessions are available. The present study aims to define a reliable standard for the extraction of multiple signatures from fMRI data, while verifying that they do not mix information about the different modalities (e.g., subjects and conditions such as tasks performed by them). In particular, condition-specific signatures should not be contaminated by subject-related information, since they aim to generalize over subjects. Practically, signatures correspond to subnetworks of directed interactions between brain regions (typically 100 covering the whole brain) supporting the subject and condition identification for single fMRI sessions. The key for robust prediction is using effective connectivity instead of functional connectivity. Our method demonstrates excellent generalization capabilities for subject identification in two datasets, using only a few sessions per subject as reference. Using another dataset with resting state and movie viewing, we show that the two signatures related to subjects and tasks correspond to distinct subnetworks, which are thus topologically orthogonal. Our results set solid foundations for applications tailored to individual subjects, such as clinical diagnostic.

Improved estimation of subject-level functional connectivity using full and partial correlation with empirical Bayes shrinkage

Reliability of subject-level resting-state functional connectivity (FC) is determined in part by the statistical techniques employed in its estimation. Methods that pool information across subjects to inform estimation of subject-level effects (e.g., Bayesian approaches) have been shown to enhance reliability of subject-level FC. However, fully Bayesian approaches are computationally demanding, while empirical Bayesian approaches typically rely on using repeated measures to estimate the variance components in the model. Here, we avoid the need for repeated measures by proposing a novel measurement error model for FC describing the different sources of variance and error, which we use to perform empirical Bayes shrinkage of subject-level FC towards the group average. In addition, since the traditional intra-class correlation coefficient (ICC) is inappropriate for biased estimates, we propose a new reliability measure denoted the mean squared error intra-class correlation coefficient (ICCMSE) to properly assess the reliability of the resulting (biased) estimates. We apply the proposed techniques to test-retest resting-state fMRI data on 461 subjects from the Human Connectome Project to estimate connectivity between 100 regions identified through independent components analysis (ICA). We consider both correlation and partial correlation as the measure of FC and assess the benefit of shrinkage for each measure, as well as the effects of scan duration. We find that shrinkage estimates of subject-level FC exhibit substantially greater reliability than traditional estimates across various scan durations, even for the most reliable connections and regardless of connectivity measure. Additionally, we find partial correlation reliability to be highly sensitive to the choice of penalty term, and to be generally worse than that of full correlations except for certain connections and a narrow range of penalty values. This suggests that the penalty needs to be chosen carefully when using partial correlations.

The goal priority network as a neural substrate of Conscientiousness

Conscientiousness is a personality trait associated with many important life outcomes, but little is known about the mechanisms that underlie it. We investigated its neural correlates using functional connectivity analysis in fMRI, which identifies brain regions that act in synchrony. We tested the hypothesis that a broad network resembling a combination of the salience and ventral attention networks, which we provisionally label the goal priority network (GPN), is a neural correlate of Conscientiousness. Self- and peer-ratings of Conscientiousness were collected in a community sample of adults who underwent a resting-state fMRI scan (N = 218). An independent components analysis yielded five components that overlapped substantially with the GPN. We examined synchrony within and between these GPN subcomponents. Synchrony within one of the components-mainly comprising regions of anterior insula, dorsal anterior cingulate cortex, and dorsolateral prefrontal cortex-was significantly associated with Conscientiousness. Connectivity between this component and the four other GPN components was also significantly associated with Conscientiousness. Our results support the hypothesis that variation in a network that enables prioritization of multiple goals may be central to Conscientiousness.

Considering factors affecting the connectome-based identification process: Comment on Waller et al

A recent study by Waller and colleagues evaluated the reliability, specificity, and generalizability of using functional connectivity data to identify individuals from a group. The authors note they were able to replicate identification rates in a larger version of the original Human Connectome Project (HCP) dataset. However, they also report lower identification accuracies when using historical neuroimaging acquisitions with low spatial and temporal resolution. The authors suggest that their results indicate connectomes derived from historical imaging data may be similar across individuals, to the extent that this connectome-based approach may be inappropriate for precision psychiatry and the goal of drawing inferences based on subject-level data. Here we note that the authors did not take into account factors affecting data quality and hence identification rates, independent of whether a low spatiotemporal resolution acquisition or a high spatiotemporal resolution acquisition is used. Specifically, we show here that the amount of data collected per subject and in-scanner motion are the predominant factors influencing identification rates, not the spatiotemporal resolution of the acquisition. To do this, we investigated identification rates in the HCP dataset as a function of the amount of data and motion. Using a dataset from the Consortium for Reliability and Reproducibility (CoRR), we investigated the impact of multiband versus non-multiband imaging parameters; that is, high spatiotemporal resolution versus low spatiotemporal resolution acquisitions. We show scan length and motion affect identification, whereas the imaging protocol does not affect these rates. Our results suggest that motion and amount of data per subject are the primary factors impacting individual connectivity profiles, but that within these constraints, individual differences in the connectome are readily observable.

Can brain state be manipulated to emphasize individual differences in functional connectivity?

While neuroimaging studies typically collapse data from many subjects, brain functional organization varies between individuals, and characterizing this variability is crucial for relating brain activity to behavioral phenotypes. Rest has become the default state for probing individual differences, chiefly because it is easy to acquire and a supposed neutral backdrop. However, the assumption that rest is the optimal condition for individual differences research is largely untested. In fact, other brain states may afford a better ratio of within- to between-subject variability, facilitating biomarker discovery. Depending on the trait or behavior under study, certain tasks may bring out meaningful idiosyncrasies across subjects, essentially enhancing the individual signal in networks of interest beyond what can be measured at rest. Here, we review theoretical considerations and existing work on how brain state influences individual differences in functional connectivity, present some preliminary analyses of within- and between-subject variability across conditions using data from the Human Connectome Project, and outline questions for future study.