BrainMap VBM: An environment for structural meta-analysis

Three layered sparse dictionary learning algorithm for enhancing the subject wise segregation of brain networks

Independent component analysis (ICA) and dictionary learning (DL) are the most successful blind source separation (BSS) methods for functional magnetic resonance imaging (fMRI) data analysis. However, ICA to higher and DL to lower extent may suffer from performance degradation by the presence of anomalous observations in the recovered time courses (TCs) and high overlaps among spatial maps (SMs). This paper addressed both problems using a novel three-layered sparse DL (TLSDL) algorithm that incorporated prior information in the dictionary update process and recovered full-rank outlier-free TCs from highly corrupted measurements. The associated sequential DL model involved factorizing each subject's data into a multi-subject (MS) dictionary and MS sparse code while imposing a low-rank and a sparse matrix decomposition restriction on the dictionary matrix. It is derived by solving three layers of feature extraction and component estimation. The first and second layers captured brain regions with low and moderate spatial overlaps, respectively. The third layer that segregated regions with significant spatial overlaps solved a sequence of vector decomposition problems using the proximal alternating linearized minimization (PALM) method and solved a decomposition restriction using the alternating directions method (ALM). It learned outlier-free dynamics that integrate spatiotemporal diversities across brains and external information. It differs from existing DL methods owing to its unique optimization model, which incorporates prior knowledge, subject-wise/multi-subject representation matrices, and outlier handling. The TLSDL algorithm was compared with existing dictionary learning algorithms using experimental and synthetic fMRI datasets to verify its performance. Overall, the mean correlation value was found to be 26 % higher for the TLSDL than for the state-of-the-art subject-wise sequential DL (swsDL) technique.

Gray matter volume alterations in de novo Parkinson's disease: A mediational role in the interplay between sleep quality and anxiety

OBJECTIVE

Parkinson's disease (PD) is increasingly recognized for its non-motor symptoms, among which emotional disturbances and sleep disorders frequently co-occur. The commonality of neuroanatomical underpinnings for these symptoms is not fully understood. This study is intended to investigate the differences in gray matter volume (GMV) between PD patients with anxiety (A-PD) and those without anxiety (NA-PD). Additionally, it seeks to uncover the interplay between GMV variations and the manifestations of anxiety and sleep quality.

METHODS

A total of 37 A-PD patients, 43 NA-PD patients, and 36 healthy controls (HCs) were recruited, all of whom underwent voxel-based morphometry (VBM) analysis. Group differences in GMV were assessed using analysis of covariance (ANCOVA). Partial correlation between GMV, anxiety symptom, and sleep quality were analyzed. Mediation analysis explored the mediating role of the volume of GMV-distinct brain regions on the relationship between sleep quality and anxiety within the PD patient cohort.

RESULTS

A-PD patients showed significantly lower GMV in the fusiform gyrus (FG) and right inferior temporal gyrus (ITG) compared to HCs and NA-PD patients. GMV in these regions correlated negatively with Hamilton Anxiety Rating Scale (HAMA) scores (right ITG: r = -0.690, p < 0.001; left FG: r = -0.509, p < 0.001; right FG: r = -0.576, p < 0.001) and positively with sleep quality in PD patients (right ITG: r = 0.592, p < 0.001; left FG: r = 0.356, p = 0.001; right FG: r = 0.470, p < 0.001). Mediation analysis revealed that GMV in the FG and right ITG mediated the relationship between sleep quality and anxiety symptoms, with substantial effect sizes accounted for by the right ITG (25.74%) and FG (left: 11.90%, right: 15.59%).

CONCLUSION

This study has shed further light on the relationship between sleep disturbances and anxiety symptoms in PD patients. Given the pivotal roles of the FG and the ITG in facial recognition and the recognition of emotion-related facial expressions, our findings indicate that compromised sleep quality, under the pathological conditions of PD, may exacerbate the reduction in GMV within these regions, impairing the recognition of emotional facial expressions and thereby intensifying anxiety symptoms.

Neural Correlates of Healthy Sustained Vowel Phonation Tasks: A Systematic Review and Meta-Analysis of Neuroimaging Studies

OBJECTIVE

This review of the methodology and results of studies involving a sustained vowel phonation task during functional Magnetic Resonance Imaging (fMRI) aims to contribute to the identification of brain regions involved in phonation for healthy subjects.

DATA SOURCES

This review was performed using the PubMed electronic database.

REVIEW METHODS

A review was conducted, according to PRISMA guidelines, between September and November 2020, using the following search term pairs: "fMRI and Phonation" and "fMRI and Voice." Activation likelihood estimation analysis was performed. A qualitative analysis was also performed to specify the frequency of activation of each region, as well as the various activation clusters within a single region.

RESULTS

Seven studies were included and analyzed. Five of the seven studies were selected for the activation likelihood estimation meta-analysis which revealed significant convergent activation for only one cluster located in the left precentral gyrus (BA4). A qualitative review provides an overview of brain activation. Primary motor and premotor areas were the only activated areas in all studies included. Other regions previously considered to be implicated in phonation were often activated in sustained vowel phonation tasks. Additionally, areas generally associated with articulation or language also showed activation.

CONCLUSION

Methodological recommendations are suggested to isolate the phonatory component and reduce variability between future studies. Based on the qualitative analysis, this review does not support a distinction between regions more related to phonation and regions more related to articulation. Further research is required seeking to isolate the vocal component and to improve insight into human brain network involved in phonation.

Activation Likelihood Estimation Neuroimaging Meta-Analysis: a Powerful Tool for Emotion Research

Over the past two decades, functional magnetic resonance imaging (fMRI) has become the primary tool for exploring neural correlates of emotion. To enhance the reliability of results in understanding the complex nature of emotional experiences, researchers combine findings from multiple fMRI studies using coordinate-based meta-analysis (CBMA). As one of the most widely employed CBMA methods worldwide, activation likelihood estimation (ALE) is of great importance in affective neuroscience and neuropsychology. This comprehensive review provides an introductory guide for implementing the ALE method in emotion research, outlining the experimental steps involved. By presenting a case study about the emotion of disgust, with regard to both its core and social processing, we offer insightful commentary as to how ALE can enable researchers to produce consistent results and, consequently, fruitfully investigate the neural mechanisms underpinning emotions, facilitating further progress in this field.

ALE meta-analyses of voxel-based morphometry studies: Parameter validation via large-scale simulations

Activation likelihood estimation (ALE) meta-analysis has been applied to structural neuroimaging data since long, but up to now, any systematic assessment of the algorithm's behavior, power and sensitivity has been based on simulations using functional neuroimaging databases as their foundation. Here, we aimed to determine whether the guidelines offered by previous evaluations can be generalized to ALE meta-analyses of voxel-based morphometry (VBM) studies. We ran 365000 distinct ALE analyses filled with simulated experiments, randomly sampling parameters from BrainMap's VBM experiment database. We then examined the algorithm's sensitivity, its susceptibility to spurious convergence, and its susceptibility to excessive contributions by individual experiments. In general, the performance of the ALE algorithm was highly comparable between imaging modalities, with the algorithm's sensitivity and specificity reaching similar levels with structural data as previously observed with functional data. Because of the lower number of foci reported and the higher number of participants usually included in structural experiments, individual studies had, on average, a higher impact towards significant clusters. To prevent significant clusters from being driven by single experiments, we recommend that researchers include at least 23 experiments in a VBM ALE dataset, instead of the previously recommended minimum of n = 17. While these recommendations do not constitute hard borders, running ALE analyses on smaller datasets would require special diligence in assessing and reporting the contributions of experiments to individual clusters.

Structural degeneration of the nucleus basalis of Meynert in mild cognitive impairment and Alzheimer's disease - Evidence from an MRI-based meta-analysis

Recent models of Alzheimer's disease (AD) suggest that neuropathological changes of the medial temporal lobe, especially entorhinal cortex, are preceded by degenerations of the cholinergic Nucleus basalis of Meynert (NbM). Evidence from imaging studies in humans, however, is limited. Therefore, we performed an activation-likelihood estimation meta-analysis on whole brain voxel-based morphometry (VBM) MRI data from 54 experiments and 2581 subjects in total. It revealed, compared to healthy older controls, reduced gray matter in the bilateral NbM in AD, but only limited evidence for such an effect in patients with mild cognitive impairment (MCI), which typically precedes AD. Both patient groups showed less gray matter in the amygdala and hippocampus, with hints towards more pronounced amygdala effects in AD. We discuss our findings in the context of studies that highlight the importance of the cholinergic basal forebrain in learning and memory throughout the lifespan, and conclude that they are partly compatible with pathological staging models suggesting initial and pronounced structural degenerations within the NbM in the progression of AD.

Deep neural network heatmaps capture Alzheimer's disease patterns reported in a large meta-analysis of neuroimaging studies

Deep neural networks currently provide the most advanced and accurate machine learning models to distinguish between structural MRI scans of subjects with Alzheimer's disease and healthy controls. Unfortunately, the subtle brain alterations captured by these models are difficult to interpret because of the complexity of these multi-layer and non-linear models. Several heatmap methods have been proposed to address this issue and analyze the imaging patterns extracted from the deep neural networks, but no quantitative comparison between these methods has been carried out so far. In this work, we explore these questions by deriving heatmaps from Convolutional Neural Networks (CNN) trained using T1 MRI scans of the ADNI data set and by comparing these heatmaps with brain maps corresponding to Support Vector Machine (SVM) activation patterns. Three prominent heatmap methods are studied: Layer-wise Relevance Propagation (LRP), Integrated Gradients (IG), and Guided Grad-CAM (GGC). Contrary to prior studies where the quality of heatmaps was visually or qualitatively assessed, we obtained precise quantitative measures by computing overlap with a ground-truth map from a large meta-analysis that combined 77 voxel-based morphometry (VBM) studies independently from ADNI. Our results indicate that all three heatmap methods were able to capture brain regions covering the meta-analysis map and achieved better results than SVM activation patterns. Among them, IG produced the heatmaps with the best overlap with the independent meta-analysis.

Trends in the sample size, statistics, and contributions to the BrainMap database of activation likelihood estimation meta-analyses: An empirical study of 10-year data

The literature of neuroimaging meta-analysis has been thriving for over a decade. A majority of them were coordinate-based meta-analyses, particularly the activation likelihood estimation (ALE) approach. A meta-evaluation of these meta-analyses was performed to qualitatively evaluate their design and reporting standards. The publications listed from the BrainMap website were screened. Six hundred and three ALE papers published during 2010-2019 were included and analysed. For reporting standards, most of the ALE papers reported their total number of Papers involved and mentioned the inclusion/exclusion criteria on Paper selection. However, most papers did not describe how data redundancy was avoided when multiple related Experiments were reported within one paper. The most prevalent repeated-measures correction methods were voxel-level FDR (54.4%) and cluster-level FWE (33.8%), with the latter quickly replacing the former since 2016. For study characteristics, sample size in terms of number of Papers included per ALE paper and number of Experiments per analysis seemed to be stable over the decade. One-fifth of the surveyed ALE papers failed to meet the recommendation of having >17 Experiments per analysis. For data sharing, most of them did not provide input and output data. In conclusion, the field has matured well in terms of rising dominance of cluster-level FWE correction, and slightly improved reporting on elimination of data redundancy and providing input data. The provision of Data and Code availability statements and flow chart of literature screening process, as well as data submission to BrainMap, should be more encouraged.

A Minimum Bayes Factor Based Threshold for Activation Likelihood Estimation

Activation likelihood estimation (ALE) is among the most used algorithms to perform neuroimaging meta-analysis. Since its first implementation, several thresholding procedures had been proposed, all referred to the frequentist framework, returning a rejection criterion for the null hypothesis according to the critical p-value selected. However, this is not informative in terms of probabilities of the validity of the hypotheses. Here, we describe an innovative thresholding procedure based on the concept of minimum Bayes factor (mBF). The use of the Bayesian framework allows to consider different levels of probability, each of these being equally significant. In order to simplify the translation between the common ALE practice and the proposed approach, we analised six task-fMRI/VBM datasets and determined the mBF values equivalent to the currently recommended frequentist thresholds based on Family Wise Error (FWE). Sensitivity and robustness toward spurious findings were also analyzed. Results showed that the cutoff log₁₀(mBF) = 5 is equivalent to the FWE threshold, often referred as voxel-level threshold, while the cutoff log₁₀(mBF) = 2 is equivalent to the cluster-level FWE (c-FWE) threshold. However, only in the latter case voxels spatially far from the blobs of effect in the c-FWE ALE map survived. Therefore, when using the Bayesian thresholding the cutoff log₁₀(mBF) = 5 should be preferred. However, being in the Bayesian framework, lower values are all equally significant, while suggesting weaker level of force for that hypothesis. Hence, results obtained through less conservative thresholds can be legitimately discussed without losing statistical rigor. The proposed technique adds therefore a powerful tool to the human-brain-mapping field.

Co-alteration Network Architecture of Major Depressive Disorder: A Multi-modal Neuroimaging Assessment of Large-scale Disease Effects

Major depressive disorder (MDD) exhibits diverse symptomology and neuroimaging studies report widespread disruption of key brain areas. Numerous theories underpinning the network degeneration hypothesis (NDH) posit that neuropsychiatric diseases selectively target brain areas via meaningful network mechanisms rather than as indistinct disease effects. The present study tests the hypothesis that MDD is a network-based disorder, both structurally and functionally. Coordinate-based meta-analysis and Activation Likelihood Estimation (CBMA-ALE) were used to assess the convergence of findings from 92 previously published studies in depression. An extension of CBMA-ALE was then used to generate a node-and-edge network model representing the co-alteration of brain areas impacted by MDD. Standardized measures of graph theoretical network architecture were assessed. Co-alteration patterns among the meta-analytic MDD nodes were then tested in independent, clinical T1-weighted structural magnetic resonance imaging (MRI) and resting-state functional (rs-fMRI) data. Differences in co-alteration profiles between MDD patients and healthy controls, as well as between controls and clinical subgroups of MDD patients, were assessed. A 65-node 144-edge co-alteration network model was derived for MDD. Testing of co-alteration profiles in replication data using the MDD nodes provided distinction between MDD and healthy controls in structural data. However, co-alteration profiles were not distinguished between patients and controls in rs-fMRI data. Improved distinction between patients and healthy controls was observed in clinically homogenous MDD subgroups in T1 data. MDD abnormalities demonstrated both structural and functional network architecture, though only structural networks exhibited between-groups differences. Our findings suggest improved utility of structural co-alteration networks for ongoing biomarker development.

Linking neuroanatomical abnormalities in autism spectrum disorder with gene expression of candidate ASD genes: A meta-analytic and network-oriented approach

BACKGROUND

Autism spectrum disorder (ASD) is a set of developmental conditions with widespread neuroanatomical abnormalities and a strong genetic basis. Although neuroimaging studies have indicated anatomical changes in grey matter (GM) morphometry, their associations with gene expression remain elusive.

METHODS

Here, we aim to understand how gene expression correlates with neuroanatomical atypicalities in ASD. To do so, we performed a coordinate-based meta-analysis to determine the common GM variation pattern in the autistic brain. From the Allen Human Brain Atlas, we selected eight genes from the SHANK, NRXN, NLGN family and MECP2, which have been implicated with ASD, particularly in regards to altered synaptic transmission and plasticity. The gene expression maps for each gene were built. We then assessed the correlation between the gene expression maps and the GM alteration maps. Lastly, we projected the obtained clusters of GM alteration-gene correlations on top of the canonical resting state networks, in order to provide a functional characterization of the structural evidence.

RESULTS

We found that gene expression of most genes correlated with GM alteration (both increase and decrease) in regions located in the default mode network. Decreased GM was also correlated with gene expression of some ASD genes in areas associated with the dorsal attention and cerebellar network. Lastly, single genes were found to be significantly correlated with increased GM in areas located in the somatomotor, limbic and ganglia/thalamus networks.

CONCLUSIONS

This approach allowed us to combine the well beaten path of genetic and brain imaging in a novel way, to specifically investigate the relation between gene expression and brain with structural damage, and individuate genes of potential interest for further investigation in the functional domain.

Structure and activity alteration in adult highland residents' cerebrum: Voxel-based morphometry and amplitude of low-frequency fluctuation study

Introduction

People living in highland areas may have factors that allow them to adapt to chronic hypoxia, but these physiological mechanisms remain unclear. This study aimed to investigate the brain mechanism in a cohort of adult residents of Tibet, a well-known plateau section in China, by observing differences in brain structure and function in non-plateau populations.

Methods

The study included 27 Tibetan and 27 non-plateau region residents who were matched in age, sex, and education. All participants underwent high-resolution three-dimensional T1 weighted imaging (3D-T1WI) and resting-state functional magnetic resonance imaging (rs-fMRI) scans on a 1.5 Tesla MR. Gray matter volumes and regional spontaneous neuronal activity (SNA) were calculated and compared between the two groups.

Results

When comparing gray matter in people living in high altitudes to those living in the flatlands, the results showed positive activation of gray matter in local brain regions (p < 0.05, false discovery rate (FDR) corrected), in the right postcentral [automated atomic labeling (aal)], left postcentral (aal), and right lingual (aal) regions. Comparing the people of high altitude vs. flat land in the brain function study (p < 0.05, FDR corrected), positive activation was found in the right superior motor area (aal) and left superior frontal (aal), and negative activation was found in the right precuneus (aal).

Conclusion

In high-altitude individuals, larger regional gray matter volumes and higher SNA may represent a compensatory mechanism to adapt to chronic hypoxia.

Neural mechanisms of brand love relationship dynamics: Is the development of brand love relationships the same as that of interpersonal romantic love relationships?

Brand love is a relationship between brands and consumers. Managing the relationship is an important issue for marketing strategy since it changes according to temporal flow. Brand love theories, including their dynamics, have been developed based on interpersonal romantic love theories. Although many brand love studies have provided useful findings, the neural mechanism of brand love remains unclear. Especially, its dynamics have not been considered from a neuroscience perspective. The present study addressed the commonalities and differentiations of activated brain regions between brand love and interpersonal romantic love relationships using a quantitative neuroimaging meta-analytic approach, from the view of brain connectivity. Regarding the mental processes of each love relationship related to these activated brain regions, decoding analysis was conducted using the NeuroQuery platform to prevent reverse inference. The results revealed that different neural mechanisms and mental processes were distinctively involved in the dynamics of each love relationship, although the anterior insula overlapped across all stages and the reinforcement learning system was driven between both love relationships in the early stage. Remarkably, regarding the distinctive mental processes, although prosocial aspects were involved in the mental processes of interpersonal romantic love relationships across all stages, they were not involved in the mental processes of brand love relationships. Conclusively, although common brain regions and mental processes between both love relationships were observed, neural mechanisms and mental processes in brand love relationship dynamics might be innately different from those in the interpersonal romantic love relationship dynamics. As this finding indicates essential distinctiveness between both these relationships, theories concerning interpersonal romantic love should be applied cautiously when investigating brand love relationship dynamics.

Invariant structural and functional brain regions associated with tinnitus: A meta-analysis

Tinnitus is a common, functionally disabling condition of often unknown etiology. Neuroimaging research to better understand tinnitus is emerging but remains limited in scope. Voxel-based physiology (VBP) studies detect tinnitus-associated pathophysiology by group-wise contrast (tinnitus vs controls) of resting-state indices of hemodynamics, metabolism, and neurovascular coupling. Voxel-based morphometry (VBM) detects tinnitus-associated neurodegeneration by group-wise contrast of structural MRI. Both VBP and VBM studies routinely report results as atlas-referenced coordinates, suitable for coordinate-based meta-analysis (CBMA). Here, 17 resting-state VBP and 8 VBM reports of tinnitus-associated regional alterations were meta-analyzed using activation likelihood estimation (ALE). Acknowledging the need for data-driven insights, ALEs were performed at two levels of statistical rigor: corrected for multiple comparisons and uncorrected. The corrected ALE applied cluster-level inference thresholding by intensity (z-score > 1.96; p < 0.05) followed by family-wise error correction for multiple comparisons (p < .05, 1000 permutations) and fail-safe correction for missing data. The corrected analysis identified one significant cluster comprising five foci in the posterior cingulate gyrus and precuneus, that is, not within the primary or secondary auditory cortices. The uncorrected ALE identified additional regions within auditory and cognitive processing networks. Taken together, tinnitus is likely a dysfunction of regions spanning multiple canonical networks that may serve to increase individuals’ interoceptive awareness of the tinnitus sound, decrease capacity to switch cognitive sets, and prevent behavioral and cognitive attention to other stimuli. It is noteworthy that the most robust tinnitus-related abnormalities are not in the auditory system, contradicting collective findings of task-activation literature in tinnitus.

Advances in human intracranial electroencephalography research, guidelines and good practices

Since the second-half of the twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into the human brain. At the interface between fundamental research and the clinic, iEEG provides both high temporal resolution and high spatial specificity but comes with constraints, such as the individual's tailored sparsity of electrode sampling. Over the years, researchers in neuroscience developed their practices to make the most of the iEEG approach. Here we offer a critical review of iEEG research practices in a didactic framework for newcomers, as well addressing issues encountered by proficient researchers. The scope is threefold: (i) review common practices in iEEG research, (ii) suggest potential guidelines for working with iEEG data and answer frequently asked questions based on the most widespread practices, and (iii) based on current neurophysiological knowledge and methodologies, pave the way to good practice standards in iEEG research. The organization of this paper follows the steps of iEEG data processing. The first section contextualizes iEEG data collection. The second section focuses on localization of intracranial electrodes. The third section highlights the main pre-processing steps. The fourth section presents iEEG signal analysis methods. The fifth section discusses statistical approaches. The sixth section draws some unique perspectives on iEEG research. Finally, to ensure a consistent nomenclature throughout the manuscript and to align with other guidelines, e.g., Brain Imaging Data Structure (BIDS) and the OHBM Committee on Best Practices in Data Analysis and Sharing (COBIDAS), we provide a glossary to disambiguate terms related to iEEG research.

Six actions to improve detection of critical features for neuroimaging coordinate-based meta-analysis preparation

Coordinate-based meta-analysis (CBMA) is a research strategy widely used in the field of human brain imaging. Although dedicated tools as BrainMap or Neurosynth had been developed in past years, some of the crucial steps necessary to identify and compose the dataset are still user-based, resulting in a not standardized approach to literature search, as well as in time-consuming and prone to errors procedures. In particular, this concern involves the assessment of voxel-wise whole brain analyses in contrast to ROI-based ones, and the identification of available lists of peaks of effect (i.e., x,y,z coordinates of the foci). Here, we propose six simple actions that can be undertaken by any researcher and by the publishing system, allowing to limit the risk of erroneous decisions on the inclusion of experimental data in the meta-analytic dataset. This straightforward and useful strategy would reduce possible bias in CBMA, therefore allowing to obtain more reliable results.

The spectrum of data sharing policies in neuroimaging data repositories

Sharing data is a scientific imperative that accelerates scientific discoveries, reinforces open science inquiry, and allows for efficient use of public investment and research resources. Considering these benefits, data sharing has been widely promoted in diverse fields and neuroscience has been no exception to this movement. For all its promise, however, the sharing of human neuroimaging data raises critical ethical and legal issues, such as data privacy. Recently, the heightened risks to data privacy posed by the rapid advances in artificial intelligence and machine learning techniques have made data sharing more challenging; the regulatory landscape around data sharing has also been evolving rapidly. Here we present an in-depth ethical and regulatory analysis that examines how neuroimaging data are currently shared against the backdrop of the relevant regulations and policies in the United States and how advanced software tools and algorithms might undermine subjects' privacy in neuroimaging data sharing. The implications of these novel technological threats to privacy in neuroimaging data sharing practices and policies will also be discussed. We then conclude with a proposal for a legal prohibition against malicious use of neuroscience data as a regulatory mechanism to address privacy risks associated with the data while maximizing the benefits of data sharing and open science practice in the field of neuroscience.

The Brain Research Hotspot Database (BRHD): A Panoramic Database of the Latest Hotspots in Brain Research

Brain science, an emerging, dynamic, multidisciplinary basic research field, is generating numerous valuable data. However, there are still several obstacles for the utilization of these data, such as data fragmentation, heterogeneity, availability, and annotation divergence. Thus, to overcome these obstacles and construct an online community, we developed a panoramic database named Brain Research Hotspot Database (BRHD). As of 30 January 2022, the database had been integrated with standardized vocabularies from various resources, including 423,681 papers, 46,344 patents, 9585 transcriptomic datasets, 261 cell markers, as well as with information regarding brain initiatives that were officially launched and well-known scholars in brain research. Based on the keywords entered by users and the search options they set, data can be accessed and retrieved through exact and fuzzy search scenarios. In addition, for brain diseases, we developed three featured functions based on deep data mining: (1) a brain disease–genome network, which collects the associations between common brain diseases, genes, and mutations reported in the literature; (2) brain and gut microbiome associations, based on the literature related to this topic, with added annotations for reference; (3) 3D brain structure, containing a high-precision brain anatomy model with visual links to quickly connect to an organ-on-a-chip database. In short, the BRHD integrates data from a variety of brain science resources to provide a friendly user interface and freely accessible viewing and downloading environment. Furthermore, the original functions developed based on these data provide references and insights for brain research.

A co-alteration parceling of the cingulate cortex

The cingulate cortex is known to be a complex structure, involved in several cognitive and emotional functions, as well as being altered by a variety of brain disorders. This heterogeneity is reflected in the multiple parceling models proposed in the literature. At the present, sub-regions of the cingulate cortex had been identified taking into account functional and structural connectivity, as well as cytological and electrochemical properties. In the present work, we propose an innovative node-wise parceling approach based on meta-analytic Bayesian co-alteration. To this aim, 193 case-control voxel-based morphometry experiments were analyzed, and the Patel's κ index was used to assess probability of morphometric co-alteration between nodes placed in the cingulate cortex and in the rest of the brain. Hierarchical clustering was then applied to identify nodes in the cingulate cortex exhibiting a similar pattern of whole-brain co-alteration. The obtained dendrogram highlighted a robust fronto-parietal cluster compatible with the default mode network, and being supported by the interplay between the retrosplenial cortex and the anterior and posterior cingulate cortex, rarely described in the literature. This ensemble was further confirmed by the analysis of functional patterns. Leveraging on co-alteration to investigate cortical organization could, therefore, allow to combine multimodal information, resolving conflicting results sometimes coming from the separate use of singular modalities. Crucially, this provides a valuable way to understand the pathological brain using data driven, whole-brain informed and context-specific evidence in a way not yet explored in the field.

A meta-analysis on neural changes of cognitive training for mental disorders in executive function tasks: increase or decrease brain activation?

BACKGROUND

Cognitive impairment is often found in patients with psychiatric disorders, and cognitive training (CT) has been shown to help these patients. To better understand the mechanisms of CT, many neuroimaging studies have investigated the neural changes associated with it. However, the results of those studies have been inconsistent, making it difficult to draw conclusions from the literature. Therefore, the objective of this meta-analysis was to identify consistent patterns in the literature of neural changes associated with CT for psychiatric disorders.

METHODS

We searched for cognitive training imaging studies in PubMed, Cochrane library, Scopus, and ProQuest electronic databases. We conducted an activation likelihood estimation (ALE) for coordinate-based meta-analysis of neuroimaging studies, conduct behavioral analysis of brain regions identified by ALE analysis, conduct behavioral analysis of brain regions identified by ALE analysis, and then created a functional meta-analytic connectivity model (fMACM) of the resulting regions.

RESULTS

Results showed that CT studies consistently reported increased activation in the left inferior frontal gyrus (IFG) and decreased activation in the left precuneus and cuneus from pre- to post- CT.

CONCLUSION

CT improves cognitive function by supporting language and memory function, and reducing neuronal resources associated with basic visual processing.

Accumulating Knowledge in the Organizational Sciences

In some fields, research findings are rigorously curated in a common language and made available to enable future use and large-scale, robust insights. Organizational researchers have begun such efforts [e.g., metaBUS ( http://metabus.org/ )] but are far from the efficient, comprehensive curation seen in areas such as cognitive neuroscience or genetics. This review provides a sample of insights from research curation efforts in organizational research, psychology, and beyond—insights not possible by even large-scale, substantive meta-analyses. Efforts are classified as either science-of-science research or large-scale, substantive research. The various methods used for information extraction (e.g., from PDF files) and classification (e.g., using consensus ontologies) is reviewed. The review concludes with a series of recommendations for developing and leveraging the available corpus of organizational research to speed scientific progress.

Grey and white matter microstructure changes in epilepsy patients with vagus nerve stimulators

OBJECTIVES

Vagus nerve stimulation (VNS) has been widely used as an effective treatment for patients with drug-resistant epilepsy (DRE). However, little is known about grey matter (GM) and white matter (WM) microstructure changes caused by VNS. This study aimed to detect consistent GM and WM alterations in epilepsy patients with vagus nerve stimulators.

METHODS

The diffusion tensor imaging data was acquired from 15 patients who underwent VNS implantation. The voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) were used to detect group differences in GM and WM microstructure and explore their correlation with postoperative seizure reduction.

RESULTS

After 3 months of stimulation, GM density reduced in right cerebellum, left superior temporal gyrus, right inferior temporal gyrus and left thalamus, and increased in left cerebellum, left inferior parietal lobule, left middle occipital gyrus and left gyrus rectus. No significant volume changes had been found in 14 subcortical nuclei. The fractional anisotropy (FA) values reduced in left superior longitudinal fasciculus and left corticospinal tract, and increased in bilateral cingulum and body of corpus callosum. The mean diffusivity (MD) values reduced in right retrolenticular part of internal capsule, right posterior corona radiata and right superior longitudinal fasciculus. The seizure reduction had positive correlation trends with the volume reduction in left nucleus accumbens and right amygdala, and MD reduction in right medial lemniscus and right posterior corona radiata.

CONCLUSIONS

The results showed that VNS could cause changes of GM density, WM FA and MD values in epilepsy patients. The volume and MD reduction in some subcortical structures might participate in the seizure frequency reduction of VNS.

Mapping gene transcription and neurocognition across human neocortex

Regulation of gene expression drives protein interactions that govern synaptic wiring and neuronal activity. The resulting coordinated activity among neuronal populations supports complex psychological processes, yet how gene expression shapes cognition and emotion remains unknown. Here, we directly bridge the microscale and macroscale by mapping gene expression patterns to functional activation patterns across the cortical sheet. Applying unsupervised learning to the Allen Human Brain Atlas and Neurosynth databases, we identify a ventromedial-dorsolateral gradient of gene assemblies that separate affective and perceptual domains. This topographic molecular-psychological signature reflects the hierarchical organization of the neocortex, including systematic variations in cell type, myeloarchitecture, laminar differentiation and intrinsic network affiliation. In addition, this molecular-psychological signature strengthens over neurodevelopment and can be replicated in two independent repositories. Collectively, our results reveal spatially covarying transcriptomic and cognitive architectures, highlighting the influence that molecular mechanisms exert on psychological processes.

Meta-analytic connectivity modelling of deception-related brain regions

Brain-based deception research began only two decades ago and has since included a wide variety of contexts and response modalities for deception paradigms. Investigations of this sort serve to better our neuroscientific and legal knowledge of the ways in which individuals deceive others. To this end, we conducted activation likelihood estimation (ALE) and meta-analytic connectivity modelling (MACM) using BrainMap software to examine 45 task-based fMRI brain activation studies on deception. An activation likelihood estimation comparing activations during deceptive versus honest behavior revealed 7 significant peak activation clusters (bilateral insula, left superior frontal gyrus, bilateral supramarginal gyrus, and bilateral medial frontal gyrus). Meta-analytic connectivity modelling revealed an interconnected network amongst the 7 regions comprising both unidirectional and bidirectional connections. Together with subsequent behavioral and paradigm decoding, these findings implicate the supramarginal gyrus as a key component for the sociocognitive process of deception.

Interhemispheric co-alteration of brain homotopic regions

Asymmetries in gray matter alterations raise important issues regarding the pathological co-alteration between hemispheres. Since homotopic areas are the most functionally connected sites between hemispheres and gray matter co-alterations depend on connectivity patterns, it is likely that this relationship might be mirrored in homologous interhemispheric co-altered areas. To explore this issue, we analyzed data of patients with Alzheimer’s disease, schizophrenia, bipolar disorder and depressive disorder from the BrainMap voxel-based morphometry database. We calculated a map showing the pathological homotopic anatomical co-alteration between homologous brain areas. This map was compared with the meta-analytic homotopic connectivity map obtained from the BrainMap functional database, so as to have a meta-analytic connectivity modeling map between homologous areas. We applied an empirical Bayesian technique so as to determine a directional pathological co-alteration on the basis of the possible tendencies in the conditional probability of being co-altered of homologous brain areas. Our analysis provides evidence that: the hemispheric homologous areas appear to be anatomically co-altered; this pathological co-alteration is similar to the pattern of connectivity exhibited by the couples of homologues; the probability to find alterations in the areas of the left hemisphere seems to be greater when their right homologues are also altered than vice versa, an intriguing asymmetry that deserves to be further investigated and explained.

BACON: A tool for reverse inference in brain activation and alteration

Over the past decades, powerful MRI‐based methods have been developed, which yield both voxel‐based maps of the brain activity and anatomical variation related to different conditions. With regard to functional or structural MRI data, forward inferences try to determine which areas are involved given a mental function or a brain disorder. A major drawback of forward inference is its lack of specificity, as it suggests the involvement of brain areas that are not specific for the process/condition under investigation. Therefore, a different approach is needed to determine to what extent a given pattern of cerebral activation or alteration is specifically associated with a mental function or brain pathology. In this study, we present a new tool called BACON (Bayes fACtor mOdeliNg) for performing reverse inference both with functional and structural neuroimaging data. BACON implements the Bayes' factor and uses the activation likelihood estimation derived‐maps to obtain posterior probability distributions on the evidence of specificity with regard to a particular mental function or brain pathology.

Parcellation-based anatomic model of the semantic network

INTRODUCTION

The semantic network is an important mediator of language, enabling both speech production and the comprehension of multimodal stimuli. A major challenge in the field of neurosurgery is preventing semantic deficits. Multiple cortical areas have been linked to semantic processing, though knowledge of network connectivity has lacked anatomic specificity. Using attentional task-based fMRI studies, we built a neuroanatomical model of this network.

METHODS

One hundred and fifty-five task-based fMRI studies related to categorization of visual words and objects, and auditory words and stories were used to generate an activation likelihood estimation (ALE). Cortical parcellations overlapping the ALE were used to construct a preliminary model of the semantic network based on the cortical parcellation scheme previously published under the Human Connectome Project. Deterministic fiber tractography was performed on 25 randomly chosen subjects from the Human Connectome Project, to determine the connectivity of the cortical parcellations comprising the network.

RESULTS

The ALE analysis demonstrated fourteen left hemisphere cortical regions to be a part of the semantic network: 44, 45, 55b, IFJa, 8C, p32pr, SFL, SCEF, 8BM, STSdp, STSvp, TE1p, PHT, and PBelt. These regions showed consistent interconnections between parcellations. Notably, the anterior temporal pole, a region often implicated in semantic function, was absent from our model.

CONCLUSIONS

We describe a preliminary cortical model for the underlying structural connectivity of the semantic network. Future studies will further characterize the neurotractographic details of the semantic network in the context of medical application.

A Cortical Parcellation Based Analysis of Ventral Premotor Area Connectivity

Introduction. The ventral premotor area (VPM) plays a crucial role in executing various aspects of motor control. These include hand reaching, joint coordination, and direction of movement in space. While many studies discuss the VPM and its relationship to the rest of the motor network, there is minimal literature examining the connectivity of the VPM outside of the motor network. Using region-based fMRI studies, we built a neuroanatomical model to account for these extra-motor connections.Methods. Thirty region-based fMRI studies were used to generate an activation likelihood estimation (ALE) using BrainMap software. Cortical parcellations overlapping the ALE were used to construct a preliminary model of the VPM connections outside the motor network. Diffusion spectrum imaging (DSI)-based fiber tractography was performed to determine the connectivity between cortical parcellations in both hemispheres, and a laterality index (LI) was calculated with resultant tract volumes. The resulting connections were described using the cortical parcellation scheme developed by the Human Connectome Project (HCP).Results. Four cortical regions were found to comprise the VPM. These four regions included 6v, 4, 3b, and 3a. Across mapped brains, these areas showed consistent interconnections between each other. Additionally, ipsilateral connections to the primary motor cortex, supplementary motor area, and dorsal premotor cortex were demonstrated. Inter-hemispheric asymmetries were identified, especially with areas 1, 55b, and MI connecting to the ipsilateral VPM regions.Conclusion. We describe a preliminary cortical model for the underlying connectivity of the ventral premotor area. Future studies should further characterize the neuroanatomic underpinnings of this network for neurosurgical applications.

Brain pathology recapitulates physiology: A network meta-analysis

Network architecture is a brain-organizational motif present across spatial scales from cell assemblies to distributed systems. Structural pathology in some neurodegenerative disorders selectively afflicts a subset of functional networks, motivating the network degeneration hypothesis (NDH). Recent evidence suggests that structural pathology recapitulating physiology may be a general property of neuropsychiatric disorders. To test this possibility, we compared functional and structural network meta-analyses drawing upon the BrainMap database. The functional meta-analysis included results from >7,000 experiments of subjects performing >100 task paradigms; the structural meta-analysis included >2,000 experiments of patients with >40 brain disorders. Structure-function network concordance was high: 68% of networks matched (pFWE < 0.01), confirming the broader scope of NDH. This correspondence persisted across higher model orders. A positive linear association between disease and behavioral entropy (p = 0.0006;R2 = 0.53) suggests nodal stress as a common mechanism. Corroborating this interpretation with independent data, we show that metabolic 'cost' significantly differs along this transdiagnostic/multimodal gradient.

Gray matter abnormalities follow non-random patterns of co-alteration in autism: Meta-connectomic evidence

BACKGROUND

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by atypical brain anatomy and connectivity. Graph-theoretical methods have mainly been applied to detect altered patterns of white matter tracts and functional brain activation in individuals with ASD. The network topology of gray matter (GM) abnormalities in ASD remains relatively unexplored.

METHODS

An innovative meta-connectomic analysis on voxel-based morphometry data (45 experiments, 1,786 subjects with ASD) was performed in order to investigate whether GM variations can develop in a distinct pattern of co-alteration across the brain. This pattern was then compared with normative profiles of structural and genetic co-expression maps. Graph measures of centrality and clustering were also applied to identify brain areas with the highest topological hierarchy and core sub-graph components within the co-alteration network observed in ASD.

RESULTS

Individuals with ASD exhibit a distinctive and topologically defined pattern of GM co-alteration that moderately follows the structural connectivity constraints. This was not observed with respect to the pattern of genetic co-expression. Hub regions of the co-alteration network were mainly left-lateralized, encompassing the precuneus, ventral anterior cingulate, and middle occipital gyrus. Regions of the default mode network appear to be central in the topology of co-alterations.

CONCLUSION

These findings shed new light on the pathobiology of ASD, suggesting a network-level dysfunction among spatially distributed GM regions. At the same time, this study supports pathoconnectomics as an insightful approach to better understand neuropsychiatric disorders.

Updating and characterizing neuroanatomical markers in high-risk subjects, recently diagnosed and chronic patients with schizophrenia: A revised coordinate-based meta-analysis

Characterizing neuroanatomical markers of different stages of schizophrenia (SZ) to assess pathophysiological models of how the disorder develops is an important target for the clinical practice. We performed a meta-analysis of voxel-based morphometry studies of genetic and clinical high-risk subjects (g-/c-HR), recently diagnosed (RDSZ) and chronic SZ patients (ChSZ). We quantified gray matter (GM) changes associated with these four conditions and compared them with contrast and conjunctional data. We performed the behavioral analysis and networks decomposition of alterations to obtain their functional characterization. Results reveal a cortical-subcortical, left-to-right homotopic progression of GM loss. The right anterior cingulate is the only altered region found altered among c-HR, RDSZ and ChSZ. Contrast analyses show left-lateralized insular, amygdalar and parahippocampal GM reduction in RDSZ, which appears bilateral in ChSZ. Functional decomposition shows involvement of the salience network, with an enlargement of the sensorimotor network in RDSZ and the thalamus-basal nuclei network in ChSZ. These findings support the current neuroprogressive models of SZ and integrate this deterioration with the clinical evolution of the disease.

Parcellation-based modeling of the supplementary motor area

INTRODUCTION

The supplementary motor area (SMA) plays an important role in the initiation and coordination of internally and externally cued movements. Such movements include reaching, grasping, speaking, and bilateral hand coordination. While many studies discuss the SMA and its relationship to other parts of the motor network, there is minimal literature examining the connectivity of the SMA outside of the motor network. Using region-based fMRI studies, we built a neuroanatomical model to account for these extra-motor connections.

METHODS

Thirty region-based fMRI studies were used to generate an activation likelihood estimation (ALE) using BrainMap software. Cortical parcellations overlapping the ALE were used to construct a preliminary model of the SMA connections outside the motor network. DSI-based fiber tractography was performed to determine the connectivity between cortical parcellations. The resulting connections were described using the cortical parcellation scheme developed by the Human Connectome Project (HCP).

RESULTS

Four left hemisphere regions were found to comprise the SMA. These included areas SFL, SCEF, 6ma, and 6mp. Across mapped brains, these areas showed consistent interconnections between each other. Additionally, ipsilateral connections to the primary motor cortex, left inferior and middle frontal gyri, the anterior cingulate gyrus, and insula were demonstrated. Connections to the contralateral SMA, anterior cingulate, lateral premotor, and inferior frontal cortices were also identified.

CONCLUSIONS

We describe a preliminary cortical model for the underlying structural connectivity of the supplementary motor area outside the motor network. Future studies should further characterize the neuroanatomic underpinnings of this network for the purposes of medical application.

Transdiagnostic, Connectome-Based Prediction of Memory Constructs Across Psychiatric Disorders

Memory deficits are observed in a range of psychiatric disorders, but it is unclear whether memory deficits arise from a shared brain correlate across disorders or from various dysfunctions unique to each disorder. Connectome-based predictive modeling is a computational method that captures individual differences in functional connectomes associated with behavioral phenotypes such as memory. We used publicly available task-based functional MRI data from patients with schizophrenia (n = 33), bipolar disorder (n = 34), attention deficit hyper-activity disorder (n = 32), and healthy controls (n = 73) to model the macroscale brain networks associated with working, short- and long-term memory. First, we use 10-fold and leave-group-out analyses to demonstrate that the same macroscale brain networks subserve memory across diagnostic groups and that individual differences in memory performance are related to individual differences within networks distributed throughout the brain, including the subcortex, default mode network, limbic network, and cerebellum. Next, we show that diagnostic groups are associated with significant differences in whole-brain functional connectivity that are distinct from the predictive models of memory. Finally, we show that models trained on the transdiagnostic sample generalize to novel, healthy participants (n = 515) from the Human Connectome Project. These results suggest that despite significant differences in whole-brain patterns of functional connectivity between diagnostic groups, the core macroscale brain networks that subserve memory are shared.

Gray matter covariations and core symptoms of autism: the EU-AIMS Longitudinal European Autism Project

BACKGROUND

Voxel-based morphometry (VBM) studies in autism spectrum disorder (autism) have yielded diverging results. This might partly be attributed to structural alterations being associating with the combined influence of several regions rather than with a single region. Further, these structural covariation differences may relate to continuous measures of autism rather than with categorical case-control contrasts. The current study aimed to identify structural covariation alterations in autism, and assessed canonical correlations between brain covariation patterns and core autism symptoms.

METHODS

We studied 347 individuals with autism and 252 typically developing individuals, aged between 6 and 30 years, who have been deeply phenotyped in the Longitudinal European Autism Project. All participants' VBM maps were decomposed into spatially independent components using independent component analysis. A generalized linear model (GLM) was used to examine case-control differences. Next, canonical correlation analysis (CCA) was performed to separately explore the integrated effects between all the brain sources of gray matter variation and two sets of core autism symptoms.

RESULTS

GLM analyses showed significant case-control differences for two independent components. The first component was primarily associated with decreased density of bilateral insula, inferior frontal gyrus, orbitofrontal cortex, and increased density of caudate nucleus in the autism group relative to typically developing individuals. The second component was related to decreased densities of the bilateral amygdala, hippocampus, and parahippocampal gyrus in the autism group relative to typically developing individuals. The CCA results showed significant correlations between components that involved variation of thalamus, putamen, precentral gyrus, frontal, parietal, and occipital lobes, and the cerebellum, and repetitive, rigid and stereotyped behaviors and abnormal sensory behaviors in autism individuals.

LIMITATIONS

Only 55.9% of the participants with autism had complete questionnaire data on continuous parent-reported symptom measures.

CONCLUSIONS

Covaried areas associated with autism diagnosis and/or symptoms are scattered across the whole brain and include the limbic system, basal ganglia, thalamus, cerebellum, precentral gyrus, and parts of the frontal, parietal, and occipital lobes. Some of these areas potentially subserve social-communicative behavior, whereas others may underpin sensory processing and integration, and motor behavior.

The pathoconnectivity network analysis of the insular cortex: A morphometric fingerprinting

Brain disorders tend to impact on many different regions in a typical way: alterations do not spread randomly; rather, they seem to follow specific patterns of propagation that show a strong overlap between different pathologies. The insular cortex is one of the brain areas more involved in this phenomenon, as it seems to be altered by a wide range of brain diseases. On these grounds we thoroughly investigated the impact of brain disorders on the insular cortices analyzing the patterns of their structural co-alteration. We therefore investigated, applying a network analysis approach to meta-analytic data, 1) what pattern of gray matter alteration is associated with each of the insular cortex parcels; 2) whether or not this pattern correlates and overlaps with its functional meta-analytic connectivity; and, 3) the behavioral profile related to each insular co-alteration pattern. All the analyses were repeated considering two solutions: one with two clusters and another with three. Our study confirmed that the insular cortex is one of the most altered cerebral regions among the cortical areas, and exhibits a dense network of co-alteration including a prevalence of cortical rather than sub-cortical brain regions. Regions of the frontal lobe are the most involved, while occipital lobe is the less affected. Furthermore, the co-alteration and co-activation patterns greatly overlap each other. These findings provide significant evidence that alterations caused by brain disorders are likely to be distributed according to the logic of network architecture, in which brain hubs lie at the center of networks composed of co-altered areas. For the first time, we shed light on existing differences between insula sub-regions even in the pathoconnectivity domain.

Finding specificity in structural brain alterations through Bayesian reverse inference

In the field of neuroimaging reverse inferences can lead us to suppose the involvement of cognitive processes from certain patterns of brain activity. However, the same reasoning holds if we substitute "brain activity" with "brain alteration" and "cognitive process" with "brain disorder." The fact that different brain disorders exhibit a high degree of overlap in their patterns of structural alterations makes forward inference-based analyses less suitable for identifying brain areas whose alteration is specific to a certain pathology. In the forward inference-based analyses, in fact, it is impossible to distinguish between areas that are altered by the majority of brain disorders and areas that are specifically affected by certain diseases. To address this issue and allow the identification of highly pathology-specific altered areas we used the Bayes' factor technique, which was employed, as a proof of concept, on voxel-based morphometry data of schizophrenia and Alzheimer's disease. This technique allows to calculate the ratio between the likelihoods of two alternative hypotheses (in our case, that the alteration of the voxel is specific for the brain disorder under scrutiny or that the alteration is not specific). We then performed temporal simulations of the alterations' spread associated with different pathologies. The Bayes' factor values calculated on these simulated data were able to reveal that the areas, which are more specific to a certain disease, are also the ones to be early altered. This study puts forward a new analytical instrument capable of innovating the methodological approach to the investigation of brain pathology.

Hubs of long-distance co-alteration characterize brain pathology

It is becoming clearer that the impact of brain diseases is more convincingly represented in terms of co-alterations rather than in terms of localization of alterations. In this context, areas characterized by a long mean distance of co-alteration may be considered as hubs with a crucial role in the pathology. We calculated meta-analytic transdiagnostic networks of co-alteration for the gray matter decreases and increases, and we evaluated the mean Euclidean, fiber-length, and topological distance of its nodes. We also examined the proportion of co-alterations between canonical networks, and the transdiagnostic variance of the Euclidean distance. Furthermore, disease-specific analyses were conducted on schizophrenia and Alzheimer's disease. The anterodorsal prefrontal cortices appeared to be a transdiagnostic hub of long-distance co-alterations. Also, the disease-specific analyses showed that long-distance co-alterations are more able than classic meta-analyses to identify areas involved in pathology and symptomatology. Moreover, the distance maps were correlated with the normative connectivity. Our findings substantiate the network degeneration hypothesis in brain pathology. At the same time, they suggest that the concept of co-alteration might be a useful tool for clinical neuroscience.

Estimating the prevalence of missing experiments in a neuroimaging meta-analysis

Coordinate-based meta-analyses (CBMA) allow researchers to combine the results from multiple functional magnetic resonance imaging experiments with the goal of obtaining results that are more likely to generalize. However, the interpretation of CBMA findings can be impaired by the file drawer problem, a type of publication bias that refers to experiments that are carried out but are not published. Using foci per contrast count data from the BrainMap database, we propose a zero-truncated modeling approach that allows us to estimate the prevalence of nonsignificant experiments. We validate our method with simulations and real coordinate data generated from the Human Connectome Project. Application of our method to the data from BrainMap provides evidence for the existence of a file drawer effect, with the rate of missing experiments estimated as at least 6 per 100 reported. The R code that we used is available at https://osf.io/ayhfv/.

From a deep learning model back to the brain-Identifying regional predictors and their relation to aging

We present a Deep Learning framework for the prediction of chronological age from structural magnetic resonance imaging scans. Previous findings associate increased brain age with neurodegenerative diseases and higher mortality rates. However, the importance of brain age prediction goes beyond serving as biomarkers for neurological disorders. Specifically, utilizing convolutional neural network (CNN) analysis to identify brain regions contributing to the prediction can shed light on the complex multivariate process of brain aging. Previous work examined methods to attribute pixel/voxel-wise contributions to the prediction in a single image, resulting in "explanation maps" that were found noisy and unreliable. To address this problem, we developed an inference scheme for combining these maps across subjects, thus creating a population-based, rather than a subject-specific map. We applied this method to a CNN ensemble trained on predicting subjects' age from raw T1 brain images in a lifespan sample of 10,176 subjects. Evaluating the model on an untouched test set resulted in mean absolute error of 3.07 years and a correlation between chronological and predicted age of r = 0.98. Using the inference method, we revealed that cavities containing cerebrospinal fluid, previously found as general atrophy markers, had the highest contribution for age prediction. Comparing maps derived from different models within the ensemble allowed to assess differences and similarities in brain regions utilized by the model. We showed that this method substantially increased the replicability of explanation maps, converged with results from voxel-based morphometry age studies and highlighted brain regions whose volumetric variability correlated the most with the prediction error.

A meta-analytic approach to mapping co-occurrent grey matter volume increases and decreases in psychiatric disorders

Numerous studies have investigated grey matter (GM) volume changes in diverse patient groups. Reports of disorder-related GM reductions are common in such work, but many studies also report evidence for GM volume increases in patients. It is unclear whether these GM increases and decreases are independent or related in some way. Here, we address this question using a novel meta-analytic network mapping approach. We used a coordinate-based meta-analysis of 64 voxel-based morphometry studies of psychiatric disorders to calculate the probability of finding a GM increase or decrease in one region given an observed change in the opposite direction in another region. Estimating this co-occurrence probability for every pair of brain regions allowed us to build a network of concurrent GM changes of opposing polarity. Our analysis revealed that disorder-related GM increases and decreases are not independent; instead, a GM change in one area is often statistically related to a change of opposite polarity in other areas, highlighting distributed yet coordinated changes in GM volume as a function of brain pathology. Most regions showing GM changes linked to an opposite change in a distal area were located in salience, executive-control and default mode networks, as well as the thalamus and basal ganglia. Moreover, pairs of regions showing coupled changes of opposite polarity were more likely to belong to different canonical networks than to the same one. Our results suggest that regional GM alterations in psychiatric disorders are often accompanied by opposing changes in distal regions that belong to distinct functional networks.

Multimodal Abnormalities of Brain Structure and Function in Major Depressive Disorder: A Meta-Analysis of Neuroimaging Studies

OBJECTIVE

Imaging studies of major depressive disorder have reported structural and functional abnormalities in a variety of spatially diverse brain regions. Quantitative meta-analyses of this literature, however, have failed to find statistically significant between-study spatial convergence, other than transdiagnostic-only effects. In the present study, the authors applied a novel multimodal meta-analytic approach to test the hypothesis that major depression exhibits spatially convergent structural and functional brain abnormalities.

METHODS

This coordinate-based meta-analysis included voxel-based morphometry (VBM) studies and resting-state voxel-based pathophysiology (VBP) studies of blood flow, glucose metabolism, regional homogeneity, and amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF). Input data were grouped into three primary meta-analytic classes: gray matter atrophy, increased function, and decreased function in patients with major depression relative to healthy control subjects. In secondary meta-analyses, the data were grouped across primary categories, and in tertiary analyses, by medication status and absence of psychiatric comorbidity. Activation likelihood estimation was used for all analyses.

RESULTS

A total of 92 publications reporting 152 experiments were identified, collectively representing 2,928 patients with major depressive disorder. The primary analyses detected no convergence across studies. The secondary analyses identified portions of the subgenual cingulate cortex, hippocampus, amygdala, and putamen as demonstrating convergent abnormalities. The tertiary analyses (clinical subtypes) showed improved convergence relative to the secondary analyses.

CONCLUSIONS

Coordinate-based meta-analysis identified spatially convergent structural (VBM) and functional (VBP) abnormalities in major depression. The findings suggest replicable neuroimaging features associated with major depression, beyond the transdiagnostic effects reported in previous meta-analyses, and support a continued research focus on the subgenual cingulate and other selected regions' role in depression.

Structural and functional alterations in the brain gray matter among first-degree relatives of schizophrenia patients: A multimodal meta-analysis of fMRI and VBM studies

OBJECTIVE

We conducted a multimodal coordinate-based meta-analysis (CBMA) to investigate structural and functional brain alterations in first-degree relatives of schizophrenia patients (FRs).

METHODS

We conducted a systematic literature search from electronic databases to find studies that examined differences between FRs and healthy controls using whole-brain functional magnetic resonance imaging (fMRI) or voxel-based morphometry (VBM). A CBMA of 30 fMRI (754 FRs; 959 controls) and 11 VBM (885 FRs; 775 controls) datasets were conducted using the anisotropic effect-size version of signed differential mapping. Further, we conducted separate meta-analyses about functional alterations in different cognitive tasks: social cognition, executive functioning, working memory, and inhibitory control.

RESULTS

FRs showed higher fMRI activation in the right frontal gyrus during cognitive tasks than healthy controls. In VBM studies, there were no differences in gray matter density between FRs and healthy controls. Furthermore, multi-modal meta-analysis obtained no differences between FRs and healthy controls. By utilizing the BrainMap database, we showed that the brain region which showed functional alterations in FRs (i) overlapped only slightly with the brain regions that were affected in the meta-analysis of schizophrenia patients and (ii) correlated positively with the brain regions that exhibited increased activity during cognitive tasks in healthy individuals.

CONCLUSIONS

Based on this meta-analysis, FRs may exhibit only minor functional alterations in the brain during cognitive tasks, and the alterations are much more restricted and only slightly overlapping with the regions that are affected in schizophrenia patients. The familial risk did not relate to structural alterations in the gray matter.

Reduced gray matter volume and cortical thickness associated with traffic-related air pollution in a longitudinally studied pediatric cohort

Early life exposure to air pollution poses a significant risk to brain development from direct exposure to toxicants or via indirect mechanisms involving the circulatory, pulmonary or gastrointestinal systems. In children, exposure to traffic related air pollution has been associated with adverse effects on cognitive, behavioral and psychomotor development. We aimed to determine whether childhood exposure to traffic related air pollution is associated with regional differences in brain volume and cortical thickness among children enrolled in a longitudinal cohort study of traffic related air pollution and child health. We used magnetic resonance imaging to obtain anatomical brain images from a nested subset of 12 year old participants characterized with either high or low levels of traffic related air pollution exposure during their first year of life. We employed voxel-based morphometry to examine group differences in regional brain volume, and with separate analyses, changes in cortical thickness. Smaller regional gray matter volumes were determined in the left pre- and post-central gyri, the cerebellum, and inferior parietal lobe of participants in the high traffic related air pollution exposure group relative to participants with low exposure. Reduced cortical thickness was observed in participants with high exposure relative to those with low exposure, primarily in sensorimotor regions of the brain including the pre- and post-central gyri and the paracentral lobule, but also within the frontal and limbic regions. These results suggest that significant childhood exposure to traffic related air pollution is associated with structural alterations in brain.

Restructuring of contralateral gray matter volume associated with cognition in patients with unilateral temporal lobe glioma before and after surgery

Glioma can cause variable alterations to the structure and function of the brain. However, there is a paucity of studies on the gray matter (GM) volume alterations in the brain region opposite the temporal glioma before and after surgery. Therefore, the present study was initiated to investigate the alternation in contralateral homotopic GM volume in patients with unilateral temporal lobe glioma and further, assess the relationship between GM volume alternations with cognition. Eight left temporal lobe glioma patients (LTPs), nine right temporal lobe glioma patients (RTPs), and 28 demographically matched healthy controls (HCs) were included. Using voxel‐based morphometry method, alternations in the contralateral homotopic GM volume in patients with unilateral temporal lobe glioma was determined. Furthermore, the correlation analysis was performed to explore the relationship between cognitive function and altered GM volume. In the preoperative analysis, compared to HCs, LTPs exhibited increased GM volume in right inferior temporal gyrus and right temporal pole (superior temporal gyrus), and, RTPs presented increased GM volume in left inferior temporal gyrus. In the postoperative analysis, compared to HCs, RTPs presented increased GM volume in left middle temporal gyrus. Furthermore, the increased GM volume was significantly positively correlated with the memory test but negatively correlated with the visuospatial test. This study preliminarily confirmed that there were compensatory changes in the GM volume in the contralateral temporal lobe in unilateral temporal lobe glioma patients. Furthermore, alterations of GM volume may be a mechanism for cognitive function compensation.

Localised grey matter atrophy in multiple sclerosis is network-based: a coordinate-based meta-analysis

AIM

To test the network degeneration hypothesis in multiple sclerosis (MS) with a two-stage coordinate-based meta-analysis by: (1) characterising regional selectivity of grey matter (GM) atrophy and (2) testing for functional connectivity involving these regions.

MATERIALS AND METHODS

Meta-analytic sources included 33 journal articles (1,666 MS patients and 1,269 healthy controls) with coordinate-based results from voxel-based morphometry analysis demonstrating GM atrophy. Mass univariate and multivariate coordinate-based meta-analyses were performed to identify a convergent pattern of GM atrophy and determine inter-regional co-activation (as a surrogate of functional connectivity), with anatomical likelihood estimation and functional meta-analytic connectivity modelling, respectively.

RESULTS

Localised GM atrophy was demonstrated in the thalamus, putamen, caudate, sensorimotor cortex, insula, superior temporal gyrus, and cingulate gyrus. This convergent pattern of atrophy displayed significant inter-regional functional co-activations.

CONCLUSION

In MS, GM atrophy was regionally selective, and these regions were functionally connected. The meta-analytic model-based results of this study are intended to guide future development of quantitative neuroimaging markers for diagnosis, evaluating disease progression, and monitoring treatment response.

A resting-state network comparison of combat-related PTSD with combat-exposed and civilian controls

Resting-state functional connectivity (rsFC) is an emerging means of understanding the neurobiology of combat-related post-traumatic stress disorder (PTSD). However, most rsFC studies to date have limited focus to cognitively related intrinsic connectivity networks (ICNs), have not applied data-driven methodologies or have disregarded the effect of combat exposure. In this study, we predicted that group independent component analysis (GICA) would reveal group-wise differences in rsFC across 50 active duty service members with PTSD, 28 combat-exposed controls (CEC), and 25 civilian controls without trauma exposure (CC). Intranetwork connectivity differences were identified across 11 ICNs, yet combat-exposed groups were indistinguishable in PTSD vs CEC contrasts. Both PTSD and CEC demonstrated anatomically diffuse differences in the Auditory Vigilance and Sensorimotor networks compared to CC. However, intranetwork connectivity in a subset of three regions was associated with PTSD symptom severity among executive (left insula; ventral anterior cingulate) and right Fronto-Parietal (perigenual cingulate) networks. Furthermore, we found that increased temporal synchronization among visuospatial and sensorimotor networks was associated with worse avoidance symptoms in PTSD. Longitudinal neuroimaging studies in combat-exposed cohorts can further parse PTSD-related, combat stress-related or adaptive rsFC changes ensuing from combat.

A neural signature of metabolic syndrome

That metabolic syndrome (MetS) is associated with age-related cognitive decline is well established. The neurobiological changes underlying these cognitive deficits, however, are not well understood. The goal of this study was to determine whether MetS is associated with regional differences in gray-matter volume (GMV) using a cross-sectional, between-group contrast design in a large, ethnically homogenous sample. T1-weighted MRIs were sampled from the genetics of brain structure (GOBS) data archive for 208 Mexican-American participants: 104 participants met or exceeded standard criteria for MetS and 104 participants were age- and sex-matched metabolically healthy controls. Participants ranged in age from 18 to 74 years (37.3 ± 13.2 years, 56.7% female). Images were analyzed in a whole-brain, voxel-wise manner using voxel-based morphometry (VBM). Three contrast analyses were performed, a whole sample analysis of all 208 participants, and two post hoc half-sample analyses split by age along the median (35.5 years). Significant associations between MetS and decreased GMV were observed in multiple, spatially discrete brain regions including the posterior cerebellum, brainstem, orbitofrontal cortex, bilateral caudate nuclei, right parahippocampus, right amygdala, right insula, lingual gyrus, and right superior temporal gyrus. Age, as shown in the post hoc analyses, was demonstrated to be a significant covariate. A further functional interpretation of the structures exhibiting lower GMV in MetS reflected a significant involvement in reward perception, emotional valence, and reasoning. Additional studies are needed to characterize the influence of MetS's individual clinical components on brain structure and to explore the bidirectional association between GMV and MetS.

Brain structural alterations are distributed following functional, anatomic and genetic connectivity

The pathological brain is characterized by distributed morphological or structural alterations in the grey matter, which tend to follow identifiable network-like patterns. We analysed the patterns formed by these alterations (increased and decreased grey matter values detected with the voxel-based morphometry technique) conducting an extensive transdiagnostic search of voxel-based morphometry studies in a large variety of brain disorders. We devised an innovative method to construct the networks formed by the structurally co-altered brain areas, which can be considered as pathological structural co-alteration patterns, and to compare these patterns with three associated types of connectivity profiles (functional, anatomical, and genetic). Our study provides transdiagnostical evidence that structural co-alterations are influenced by connectivity constraints rather than being randomly distributed. Analyses show that although all the three types of connectivity taken together can account for and predict with good statistical accuracy, the shape and temporal development of the co-alteration patterns, functional connectivity offers the better account of the structural co-alteration, followed by anatomic and genetic connectivity. These results shed new light on the possible mechanisms at the root of neuropathological processes and open exciting prospects in the quest for a better understanding of brain disorders.

Empirical examination of the replicability of associations between brain structure and psychological variables

Linking interindividual differences in psychological phenotype to variations in brain structure is an old dream for psychology and a crucial question for cognitive neurosciences. Yet, replicability of the previously-reported 'structural brain behavior' (SBB)-associations has been questioned, recently. Here, we conducted an empirical investigation, assessing replicability of SBB among heathy adults. For a wide range of psychological measures, the replicability of associations with gray matter volume was assessed. Our results revealed that among healthy individuals 1) finding an association between performance at standard psychological tests and brain morphology is relatively unlikely 2) significant associations, found using an exploratory approach, have overestimated effect sizes and 3) can hardly be replicated in an independent sample. After considering factors such as sample size and comparing our findings with more replicable SBB-associations in a clinical cohort and replicable associations between brain structure and non-psychological phenotype, we discuss the potential causes and consequences of these findings.

The alteration landscape of the cerebral cortex

Growing evidence is challenging the assumption that brain disorders are diagnostically clear-cut categories. Transdiagnostic studies show that a set of cerebral areas is frequently altered in a variety of psychiatric as well as neurological syndromes. In order to provide a map of the altered areas in the pathological brain we devised a metric, called alteration entropy (A-entropy), capable of denoting the "structural alteration variety" of an altered region. Using the whole voxel-based morphometry database of BrainMap, we were able to differentiate the brain areas exhibiting a high degree of overlap between different neuropathologies (or high value of A-entropy) from those exhibiting a low degree of overlap (or low value of A-entropy). The former, which are parts of large-scale brain networks with attentional, emotional, salience, and premotor functions, are thought to be more vulnerable to a great range of brain diseases; while the latter, which include the sensorimotor, visual, inferior temporal, and supramarginal regions, are thought to be more informative about the specific impact of brain diseases. Since low A-entropy areas appear to be altered by a smaller number of brain disorders, they are more informative than the areas characterized by high values of A-entropy. It is also noteworthy that even the areas showing low values of A-entropy are substantially altered by a variety of brain disorders. In fact, no cerebral area appears to be only altered by a specific disorder. Our study shows that the overlap of areas with high A-entropy provides support for a transdiagnostic approach to brain disorders but, at the same time, suggests that fruitful differences can be traced among brain diseases, as some areas can exhibit an alteration profile more specific to certain disorders than to others.