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Resting-state functional magnetic resonance imaging (R-fMRI) applications can entail a higher temporal-sampling rate that trades off spatial resolution, thereby challenging effective scientific studies. To enable higher spatial resolution, current schemes speedup per-timeframe scanning by reconstruction from simultaneous multislice (SMS) magnetic resonance imaging (MRI) with k-space undersampling (sometimes temporal undersampling), while using prior models on the signal. We propose a novel algorithmic framework to reconstruct R-fMRI (SMS with controlled aliasing) that has, both, k-space undersampling and temporal undersampling. We propose a coupled spatiotemporal sparse model, incorporating (i) a robust spatially-regularized temporal-dictionary prior and (ii) a spatiotemporal wavelet prior, which we fit efficiently using variational Bayesian expectation maximization with nested minorization (VBEMNM). We show that our framework has the potential to enable higher spatial resolution without increasing scan time in R-fMRI that has inherently weak signals and is therefore prone to large physiological fluctuations, acquisition noise, and imaging artifacts. Qualitative and quantitative evaluation on retrospectively undersampled brain R-fMRI shows that estimates of resting-state networks from our framework and the boost in temporal stability given by our framework compares favourably to existing methods for R-fMRI reconstruction.

Purpose: In recent years, machine learning techniques have received increasing attention as a promising approach to differentiating patients from healthy subjects. Therefore, some resting-state functional magnetic resonance neuroimaging (R-fMRI) studies have used interregional functional connections as discriminative features. The aim of this study was to investigate ADHD-related spatially distributed discriminative features derived from whole-brain resting-state functional connectivity patterns using machine learning. Patients and Methods: We measured the interregional functional connections of the R-fMRI data from 40 ADHD patients and 28 matched typically developing controls. Machine learning was used to discriminate ADHD patients from controls. Classification performance was assessed by permutation tests. Results: The results from the model with the highest classification accuracy showed that 85.3% of participants were correctly identified using leave-one-out cross-validation (LOOV) with support vector machine (SVM). The majority of the most discriminative functional connections were located within or between the cerebellum, default mode network (DMN) and frontoparietal regions. Approximately half of the most discriminative connections were associated with the cerebellum. The cerebellum, right superior orbitofrontal cortex, left olfactory cortex, left gyrus rectus, right superior temporal pole, right calcarine gyrus and bilateral inferior occipital cortex showed the highest discriminative power in classification. Regarding the brain–behaviour relationships, some functional connections between the cerebellum and DMN regions were significantly correlated with behavioural symptoms in ADHD (P < 0.05). Conclusion: This study indicated that whole-brain resting-state functional connections might provide potential neuroimaging-based information for clinically assisting the diagnosis of ADHD. [ABSTRACT FROM AUTHOR]

Background: Neuroimaging studies have shown that the high synchrony of spontaneous neural activity in the homotopic regions between hemispheres is an important functional structural feature of normal human brains, and this feature is abnormal in the patients with various mental disorders. However, little is known about this feature in obsessive–compulsive disorder (OCD). This study aimed to further analyze the underlying neural mechanisms of OCD and to explore whether clinical characteristics are correlated with the alerted homotopic connectivity in patients with OCD.Methods: Using voxel-mirrored homotopic connectivity (VMHC) during resting state, we compared 46 OCD patients and 46 healthy controls (HCs) matched for age, gender, and education level. A partial correlation analysis was used to investigate the relationship between altered VMHC and clinical characteristics in patients with OCD.Results: Patients with OCD showed lower VMHC than HCs in fusiform gyrus/inferior occipital gyrus, lingual gyrus, postcentral gyrus/precentral gyrus, putamen, and orbital frontal gyrus. A significant positive correlation was observed between altered VMHC in the angular gyrus/middle occipital gyrus and illness duration in patients.Conclusions: Interhemispheric functional imbalance may be an essential aspect of the pathophysiological mechanism of OCD, which is reflected not only in the cortico-striato-thalamo-cortical (CSTC) loop but also elsewhere in the brain.

Background: Neuroimaging studies have shown that the high synchrony of spontaneous neural activity in the homotopic regions between hemispheres is an important functional structural feature of normal human brains, and this feature is abnormal in the patients with various mental disorders. However, little is known about this feature in obsessive–compulsive disorder (OCD). This study aimed to further analyze the underlying neural mechanisms of OCD and to explore whether clinical characteristics are correlated with the alerted homotopic connectivity in patients with OCD. Methods: Using voxel-mirrored homotopic connectivity (VMHC) during resting state, we compared 46 OCD patients and 46 healthy controls (HCs) matched for age, gender, and education level. A partial correlation analysis was used to investigate the relationship between altered VMHC and clinical characteristics in patients with OCD. Results: Patients with OCD showed lower VMHC than HCs in fusiform gyrus/inferior occipital gyrus, lingual gyrus, postcentral gyrus/precentral gyrus, putamen, and orbital frontal gyrus. A significant positive correlation was observed between altered VMHC in the angular gyrus/middle occipital gyrus and illness duration in patients. Conclusions: Interhemispheric functional imbalance may be an essential aspect of the pathophysiological mechanism of OCD, which is reflected not only in the cortico-striato-thalamo-cortical (CSTC) loop but also elsewhere in the brain. [ABSTRACT FROM AUTHOR]

Abstract: The human brain is a large, interacting dynamic network, and its architecture of coupling among brain regions varies across time (termed the “chronnectome”). However, very little is known about whether and how the dynamic properties of the chronnectome can characterize individual uniqueness, such as identifying individuals as a “fingerprint” of the brain. Here, we employed multiband resting‐state functional magnetic resonance imaging data from the Human Connectome Project (N = 105) and a sliding time‐window dynamic network analysis approach to systematically examine individual time‐varying properties of the chronnectome. We revealed stable and remarkable individual variability in three dynamic characteristics of brain connectivity (i.e., strength, stability, and variability), which was mainly distributed in three higher order cognitive systems (i.e., default mode, dorsal attention, and fronto‐parietal) and in two primary systems (i.e., visual and sensorimotor). Intriguingly, the spatial patterns of these dynamic characteristics of brain connectivity could successfully identify individuals with high accuracy and could further significantly predict individual higher cognitive performance (e.g., fluid intelligence and executive function), which was primarily contributed by the higher order cognitive systems. Together, our findings highlight that the chronnectome captures inherent functional dynamics of individual brain networks and provides implications for individualized characterization of health and disease. [ABSTRACT FROM AUTHOR]

Sharing drafts of scientific manuscripts on preprint hosting services for early exposure and pre-publication feedback is a well-accepted practice in fields such as physics, astronomy, or mathematics. The field of neuroscience, however, has yet to adopt the preprint model. A reason for this reluctance might partly be the lack of central preprint services for the field of neuroscience. To address this issue, we announce the launch of Preprints of the R-fMRI Network (PRN), a community funded preprint hosting service. PRN provides free-submission and free hosting of manuscripts for resting state functional magnetic resonance imaging (R-fMRI) and neuroscience related studies. Submitted articles are openly discussed and receive feedback from readers and a panel of invited consultants from the R-fMRI Network. All manuscripts and feedback are freely accessible online with citable permanent URL for open-access. The goal of PRN is to supplement the peer reviewed journal publication system – by more rapidly communicating the latest research achievements throughout the world. We hope PRN would help the field to embrace the preprint model and thus further accelerate R-fMRI and neuroscience related studies, eventually enhancing human mental health.

Sharing drafts of scientific manuscripts on preprint hosting services for early exposure and pre-publication feedback is a well-accepted practice in fields such as physics, astronomy, or mathematics. The field of neuroscience, however, has yet to adopt the preprint model. A reason for this reluctance might partly be the lack of central preprint services for the field of neuroscience. To address this issue, we announce the launch of Preprints of the R-fMRI Network (PRN), a community funded preprint hosting service. PRN provides free-submission and free hosting of manuscripts for resting state functional magnetic resonance imaging (R-fMRI) and neuroscience related studies. Submissions will be peer viewed and receive feedback from readers and a panel of invited consultants of the R-fMRI Network. All manuscripts and feedback will be freely available online with citable permanent URL for open-access. The goal of PRN is to supplement the “peer reviewed” journal publication system – by more rapidly communicating the latest research achievements throughout the world. We hope PRN will help the field to embrace the preprint model and thus further accelerate R-fMRI and neuroscience related studies, eventually enhancing human mental health.

Motivated by recent progress in signal processing on graphs, we have developed a matched signal detection (MSD) theory for signals with intrinsic structures described by weighted graphs. First, we regard graph Laplacian eigenvalues as frequencies of graph-signals and assume that the signal is in a subspace spanned by the first few graph Laplacian eigenvectors associated with lower eigenvalues. The conventional matched subspace detector can be applied to this case. Furthermore, we study signals that may not merely live in a subspace. Concretely, we consider signals with bounded variation on graphs and more general signals that are randomly drawn from a prior distribution. For bounded variation signals, the test is a weighted energy detector. For the random signals, the test statistic is the difference of signal variations on associated graphs, if a degenerate Gaussian distribution specified by the graph Laplacian is adopted. We evaluate the effectiveness of the MSD on graphs both with simulated and real data sets. Specifically, we apply MSD to the brain imaging data classification problem of Alzheimer's disease (AD) based on two independent data sets: 1) positron emission tomography data with Pittsburgh compound-B tracer of 30 AD and 40 normal control (NC) subjects, and 2) resting-state functional magnetic resonance imaging (R-fMRI) data of 30 early mild cognitive impairment and 20 NC subjects. Our results demonstrate that the MSD approach is able to outperform the traditional methods and help detect AD at an early stage, probably due to the success of exploiting the manifold structure of the data. [ABSTRACT FROM AUTHOR]

Objective: The cerebellum plays a critical role in cognition and behavior. Altered function of the cerebellum has been related to schizophrenia and psychosis but it is not known how this applies to spontaneous resting state activity in young people with familial risk for psychosis.Methods: We conducted resting-state functional MRI (R-fMRI) in 72 (29 male) young adults with a history of psychosis in one or both parents (FR) but without their own psychosis, and 72 (29 male) similarly healthy control subjects without parental psychosis. Both groups in the Oulu Brain and Mind Study were drawn from the Northern Finland Birth Cohort 1986. Participants were 20-25 years old. Parental psychosis was established using the Care Register for Health Care. R-fMRI data pre-processing was conducted using independent component analysis with 30 and 70 components. A dual regression technique was used to detect between-group differences in the cerebellum with p<0.05 threshold corrected for multiple comparisons.Results: FR participants demonstrated statistically significantly increased activity compared to control subjects in the anterior lobe of the right cerebellum in the analysis with 70 components. The volume of the increased activity was 73 mm(3). There was no difference between the groups in the analysis with 30 components.Conclusion: The finding suggests that increased activity of the anterior lobe of the right cerebellum may be associated with increased vulnerability to psychosis. The finding is novel, and needs replication to be confirmed. [ABSTRACT FROM AUTHOR]

Children exposed to natural disasters are vulnerable to the development of posttraumatic stress disorder (PTSD). Recent studies of other neuropsychiatric disorders have used graph-based theoretical analysis to investigate the topological properties of the functional brain connectome. However, little is known about this connectome in pediatric PTSD. Twenty-eight pediatric PTSD patients and 26 trauma-exposed non-PTSD patients were recruited from 4,200 screened subjects after the 2008 Sichuan earthquake to undergo a resting-state functional magnetic resonance imaging scan. Functional connectivity between 90 brain regions from the automated anatomical labeling atlas was established using partial correlation coefficients, and the whole-brain functional connectome was constructed by applying a threshold to the resultant 90 * 90 partial correlation matrix. Graph theory analysis was then used to examine the group-specific topological properties of the two functional connectomes. Both the PTSD and non-PTSD control groups exhibited 'small-world' brain network topology. However, the functional connectome of the PTSD group showed a significant increase in the clustering coefficient and a normalized characteristic path length and local efficiency, suggesting a shift toward regular networks. Furthermore, the PTSD connectomes showed both enhanced nodal centralities, mainly in the default mode- and salience-related regions, and reduced nodal centralities, mainly in the central-executive network regions. The clustering coefficient and nodal efficiency of the left superior frontal gyrus were positively correlated with the Clinician-Administered PTSD Scale. These disrupted topological properties of the functional connectome help to clarify the pathogenesis of pediatric PTSD and could be potential biomarkers of brain abnormalities. Hum Brain Mapp 36:3677-3686, 2015. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Graph theory-based analysis has been widely employed in brain imaging studies, and altered topological properties of brain connectivity have emerged as important features of mental diseases such as schizophrenia. However, most previous studies have focused on graph metrics of stationary brain graphs, ignoring that brain connectivity exhibits fluctuations over time. Here we develop a new framework for accessing dynamic graph properties of time-varying functional brain connectivity in resting-state fMRI data and apply it to healthy controls (HCs) and patients with schizophrenia (SZs). Specifically, nodes of brain graphs are defined by intrinsic connectivity networks (ICNs) identified by group independent component analysis (ICA). Dynamic graph metrics of the time-varying brain connectivity estimated by the correlation of sliding time-windowed ICA time courses of ICNs are calculated. First- and second-level connectivity states are detected based on the correlation of nodal connectivity strength between time-varying brain graphs. Our results indicate that SZs show decreased variance in the dynamic graph metrics. Consistent with prior stationary functional brain connectivity works, graph measures of identified first-level connectivity states show lower values in SZs. In addition, more first-level connectivity states are disassociated with the second-level connectivity state which resembles the stationary connectivity pattern computed by the entire scan. Collectively, the findings provide new evidence about altered dynamic brain graphs in schizophrenia, which may underscore the abnormal brain performance in this mental illness. [ABSTRACT FROM AUTHOR]

Objective: The central executive network controls and manages high-level cognitive functions. Abnormal activation in the central executive network has been related to psychosis and schizophrenia but it is not established how this applies to people with familial risk for psychosis (FR).Methods: We conducted a resting-state functional MRI (R-fMRI) in 72 (29 males) young adults with a history of psychosis in one or both parents (FR) but without psychosis themselves, and 72 (29 males) similarly healthy control subjects without parental psychosis. Both groups in the Oulu Brain and Mind Study were drawn from the Northern Finland Birth Cohort 1986. Participants were 20-25years old. Parental psychosis was established using the Care Register for Health Care. R-fMRI data pre-processing was conducted using independent component analysis with 30 and 70 components. A dual regression technique was used to detect between-group differences in the central executive network with p<0.05 threshold corrected for multiple comparisons.Results: FR participants demonstrated statistically significantly lower activity compared to control subjects in the right inferior frontal gyrus, a key area of central executive network corresponding to Brodmann areas 44 and 45, known as Broca's area. The volume of the lower activation area with 30 components was 896mm(3) and with 70 components was 1151mm(3).Conclusion: The activity of the central executive network differed in the right inferior frontal gyrus between FR and control groups. This suggests that abnormality of the right inferior frontal gyrus may be a central part of vulnerability for psychosis. [ABSTRACT FROM AUTHOR]

Neuroimaging studies have shown that functional brain networks composed from select regions of interest (ROIs) have a modular community structure. However, the organization of functional network connectivity (FNC), comprising a purely data-driven network built from spatially independent brain components, is not yet clear. The aim of this study is to explore the modular organization of FNC in both healthy controls (HCs) and patients with schizophrenia (SZs). Resting state functional magnetic resonance imaging (R-fMRI) data of HCs and SZs were decomposed into independent components (ICs) by group independent component analysis (ICA). Then weighted brain networks (in which nodes are brain components) were built based on correlations among of ICA time courses. Clustering coefficients and connectivity strength of the networks were computed. A dynamic branch cutting algorithm was used to identify modules of the FNC in HCs and SZs. Results show stronger connectivity strength and higher clustering coefficient in HCs with more and smaller modules in SZs. In addition, HCs and SZs had some different hubs. Our findings demonstrate altered modular architecture of the FNC in schizophrenia and provide insights into abnormal topological organization of intrinsic brain networks in this mental illness.

Highlights: [•] Representation of structural connectomes by DICCCOL based on DTI data. [•] Construction of whole-brain quasi-stable functional connectomes from fMRI data. [•] Learn atomic connectome patterns (ACPs) via effective sparse representations. [•] Characterization of task-performance and task-free states by ACPs. [•] Novel insights into the functional architectures of the brain. [Copyright &y& Elsevier]

Abstract: Over a decade ago, the fMRI Data Center (fMRIDC) pioneered open-access data sharing in the task-based functional neuroimaging community. Well ahead of its time, the fMRIDC effort encountered logistical, sociocultural and funding barriers that impeded the field-wise instantiation of open-access data sharing. In 2009, ambitions for open-access data sharing were revived in the resting state functional MRI community in the form of two grassroots initiatives: the 1000 Functional Connectomes Project (FCP) and its successor, the International Neuroimaging Datasharing Initiative (INDI). Beyond providing open access to thousands of clinical and non-clinical imaging datasets, the FCP and INDI have demonstrated the feasibility of large-scale data aggregation for hypothesis generation and testing. Yet, the success of the FCP and INDI should not be confused with widespread embracement of open-access data sharing. Reminiscent of the challenges faced by fMRIDC, key controversies persist and include participant privacy, the role of informatics, and the logistical and cultural challenges of establishing an open science ethos. We discuss the FCP and INDI in the context of these challenges, highlighting the promise of current initiatives and suggesting solutions for possible pitfalls. [Copyright &y& Elsevier]

Abstract: Altered brain connectivity has emerged as a central feature of schizophrenia. Low frequency oscillations and connectivity strength (CS) of resting state brain networks are altered in patients with schizophrenia (SZs). However, the relationship between these two measures has not yet been studied. Such work may be helpful in understanding the so-called “rich club” organization (i.e. high-CS nodes are more densely connected among themselves than are nodes of a lower CS in the human brain) in healthy controls (HCs) and SZs. Here we present a study of HCs and SZs examining low frequency oscillations and CS by first decomposing resting state fMRI (R-fMRI) data into independent components (ICs) using group independent component analysis (ICA) and computing the low frequency power ratio (LFPR) of each ICA time course. Weighted brain graphs consisting of ICs were built based on correlations between ICA time courses. Positive CS and negative CS of each node in the brain graphs were then examined. The correlations between LFPR and CSs as well as “rich club” coefficients of group mean brain graphs were assessed. Results demonstrate that the LFPR of some ICs were lower in SZs compared to HCs. In addition, LFPR was correlated with positive CS in HCs, but to a lesser extent in SZs. HCs showed higher normalized rich club parameter than SZs. The findings provide new insight into disordered intrinsic brain graphs in schizophrenia. [Copyright &y& Elsevier]

Objective: Some pharmacological treatments are ineffective in parts of patients with major depressive disorder (MDD), hence this needs prediction of effective treatment responses. The study aims to examine the relationship between dynamic functional connectivity (dFC) of the hippocampal subregion and antidepressant improvement of MDD patients and to estimate the capability of dFC to predict antidepressant efficacy., Methods: The data were from 70 MDD patients and 43 healthy controls (HC); the dFC of hippocampal subregions was estimated by sliding-window approach based on resting-state functional magnetic resonance imaging (R-fMRI). After 3 months treatment, 36 patients underwent second R-fMRI scan and were then divided into the response group and non-response group according to clinical responses., Results: The result manifested that MDD patients exhibited lower mean dFC of the left rostral hippocampus (rHipp.l) compared with HC. After 3 months therapy, the response group showed lower dFC of rHipp.l compared with the non-response group. The dFC of rHipp.l was also negatively correlated with the reduction rate of Hamilton Depression Rating Scale., Conclusion: These findings highlighted the importance of rHipp in MDD from the dFC perspective. Detection and estimation of these changes might demonstrate helpful for comprehending the pathophysiological mechanism and for assessment of treatment reaction of MDD.

Despite a growing neuroimaging literature on the pathophysiology of major depressive disorder (MDD), reproducible findings are lacking, probably reflecting mostly small sample sizes and heterogeneity in analytic approaches. To address these issues, the Depression Imaging REsearch ConsorTium (DIRECT) was launched. The REST-meta-MDD project, pooling 2428 functional brain images processed with a standardized pipeline across all participating sites, has been the first effort from DIRECT. In this review, we present an overview of the motivations, rationale, and principal findings of the studies so far from the REST-meta-MDD project. Findings from the first round of analyses of the pooled repository have included alterations in functional connectivity within the default mode network, in whole-brain topological properties, in dynamic features, and in functional lateralization. These well-powered exploratory observations have also provided the basis for future longitudinal hypothesis-driven research. Following these fruitful explorations, DIRECT has proceeded to its second stage of data sharing that seeks to examine ethnicity in brain alterations in MDD by extending the exclusive Chinese original sample to other ethnic groups through international collaborations. A state-of-the-art, surface-based preprocessing pipeline has also been introduced to improve sensitivity. Functional images from patients with bipolar disorder and schizophrenia will be included to identify shared and unique abnormalities across diagnosis boundaries. In addition, large-scale longitudinal studies targeting brain network alterations following antidepressant treatment, aggregation of diffusion tensor images, and the development of functional magnetic resonance imaging-guided neuromodulation approaches are underway. Through these endeavours, we hope to accelerate the translation of functional neuroimaging findings to clinical use, such as evaluating longitudinal effects of antidepressant medications and developing individualized neuromodulation targets, while building an open repository for the scientific community., Competing Interests: One of the authors, Dr Qi-Yong Gong, is also the editor-in-chief of Psychoradiology. He was blinded from reviewing or making decisions on the manuscript., (© The Author(s) 2022. Published by Oxford University Press on behalf of West China School of Medicine/West China Hospital (WCSM/WCH) of Sichuan University.)

• Faster R-fMRI imaging allows higher spatial resolution and more reliable functional connectivity analysis. • We propose a novel undersampling scheme in k-space and time (k-t) both to provide the necessary speedup. • We propose a novel dictionary-based model on the signal, which is robust, spatially regularized, and subject invariant by leveraging an equivalence-class structure on the dictionary. • We propose a novel Bayesian inference framework based on variational Bayesian expectation maximization with nested minorization (VB-EM-NM), which allows us to estimate per-voxel uncertainty in the reconstruction. • Empirical evaluation of (i) R-fMRI reconstructions from simulated data and (ii) functional-network estimates from reconstructions of brain R-fMRI demonstrate that our framework improves over the state of the art, and, additionally, enables significantly higher spatial resolution. Higher spatial resolution in resting-state functional magnetic resonance imaging (R-fMRI) can give reliable information about the functional networks in the cerebral cortex. Typical methods can achieve higher spatial or temporal resolution by speeding up scans using either (i) complex pulse-sequence designs or (ii) k-space undersampling coupled with priors on the signal. We propose to undersample the R-fMRI acquisition in k-space and time to speedup scans in order to improve spatial resolution. We propose a novel model-based R-fMRI reconstruction framework using a robust, subject-invariant, spatially regularized dictionary prior on the signal. Furthermore, we propose a novel inference framework based on variational Bayesian expectation maximization with nested minorization (VB-EM-NM). Our inference framework allows us to provide an estimate of uncertainty of the reconstruction, unlike typical reconstruction methods. Empirical evaluation of (i) simulated R-fMRI reconstruction and (ii) functional-network estimates from brain R-fMRI reconstructions demonstrate that our framework improves over the state of the art, and, additionally, enables significantly higher spatial resolution. [ABSTRACT FROM AUTHOR]

Background: Dysconnectivity hypothesis posits that schizophrenia relates to abnormalities in neuronal connectivity. However, little is known about the alterations of the interhemispheric resting-state functional connectivity (FC) in patients with paranoid schizophrenia. In the present study, we used a newly developed voxel-mirrored homotopic connectivity (VMHC) method to investigate the interhemispheric FC of the whole brain in patients with paranoid schizophrenia at rest., Methods: Forty-nine first-episode, drug-naive patients with paranoid schizophrenia and 50 age-, gender-, and education-matched healthy subjects underwent a resting-state functional magnetic resonance imaging (fMRI) scans. An automated VMHC approach was used to analyze the data., Results: Patients exhibited lower VMHC than healthy subjects in the precuneus (PCu), the precentral gyrus, the superior temporal gyrus (STG), the middle occipital gyrus (MOG), and the fusiform gyrus/cerebellum lobule VI. No region showed greater VMHC in the patient group than in the control group. Significantly negative correlation was observed between VMHC in the precentral gyrus and the PANSS positive/total scores, and between VMHC in the STG and the PANSS positive/negative/total scores., Conclusions: Our results suggest that interhemispheric resting-state FC of VMHC is reduced in paranoid schizophrenia with clinical implications for psychiatric symptomatology thus further contribute to the dysconnectivity hypothesis of schizophrenia., (© 2013.)