fMRIPrep: a robust preprocessing pipeline for functional MRI

Theory of Mind Following the Violation of Strong and Weak Prior Beliefs

Recent work in psychology and neuroscience has revealed differences in impression updating across social distance and group membership. Observers tend to maintain prior impressions of close (vs. distant) and ingroup (vs. outgroup) others in light of new information, and this belief maintenance is at times accompanied by increased activity in Theory of Mind regions. It remains an open question whether differences in the strength of prior beliefs, in a context absent social motivation, contribute to neural differences during belief updating. We devised a functional magnetic resonance imaging study to isolate the impact of experimentally induced prior beliefs on mentalizing activity. Participants learned about targets who performed 2 or 4 same-valenced behaviors (leading to the formation of weak or strong priors), before performing 2 counter-valenced behaviors. We found a greater change in activity in dorsomedial prefrontal cortex (DMPFC) and right temporo-parietal junction following the violation of strong versus weak priors, and a greater change in activity in DMPFC and left temporo-parietal junction following the violation of positive versus negative priors. These results indicate that differences in neural responses to unexpected behaviors from close versus distant others, and ingroup versus outgroup members, may be driven in part by differences in the strength of prior beliefs.

Hyperconnection and hyperperfusion of overlapping brain regions in patients with menstrual-related migraine: a multimodal neuroimaging study

PURPOSE

Menstrual-related migraine (MRM) results in moderate to severe intensity headaches accompanied by physical and emotional disability over time in women. Neuroimaging methodologies have advanced our understanding of migraine; however, the neural mechanisms of MRM are not clearly understood.

METHODS

In this study, fourteen MRM patients in the interictal phase and fifteen age- and education-matched healthy control females were recruited. Resting-state functional magnetic resonance imaging (fMRI) and pulsed arterial spin labeling (PASL) MRI were collected for both the subject groups outside of their menstrual periods. Eigenvector centrality mapping (ECM) was performed on resting-state fMRI, and the relative cerebral blood flow (relCBF) was assessed using PASL-MRI.

RESULTS

MRM patients showed a significantly increased eigenvector centrality in the right medial frontal gyrus compared to healthy controls. Seed-based ECM analysis revealed that increased centrality was associated with the right medial frontal gyrus's hyperconnectivity with the left insula and the right supplementary motor area. The perfusion MRI revealed significantly increased relCBF in the hyperconnected regions. Furthermore, the hyperconnection positively correlated with the attack frequency, while the hyperperfusion showed a positive correlation with the disease duration.

CONCLUSION

The results suggest that menstrual-related migraine is associated with cerebral hyperconnection and hyperperfusion in critical pain-processing brain regions. Furthermore, this elevated cerebral activity is correlated with different aspects of functional impairment in MRM patients suggesting that perfusion analysis, along with whole-brain connectivity analysis, can provide a comprehensive understanding of neural mechanisms of MRM.

Neural correlates of shared sensory symptoms in autism and attention-deficit/hyperactivity disorder

Symptoms of autism spectrum disorder and attention-deficit/hyperactivity disorder often co-occur. Among these, sensory impairment, which is a core diagnostic feature of autism spectrum disorder, is often observed in children with attention-deficit/hyperactivity disorder. However, the underlying mechanisms of symptoms that are shared across disorders remain unknown. To examine the neural correlates of sensory symptoms that are associated with autism spectrum disorder and attention-deficit/hyperactivity disorder, we analysed resting-state functional MRI data obtained from 113 people with either autism spectrum disorder or attention-deficit/hyperactivity disorder (n = 78 autism spectrum disorder, mean age = 29.5; n = 35 attention-deficit/hyperactivity disorder, mean age = 31.2) and 96 neurotypical controls (mean age = 30.6, range: 20–55 years) using a cross-sectional study design. First, we used a multi-dimensional approach to examine intrinsic brain functional connectivity related to sensory symptoms in four domains (i.e. low registration, sensation seeking, sensory sensitivity and sensation avoidance), after controlling for age, handedness and head motion. Then, we used a partial least squares correlation to examine the link between sensory symptoms related to intrinsic brain functional connectivity and neurodevelopmental symptoms measured using the Autism Spectrum Quotient and Conners’ Adult Attention-Deficit/Hyperactivity Disorder Rating Scale, regardless of diagnosis. To test whether observed associations were specific to sensory symptoms related to intrinsic brain functional connectivity, we conducted a control analysis using a bootstrap framework. The results indicated that transdiagnostic yet distinct intrinsic brain functional connectivity neural bases varied according to the domain of the examined sensory symptom. Partial least squares correlation analysis revealed two latent components (latent component 1: q < 0.001 and latent component 2: q < 0.001). For latent component 1, a set of intrinsic brain functional connectivity was predominantly associated with neurodevelopmental symptom-related composite score (r = 0.64, P < 0.001), which was significantly correlated with Conners’ Adult Attention-Deficit/Hyperactivity Disorder Rating Scale total T scores (r = −0.99, q < 0.001). For latent component 2, another set of intrinsic brain functional connectivity was positively associated with neurodevelopmental symptom-related composite score (r = 0.58, P < 0.001), which was eventually positively associated with Autism Spectrum Quotient total scores (r = 0.92, q < 0.001). The bootstrap analysis showed that the relationship between intrinsic brain functional connectivity and neurodevelopmental symptoms was relative to sensory symptom-related intrinsic brain functional connectivity (latent component 1: P = 0.003 and latent component 2: P < 0.001). The current results suggest that sensory symptoms in individuals with autism spectrum disorder and those with attention-deficit/hyperactivity disorder have shared neural correlates. The neural correlates of the sensory symptoms were associated with the severity of both autism spectrum disorder and attention-deficit/hyperactivity disorder symptoms, regardless of diagnosis.

Allocentric representation in the human amygdala and ventral visual stream

The hippocampus and the entorhinal cortex are considered the main brain structures for allocentric representation of the external environment. Here, we show that the amygdala and the ventral visual stream are involved in allocentric representation. Thirty-one young men explored 35 virtual environments during high-resolution functional magnetic resonance imaging (fMRI) of the medial temporal lobe (MTL) and were subsequently tested on recall of the allocentric pattern of the objects in each environment-in other words, the positions of the objects relative to each other and to the outer perimeter. We find increasingly unique brain activation patterns associated with increasing allocentric accuracy in distinct neural populations in the perirhinal cortex, parahippocampal cortex, fusiform cortex, amygdala, hippocampus, and entorhinal cortex. In contrast to the traditional view of a hierarchical MTL network with the hippocampus at the top, we demonstrate, using recently developed graph analyses, a hierarchical allocentric MTL network without a main connector hub.

Common Brain Networks Between Major Depressive-Disorder Diagnosis and Symptoms of Depression That Are Validated for Independent Cohorts

Large-scale neuroimaging data acquired and shared by multiple institutions are essential to advance neuroscientific understanding of pathophysiological mechanisms in psychiatric disorders, such as major depressive disorder (MDD). About 75% of studies that have applied machine learning technique to neuroimaging have been based on diagnoses by clinicians. However, an increasing number of studies have highlighted the difficulty in finding a clear association between existing clinical diagnostic categories and neurobiological abnormalities. Here, using resting-state functional magnetic resonance imaging, we determined and validated resting-state functional connectivity related to depression symptoms that were thought to be directly related to neurobiological abnormalities. We then compared the resting-state functional connectivity related to depression symptoms with that related to depression diagnosis that we recently identified. In particular, for the discovery dataset with 477 participants from 4 imaging sites, we removed site differences using our recently developed harmonization method and developed a brain network prediction model of depression symptoms (Beck Depression Inventory-II [BDI] score). The prediction model significantly predicted BDI score for an independent validation dataset with 439 participants from 4 different imaging sites. Finally, we found 3 common functional connections between those related to depression symptoms and those related to MDD diagnosis. These findings contribute to a deeper understanding of the neural circuitry of depressive symptoms in MDD, a hetero-symptomatic population, revealing the neural basis of MDD.

Higher Executive Control Network Coherence Buffers Against Puberty-Related Increases in Internalizing Symptoms During the COVID-19 Pandemic

BACKGROUND

Early pubertal maturation has been posited to be a biopsychosocial risk factor for the onset of internalizing psychopathology in adolescence; further, early-maturing youths exhibit heightened reactivity to stressful events. School closures and enforced social distancing, as well as health and financial uncertainties, during the COVID-19 pandemic are expected to adversely affect mental health in youths, particularly adolescents who are already at risk for experiencing emotional difficulties. The executive control network (ECN) supports cognitive processes required to successfully navigate novel challenges and regulate emotions in stressful contexts.

METHODS

We examined whether functional coherence of the ECN, measured using resting-state functional magnetic resonance imaging 5 years before the pandemic (T1), is a neurobiological marker of resilience to increases in the severity of internalizing symptoms during COVID-19 in adolescents who were in more advanced stages of puberty at T1 relative to their same-age peers (N = 85, 49 female).

RESULTS

On average, participants reported an increase in symptoms from the 3 months before pandemic to the 2 most recent weeks during the pandemic. We found that early-maturing youths exhibited greater increases in internalizing symptoms during the pandemic if their ECN coherence was low; in contrast, relative pubertal stage was not associated with changes in internalizing symptoms in adolescents with higher ECN coherence at T1.

CONCLUSIONS

These findings highlight the role of the functional architecture of the brain that supports executive functioning in protecting against risk factors that may exacerbate symptoms of internalizing psychopathology during periods of stress and uncertainty.

Ultra-high field fMRI reveals origins of feedforward and feedback activity within laminae of human ocular dominance columns

Ultra-high field MRI can functionally image the cerebral cortex of human subjects at the submillimeter scale of cortical columns and laminae. Here, we investigate both in concert, by imaging ocular dominance columns (ODCs) in primary visual cortex (V1) across different cortical depths. We ensured that putative ODC patterns in V1 (a) are stable across runs, sessions, and scanners located in different continents, (b) have a width (~1.3 mm) expected from post-mortem and animal work and (c) are absent at the retinotopic location of the blind spot. We then dissociated the effects of bottom-up thalamo-cortical input and attentional feedback processes on activity in V1 across cortical depth. Importantly, the separation of bottom-up information flows into ODCs allowed us to validly compare attentional conditions while keeping the stimulus identical throughout the experiment. We find that, when correcting for draining vein effects and using both model-based and model-free approaches, the effect of monocular stimulation is largest at deep and middle cortical depths. Conversely, spatial attention influences BOLD activity exclusively near the pial surface. Our findings show that simultaneous interrogation of columnar and laminar dimensions of the cortical fold can dissociate thalamocortical inputs from top-down processing, and allow the investigation of their interactions without any stimulus manipulation.

Neural mechanisms of acute stress and trait anxiety in adolescents

Adolescence is a critical period of heightened stress sensitivity and elevated vulnerability for developing mental illness, suggesting a possible association between stress exposure and the etiology of psychiatric disorders. In adults, aberrant neurobiological responses to acute stress relate to anxiety symptoms, yet less is known about the neural stress response in adolescents and how it relates to biological and psychological variables. Here we characterize the neurobiology of stress response in adolescents using multiple modalities, including neuroimaging, subjective stress ratings, heart rate, and cortisol data. We evaluated stress response in adolescents using the Montreal Imaging Stress Task (MIST), an acute psychosocial stressor commonly administered in adult functional magnetic resonance imaging (fMRI) studies but not previously utilized with this population. FMRI data were acquired from 101 adolescents (44 female; 9-16 years) exhibiting varied trait anxiety severity. The MIST elicited decreased high-frequency heart rate variability and increased heart rate, subjective stress and cortisol. Whole-brain analyses comparing fMRI activity during experimental versus control MIST conditions revealed stress-related activation in regions including the anterior insula, dorsal anterior cingulate cortex, and dorsolateral prefrontal cortex and deactivations in the hippocampus, ventral striatum, and putamen. Region of Interest analyses found that during acute stress (a) hippocampal deactivation corresponded to heightened cortisol release, (b) trait anxiety was associated with increased hippocampal and ventral striatum activation and decreased putamen activity, and (c) males exhibited greater putamen deactivation than females. These results provide novel evidence that the MIST is an effective stressor for adolescents. Associations between the neural acute stress response, other biological factors, and trait anxiety highlight the importance of these neurobiological mechanisms in understanding anxiety disorders.

PREEMACS: Pipeline for preprocessing and extraction of the macaque brain surface

Accurate extraction of the cortical brain surface is critical for cortical thickness estimation and a key element to perform multimodal imaging analysis, where different metrics are integrated and compared in a common space. While brain surface extraction has become widespread practice in human studies, several challenges unique to neuroimaging of non-human primates (NHP) have hindered its adoption for the study of macaques. Although, some of these difficulties can be addressed at the acquisition stage, several common artifacts can be minimized through image preprocessing. Likewise, there are several image analysis pipelines for human MRIs, but very few automated methods for extraction of cortical surfaces have been reported for NHPs and none have been tested on data from diverse sources. We present PREEMACS, a pipeline that standardizes the preprocessing of structural MRI images (T1- and T2-weighted) and carries out an automatic surface extraction of the macaque brain. Building upon and extending pre-existing tools, the first module performs volume orientation, image cropping, intensity non-uniformity correction, and volume averaging, before skull-stripping through a convolutional neural network. The second module performs quality control using an adaptation of MRIqc method to extract objective quality metrics that are then used to determine the likelihood of accurate brain surface estimation. The third and final module estimates the white matter (wm) and pial surfaces from the T1-weighted volume (T1w) using an NHP customized version of FreeSurfer aided by the T2-weighted volumes (T2w). To evaluate the generalizability of PREEMACS, we tested the pipeline using 57 T1w/T2w NHP volumes acquired at 11 different sites from the PRIME-DE public dataset. Results showed an accurate and robust automatic brain surface extraction from images that passed the quality control segment of our pipeline. This work offers a robust, efficient and generalizable pipeline for the automatic standardization of MRI surface analysis on NHP.

Topological Abnormalities of Functional Brain Network in Early-Stage Parkinson's Disease Patients With Mild Cognitive Impairment

Recent studies have demonstrated structural and functional alterations in Parkinson's disease (PD) with mild cognitive impairment (MCI). However, the topological patterns of functional brain networks in newly diagnosed PD patients with MCI are unclear so far. In this study, we used functional magnetic resonance imaging (fMRI) and graph theory approaches to explore the functional brain network in 45 PD patients with MCI (PD-MCI), 22 PD patients without MCI (PD-nMCI), and 18 healthy controls (HC). We found that the PD-MCI, PD-nMCI, and HC groups exhibited a small-world architecture in the functional brain network. However, early-stage PD-MCI patients had decreased clustering coefficient, increased characteristic path length, and changed nodal centrality in the default mode network (DMN), control network (CN), somatomotor network (SMN), and visual network (VN), which might contribute to factors for MCI symptoms in PD patients. Our results demonstrated that PD-MCI patients were associated with disrupted topological organization in the functional network, thus providing a topological network insight into the role of information exchange in the underlying development of MCI symptoms in PD patients.

Similarity in functional brain connectivity at rest predicts interpersonal closeness in the social network of an entire village

People often have the intuition that they are similar to their friends, yet evidence for homophily (being friends with similar others) based on self-reported personality is inconsistent. Functional connectomes-patterns of spontaneous synchronization across the brain-are stable within individuals and predict how people tend to think and behave. Thus, they may capture interindividual variability in latent traits that are particularly similar among friends but that might elude self-report. Here, we examined interpersonal similarity in functional connectivity at rest-that is, in the absence of external stimuli-and tested if functional connectome similarity is associated with proximity in a real-world social network. The social network of a remote village was reconstructed; a subset of residents underwent functional magnetic resonance imaging. Similarity in functional connectomes was positively related to social network proximity, particularly in the default mode network. Controlling for similarities in demographic and personality data (the Big Five personality traits) yielded similar results. Thus, functional connectomes may capture latent interpersonal similarities between friends that are not fully captured by commonly used demographic or personality measures. The localization of these results suggests how friends may be particularly similar to one another. Additionally, geographic proximity moderated the relationship between neural similarity and social network proximity, suggesting that such associations are particularly strong among people who live particularly close to one another. These findings suggest that social connectivity is reflected in signatures of brain functional connectivity, consistent with the common intuition that friends share similarities that go beyond, for example, demographic similarities.

Using functional connectivity changes associated with cognitive fatigue to delineate a fatigue network

Cognitive fatigue, or fatigue related to mental work, is a common experience. A growing body of work using functional neuroimaging has identified several regions that appear to be related to cognitive fatigue and that potentially comprise a "fatigue network". These include the striatum of the basal ganglia, the dorsolateral prefrontal cortex (DLPFC), the dorsal anterior cingulate cortex (dACC), the ventro-medial prefrontal cortex (vmPFC) and the anterior insula. However, no work has been conducted to assess whether the connectivity between these regions changes as a function of cognitive fatigue. We used a task-based functional neuroimaging paradigm to induce fatigue in 39 healthy individuals, regressed the signal associated with the task out of the data, and investigated how the functional connectivity between these regions changed as cognitive fatigue increased. We observed functional connectivity between these regions and other frontal regions largely decreased as cognitive fatigue increased while connectivity between these seeds and more posterior regions increased. Furthermore the striatum, the DLPFC, the insula and the vmPFC appeared to be central 'nodes' or hubs of the fatigue network. These findings represent the first demonstration that the functional connectivity between these areas changes as a function of cognitive fatigue.

Dynamic functional networks in idiopathic normal pressure hydrocephalus: Alterations and reversibility by CSF tap test

Idiopathic Normal Pressure Hydrocephalus (iNPH)—the leading cause of reversible dementia in aging—is characterized by ventriculomegaly and gait, cognitive and urinary impairments. Despite its high prevalence estimated at 6% among the elderlies, iNPH remains underdiagnosed and undertreated due to the lack of iNPH‐specific diagnostic markers and limited understanding of pathophysiological mechanisms. INPH diagnosis is also complicated by the frequent occurrence of comorbidities, the most common one being Alzheimer's disease (AD). Here we investigate the resting‐state functional magnetic resonance imaging dynamics of 26 iNPH patients before and after a CSF tap test, and of 48 normal older adults. Alzheimer's pathology was evaluated by CSF biomarkers. We show that the interactions between the default mode, and the executive‐control, salience and attention networks are impaired in iNPH, explain gait and executive disturbances in patients, and are not driven by AD‐pathology. In particular, AD molecular biomarkers are associated with functional changes distinct from iNPH functional alterations. Finally, we demonstrate a partial normalization of brain dynamics 24 hr after a CSF tap test, indicating functional plasticity mechanisms. We conclude that functional changes involving the default mode cross‐network interactions reflect iNPH pathophysiological mechanisms and track treatment response, possibly contributing to iNPH differential diagnosis and better clinical management.

Improved Task-based Functional MRI Language Mapping in Patients with Brain Tumors through Marchenko-Pastur Principal Component Analysis Denoising

Background Functional MRI improves preoperative planning in patients with brain tumors, but task-correlated signal intensity changes are only 2%-3% above baseline. This makes accurate functional mapping challenging. Marchenko-Pastur principal component analysis (MP-PCA) provides a novel strategy to separate functional MRI signal from noise without requiring user input or prior data representation. Purpose To determine whether MP-PCA denoising improves activation magnitude for task-based functional MRI language mapping in patients with brain tumors. Materials and Methods In this Health Insurance Portability and Accountability Act-compliant study, MP-PCA performance was first evaluated by using simulated functional MRI data with a known ground truth. Right-handed, left-language-dominant patients with brain tumors who successfully performed verb generation, sentence completion, and finger tapping functional MRI tasks were retrospectively identified between January 2017 and August 2018. On the group level, for each task, histograms of z scores for original and MP-PCA denoised data were extracted from relevant regions and contralateral homologs were seeded by a neuroradiologist blinded to functional MRI findings. Z scores were compared with paired two-sided t tests, and distributions were compared with effect size measurements and the Kolmogorov-Smirnov test. The number of voxels with a z score greater than 3 was used to measure task sensitivity relative to task duration. Results Twenty-three patients (mean age ± standard deviation, 43 years ± 18; 13 women) were evaluated. MP-PCA denoising led to a higher median z score of task-based functional MRI voxel activation in left hemisphere cortical regions for verb generation (from 3.8 ± 1.0 to 4.5 ± 1.4; P < .001), sentence completion (from 3.7 ± 1.0 to 4.3 ± 1.4; P < .001), and finger tapping (from 6.9 ± 2.4 to 7.9 ± 2.9; P < .001). Median z scores did not improve in contralateral homolog regions for verb generation (from -2.7 ± 0.54 to -2.5 ± 0.40; P = .90), sentence completion (from -2.3 ± 0.21 to -2.4 ± 0.37; P = .39), or finger tapping (from -2.3 ± 1.20 to -2.7 ± 1.40; P = .07). Individual functional MRI task durations could be truncated by at least 40% after MP-PCA without degradation of clinically relevant correlations between functional cortex and functional MRI tasks. Conclusion Denoising with Marchenko-Pastur principal component analysis led to higher task correlations in relevant cortical regions during functional MRI language mapping in patients with brain tumors. © RSNA, 2020 Online supplemental material is available for this article.

Automatic Brain Extraction for Rodent MRI Images

Rodent models are increasingly important in translational neuroimaging research. In rodent neuroimaging, particularly magnetic resonance imaging (MRI) studies, brain extraction is a critical data preprocessing component. Current brain extraction methods for rodent MRI usually require manual adjustment of input parameters due to widely different image qualities and/or contrasts. Here we propose a novel method, termed SHape descriptor selected Extremal Regions after Morphologically filtering (SHERM), which only requires a brain template mask as the input and is capable of automatically and reliably extracting the brain tissue in both rat and mouse MRI images. The method identifies a set of brain mask candidates, extracted from MRI images morphologically opened and closed sequentially with multiple kernel sizes, that match the shape of the brain template. These brain mask candidates are then merged to generate the brain mask. This method, along with four other state-of-the-art rodent brain extraction methods, were benchmarked on four separate datasets including both rat and mouse MRI images. Without involving any parameter tuning, our method performed comparably to the other four methods on all datasets, and its performance was robust with stably high true positive rates and low false positive rates. Taken together, this study provides a reliable automatic brain extraction method that can contribute to the establishment of automatic pipelines for rodent neuroimaging data analysis.

Neural Substrates of Food Valuation and Its Relationship With BMI and Healthy Eating in Higher BMI Individuals

Considerable evidence points to a link between body mass index (BMI), eating behavior, and the brain's reward system. However, much of this research focuses on food cue reactivity without examining the subjective valuation process as a potential mechanism driving individual differences in BMI and eating behavior. The current pre-registered study (https://osf.io/n4c95/) examined the relationship between BMI, healthy eating, and subjective valuation of healthy and unhealthy foods in a community sample of individuals with higher BMI who intended to eat more healthily. Particularly, we examined: (1) alterations in neurocognitive measures of subjective valuation related to BMI and healthy eating; (2) differences in the neurocognitive valuation for healthy and unhealthy foods and their relation to BMI and healthy eating; (3) and whether we could conceptually replicate prior findings demonstrating differences in neural reactivity to palatable vs. plain foods. To this end, we scanned 105 participants with BMIs ranging from 23 to 42 using fMRI during a willingness-to-pay task that quantifies trial-by-trial valuation of 30 healthy and 30 unhealthy food items. We measured out of lab eating behavior via the Automated Self-Administered 24 H Dietary Assessment Tool, which allowed us to calculate a Healthy Eating Index (HEI). We found that our sample exhibited robust, positive linear relationships between self-reported value and neural responses in regions previously implicated in studies of subjective value, suggesting an intact valuation system. However, we found no relationship between valuation and BMI nor HEI, with Bayes Factor indicating moderate evidence for a null relationship. Separating the food types revealed that healthy eating, as measured by the HEI, was inversely related to subjective valuation of unhealthy foods. Imaging data further revealed a stronger linkage between valuation of healthy (compared to unhealthy) foods and corresponding response in the ventromedial prefrontal cortex (vmPFC), and that the interaction between healthy and unhealthy food valuation in this region is related to HEI. Finally, our results did not replicate reactivity differences demonstrated in prior work, likely due to differences in the mapping between food healthiness and palatability. Together, our findings point to disruptions in the valuation of unhealthy foods in the vmPFC as a potential mechanism influencing healthy eating.

File-based localization of numerical perturbations in data analysis pipelines

BACKGROUND

Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear.

METHOD

We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation.

RESULTS

By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings.

Generalizable brain network markers of major depressive disorder across multiple imaging sites

Many studies have highlighted the difficulty inherent to the clinical application of fundamental neuroscience knowledge based on machine learning techniques. It is difficult to generalize machine learning brain markers to the data acquired from independent imaging sites, mainly due to large site differences in functional magnetic resonance imaging. We address the difficulty of finding a generalizable marker of major depressive disorder (MDD) that would distinguish patients from healthy controls based on resting-state functional connectivity patterns. For the discovery dataset with 713 participants from 4 imaging sites, we removed site differences using our recently developed harmonization method and developed a machine learning MDD classifier. The classifier achieved an approximately 70% generalization accuracy for an independent validation dataset with 521 participants from 5 different imaging sites. The successful generalization to a perfectly independent dataset acquired from multiple imaging sites is novel and ensures scientific reproducibility and clinical applicability.

Research Review: Brain network connectivity and the heterogeneity of depression in adolescence - a precision mental health perspective

BACKGROUND

Adolescence is a period of high risk for the onset of depression, characterized by variability in symptoms, severity, and course. During adolescence, the neurocircuitry implicated in depression continues to mature, suggesting that it is an important period for intervention. Reflecting the recent emergence of 'precision mental health' - a person-centered approach to identifying, preventing, and treating psychopathology - researchers have begun to document associations between heterogeneity in features of depression and individual differences in brain circuitry, most frequently in resting-state functional connectivity (RSFC).

METHODS

In this review, we present emerging work examining pre- and post-treatment measures of network connectivity in depressed adolescents; these studies reveal potential intervention-specific neural markers of treatment efficacy. We also review findings from studies examining associations between network connectivity and both types of depressive symptoms and response to treatment in adults, and indicate how this work can be extended to depressed adolescents. Finally, we offer recommendations for research that we believe will advance the science of precision mental health of adolescence.

RESULTS

Nascent studies suggest that linking RSFC-based pathophysiological variation with effects of different types of treatment and changes in mood following specific interventions will strengthen predictions of prognosis and treatment response. Studies with larger sample sizes and direct comparisons of treatments are required to determine whether RSFC patterns are reliable neuromarkers of treatment response for depressed adolescents. Although we are not yet at the point of using RSFC to guide clinical decision-making, findings from research examining the stability and reliability of RSFC point to a favorable future for network-based clinical phenotyping.

CONCLUSIONS

Delineating the correspondence between specific clinical characteristics of depression (e.g., symptoms, severity, and treatment response) and patterns of network-based connectivity will facilitate the development of more tailored and effective approaches to the assessment, prevention, and treatment of depression in adolescents.

Longitudinal functional brain network reconfiguration in healthy aging

Healthy aging is associated with changes in cognitive performance and functional brain organization. In fact, cross-sectional studies imply lower modularity and significant heterogeneity in modular architecture across older subjects. Here, we used a longitudinal dataset consisting of four occasions of resting-state-fMRI and cognitive testing (spanning 4 years) in 150 healthy older adults. We applied a graph-theoretic analysis to investigate the time-evolving modular structure of the whole-brain network, by maximizing the multilayer modularity across four time points. Global flexibility, which reflects the tendency of brain nodes to switch between modules across time, was significantly higher in healthy elderly than in a temporal null model. Further, global flexibility, as well as network-specific flexibility of the default mode, frontoparietal control, and somatomotor networks, were significantly associated with age at baseline. These results indicate that older age is related to higher variability in modular organization. The temporal metrics were not associated with simultaneous changes in processing speed or learning performance in the context of memory encoding. Finally, this approach provides global indices for longitudinal change across a given time span and it may contribute to uncovering patterns of modular variability in healthy and clinical aging populations.

Emergence and organization of adult brain function throughout child development

Adult cognitive neuroscience has guided the study of human brain development by identifying regions associated with cognitive functions at maturity. The activity, connectivity, and structure of a region can be compared across ages to characterize the developmental trajectory of the corresponding function. However, developmental differences may reflect both the maturation of the function and also its organization across the brain. That is, a function may be present in children but supported by different brain regions, leading its maturity to be underestimated. Here we test the presence, maturity, and localization of adult functions in children using shared response modeling, a machine learning approach for functional alignment. After learning a lower-dimensional feature space from fMRI activity as adults watched a movie, we translated these shared features into the anatomical brain space of children 3–12 years old. To evaluate functional maturity, we correlated this reconstructed activity with children’s actual fMRI activity as they watched the same movie. We found reliable correlations throughout cortex, even in the youngest children. The strength of the correlation in the precuneus, inferior frontal gyrus, and lateral occipital cortex predicted chronological age. These age-related changes were driven by three types of developmental trajectories: emergence from absence to presence, consistency in anatomical expression, and reorganization from one anatomical region to another. We also found evidence that the processing of pain-related events in the movie underwent reorganization across childhood. This data-driven, naturalistic approach provides a new perspective on the development of functional neuroanatomy throughout childhood.

DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains

Deep neural networks (DNNs) have attained human-level performance on dozens of challenging tasks via an end-to-end deep learning strategy. Deep learning allows data representations that have multiple levels of abstraction; however, it does not explicitly provide any insights into the internal operations of DNNs. Deep learning's success is appealing to neuroscientists not only as a method for applying DNNs to model biological neural systems but also as a means of adopting concepts and methods from cognitive neuroscience to understand the internal representations of DNNs. Although general deep learning frameworks, such as PyTorch and TensorFlow, could be used to allow such cross-disciplinary investigations, the use of these frameworks typically requires high-level programming expertise and comprehensive mathematical knowledge. A toolbox specifically designed as a mechanism for cognitive neuroscientists to map both DNNs and brains is urgently needed. Here, we present DNNBrain, a Python-based toolbox designed for exploring the internal representations of DNNs as well as brains. Through the integration of DNN software packages and well-established brain imaging tools, DNNBrain provides application programming and command line interfaces for a variety of research scenarios. These include extracting DNN activation, probing and visualizing DNN representations, and mapping DNN representations onto the brain. We expect that our toolbox will accelerate scientific research by both applying DNNs to model biological neural systems and utilizing paradigms of cognitive neuroscience to unveil the black box of DNNs.

Behavioral, Physiological, and Neural Signatures of Surprise during Naturalistic Sports Viewing

Surprise signals a discrepancy between past and current beliefs. It is theorized to be linked to affective experiences, the creation of particularly resilient memories, and segmentation of the flow of experience into discrete perceived events. However, the ability to precisely measure naturalistic surprise has remained elusive. We used advanced basketball analytics to derive a quantitative measure of surprise and characterized its behavioral, physiological, and neural correlates in human subjects observing basketball games. We found that surprise was associated with segmentation of ongoing experiences, as reflected by subjectively perceived event boundaries and shifts in neocortical patterns underlying belief states. Interestingly, these effects differed by whether surprising moments contradicted or bolstered current predominant beliefs. Surprise also positively correlated with pupil dilation, activation in subcortical regions associated with dopamine, game enjoyment, and long-term memory. These investigations support key predictions from event segmentation theory and extend theoretical conceptualizations of surprise to real-world contexts.

Abstract Neural Representations of Category Membership beyond Information Coding Stimulus or Response

For decades, researchers have debated whether mental representations are symbolic or grounded in sensory inputs and motor programs. Certainly, aspects of mental representations are grounded. However, does the brain also contain abstract concept representations that mediate between perception and action in a flexible manner not tied to the details of sensory inputs and motor programs? Such conceptual pointers would be useful when concepts remain constant despite changes in appearance and associated actions. We evaluated whether human participants acquire such representations using fMRI. Participants completed a probabilistic concept learning task in which sensory, motor, and category variables were not perfectly coupled or entirely independent, making it possible to observe evidence for abstract representations or purely grounded representations. To assess how the learned concept structure is represented in the brain, we examined brain regions implicated in flexible cognition (e.g., pFC and parietal cortex) that are most likely to encode an abstract representation removed from sensory-motor details. We also examined sensory-motor regions that might encode grounded sensory-motor-based representations tuned for categorization. Using a cognitive model to estimate participants' category rule and multivariate pattern analysis of fMRI data, we found the left pFC and MT coded for category in the absence of information coding for stimulus or response. Because category was based on the stimulus, finding an abstract representation of category was not inevitable. Our results suggest that certain brain areas support categorization behavior by constructing concept representations in a format akin to a symbol that differs from stimulus-motor codes.

A collaborative resource platform for non-human primate neuroimaging

Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.

Exploratory study of how Cognitive Multisensory Rehabilitation restores parietal operculum connectivity and improves upper limb movements in chronic stroke

Cognitive Multisensory Rehabilitation (CMR) is a promising therapy for upper limb recovery in stroke, but the brain mechanisms are unknown. We previously demonstrated that the parietal operculum (parts OP1/OP4) is activated with CMR exercises. In this exploratory study, we assessed the baseline difference between OP1/OP4 functional connectivity (FC) at rest in stroke versus healthy adults to then explore whether CMR affects OP1/OP4 connectivity and sensorimotor recovery after stroke. We recruited 8 adults with chronic stroke and left hemiplegia/paresis and 22 healthy adults. Resting-state FC with the OP1/OP4 region-of-interest in the affected hemisphere was analysed before and after 6 weeks of CMR. We evaluated sensorimotor function and activities of daily life pre- and post-CMR, and at 1-year post-CMR. At baseline, we found decreased FC between the right OP1/OP4 and 34 areas distributed across all lobes in stroke versus healthy adults. After CMR, only four areas had decreased FC compared to healthy adults. Compared to baseline (pre-CMR), participants improved on motor function (MESUPES arm p = 0.02; MESUPES hand p = 0.03; MESUPES total score p = 0.006); on stereognosis (p = 0.03); and on the Frenchay Activities Index (p = 0.03) at post-CMR and at 1-year follow-up. These results suggest enhanced sensorimotor recovery post-stroke after CMR. Our results justify larger-scale studies.

Neural Indicators Of Food Cue Reactivity, Regulation, And Valuation And Their Associations With Body Composition And Daily Eating Behavior

Exposure to food cues activates the brain's reward system and undermines efforts to regulate impulses to eat. During explicit regulation, lateral prefrontal cortex activates and modulates activity in reward regions and decreases food cravings. However, it is unclear the extent to which between-person differences in recruitment of regions associated with reward processing, subjective valuation, and regulation during food cue exposure-absent instructions to regulate-predict body composition and daily eating behaviors. In this preregistered study, we pooled data from five fMRI samples (N = 262) to examine whether regions associated with reward, valuation, and regulation, as well as whole-brain pattern expression indexing these processes, were recruited during food cue exposure and associated with body composition and real-world eating behavior. Regression models for a single a priori analytic path indicated that univariate and multivariate measures of reward and valuation were associated with individual differences in BMI and enactment of daily food cravings. Specification curve analyses further revealed reliable associations between univariate and multivariate neural indicators of reactivity, regulation, and valuation, and all outcomes. These findings highlight the utility of these methods to elucidate brain-behavior associations and suggest that multiple processes are implicated in proximal and distal markers of eating behavior.

Rapid Rule-Based Reward Reversal and the Lateral Orbitofrontal Cortex

Humans and other primates can reverse their choice of stimuli in one trial when the rewards delivered by the stimuli change or reverse. Rapidly changing our behavior when the rewards change is important for many types of behavior, including emotional and social behavior. It is shown in a one-trial rule-based Go-NoGo deterministic visual discrimination reversal task to obtain points, that the human right lateral orbitofrontal cortex and adjoining inferior frontal gyrus is activated on reversal trials, when an expected reward is not obtained, and the non-reward allows the human to switch choices based on a rule. This reward reversal goes beyond model-free reinforcement learning. This functionality of the right lateral orbitofrontal cortex shown here in very rapid, one-trial, rule-based changes in human behavior when a reward is not received is related to the emotional and social changes that follow orbitofrontal cortex damage, and to depression in which this non-reward system is oversensitive and over-connected.

Natural bladder filling alters resting brain function at multiple spatial scales: a proof-of-concept MAPP Network Neuroimaging Study

Neural circuitry regulating urine storage in humans has been largely inferred from fMRI during urodynamic studies driven by catheter infusion of fluid into the bladder. However, urodynamic testing may be confounded by artificially filling the bladder repeatedly at a high rate and examining associated time-locked changes in fMRI signals. Here we describe and test a more ecologically-valid paradigm to study the brain response to bladder filling by (1) filling the bladder naturally with oral water ingestion, (2) examining resting state fMRI (rs-fMRI) which is more natural since it is not linked with a specific stimulus, and (3) relating rs-fMRI measures to self-report (urinary urge) and physiologic measures (voided volume). To establish appropriate controls and analyses for future clinical studies, here we analyze data collected from healthy individuals (N = 62) as part of the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network. Participants orally ingested approximately 350 mL of water, and had a 10 min “fuller bladder” rs-fMRI scan approximately 1 h later. A second 10 min “empty bladder” rs-fMRI scan was conducted immediately following micturition. We examined multiple spatial scales of brain function, including local activity, circuits, and networks. We found changes in brain function distributed across micturition loci (e.g., subregions of the salience, sensorimotor, and default networks) that were significantly related to the stimulus (volume) and response (urinary urge). Based on our results, this paradigm can be applied in the future to study the neurobiological underpinnings of urologic conditions.

Brain Activity Associated With Regulating Food Cravings Predicts Changes in Self-Reported Food Craving and Consumption Over Time

Neural patterns associated with viewing energy-dense foods can predict changes in eating-related outcomes. However, most research on this topic is limited to one follow-up time point, and single outcome measures. The present study seeks to add to that literature by employing a more refined assessment of food craving and consumption outcomes along with a more detailed neurobiological model of behavior change over several time points. Here, a community sample of 88 individuals (age: M = 39.17, SD = 3.47; baseline BMI: M = 31.5, SD = 3.9, range 24–42) with higher body mass index (BMI) performed a food craving reactivity and regulation task while undergoing functional magnetic resonance imaging. At that time—and 1, 3, and 6 months later—participants reported craving for and consumption of healthy and unhealthy foods via the Food Craving Inventory (FCI) and ASA24 (N at 6 months = 52–55 depending on the measure). A priori hypotheses that brain activity associated with both viewing and regulating personally desired unhealthy, energy-dense foods would be associated with self-reported craving for and consumption of unhealthy foods at baseline were not supported by the data. Instead, regression models controlling for age, sex, and BMI demonstrated that brain activity across several regions measured while individuals were regulating their desires for unhealthy food was associated with the self-reported craving for and consumption of healthy food. The hypothesis that vmPFC activity would predict patterns of healthier eating was also not supported. Instead, linear mixed models controlling for baseline age and sex, as well as changes in BMI, revealed that more regulation-related activity in the dlPFC, dACC, IFG, and vmPFC at baseline predicted decreases in the craving for and consumption of healthy foods over the course of 6 months.

An fMRI dataset in response to "The Grand Budapest Hotel", a socially-rich, naturalistic movie

Naturalistic stimuli evoke strong, consistent, and information-rich patterns of brain activity, and engage large extents of the human brain. They allow researchers to compare highly similar brain responses across subjects, and to study how complex representations are encoded in brain activity. Here, we describe and share a dataset where 25 subjects watched part of the feature film "The Grand Budapest Hotel" by Wes Anderson. The movie has a large cast with many famous actors. Throughout the story, the camera shots highlight faces and expressions, which are fundamental to understand the complex narrative of the movie. This movie was chosen to sample brain activity specifically related to social interactions and face processing. This dataset provides researchers with fMRI data that can be used to explore social cognitive processes and face processing, adding to the existing neuroimaging datasets that sample brain activity with naturalistic movies.

Cortical gradients of functional connectivity are robust to state-dependent changes following sleep deprivation

Sleep deprivation leads to significant impairments in cognitive performance and changes to the interactions between large scale cortical networks, yet the hierarchical organization of cortical activity across states is still being explored. We used functional magnetic resonance imaging to assess activations and connectivity during cognitive tasks in 20 healthy young adults, during three states: (i) following a normal night of sleep, (ii) following 24hr of total sleep deprivation, and (iii) after a morning recovery nap. Situating cortical activity during cognitive tasks along hierarchical organizing gradients based upon similarity of functional connectivity patterns, we found that regional variations in task-activations were captured by an axis differentiating areas involved in executive control from default mode regions and paralimbic cortex. After global signal regression, the range of functional differentiation along this axis at baseline was significantly related to decline in working memory performance (2-back task) following sleep deprivation, as well as the extent of recovery in performance following a nap. The relative positions of cortical regions within gradients did not significantly change across states, except for a lesser differentiation of the visual system and increased coupling of the posterior cingulate cortex with executive control areas after sleep deprivation. This was despite a widespread increase in the magnitude of functional connectivity across the cortex following sleep deprivation. Cortical gradients of functional differentiation thus appear relatively insensitive to state-dependent changes following sleep deprivation and recovery, suggesting that there are no large-scale changes in cortical functional organization across vigilance states. Certain features of particular gradient axes may be informative for the extent of decline in performance on more complex tasks following sleep deprivation, and could be beneficial over traditional voxel- or parcel-based approaches in identifying realtionships between state-dependent brain activity and behavior.

Stability and similarity of the pediatric connectome as developmental measures

Patterns of functional connectivity are unique at the individual level, enabling test-retest matching algorithms to identify a subject from among a group using only their functional connectome. Recent findings show that accuracies of these algorithms in children increase with age. Relatedly, the persistence of functional connectivity (FC) patterns across tasks and rest also increases with age. This study investigated the hypothesis that within-subject stability and between-subject similarity of the whole-brain pediatric connectome are developmentally relevant outcomes. Using data from 210 help-seeking children and adolescents, ages 6-21 years (Healthy Brain Network Biobank), we computed whole-brain FC matrices for each participant during two different movies (MovieDM and MovieTP) and two runs of task-free rest (all from a single scan session) and fed these matrices to a test-retest matching algorithm. We replicated the finding that matching accuracies for children and youth (ages 6-21 years) are low (18-44%), and that cross-state and cross-movie accuracies were the lowest. Results also showed that parcellation resolution and the number of volumes used in each matrix affect fingerprinting accuracies. Next, we calculated three measures of whole-connectome stability for each subject: cross-rest (Rest1-Rest2), cross-state (MovieDM-Rest1), and cross-movie (MovieDM-MovieTP), and three measures of within-state between-subject connectome similarity for Rest1, MovieDM, and MovieTP. We show that stability and similarity were correlated, but that these measures were not related to age. A principal component analysis of these measures yielded two components that we used to test for brain-behavior correlations with IQ, general psychopathology, and social skills measures (n = 119). The first component was significantly correlated with the social skills measure (r=-0.26, p = 0.005). Post hoc correlations showed that the social skills measure correlated with both cross-rest stability (r=-0.29, p = 0.001) and with connectome similarity during MovieDM (r=-0.28, p = 0.002). These findings suggest that the stability and similarity of the whole-brain connectome relate to the development of social skills. We infer that the maturation of the functional connectome simultaneously achieves patterns of FC that are distinct at the individual subject level, that are shared across individuals, and that are persistent across states and across runs-features which presumably combine to optimize neural processing during development. Future longitudinal work could reveal the developmental trajectories of stability and similarity of the connectome.

Cognitive Fatigue Is Associated with Altered Functional Connectivity in Interoceptive and Reward Pathways in Multiple Sclerosis

Cognitive fatigue is common and debilitating among persons with multiple sclerosis (pwMS). Neural mechanisms underlying fatigue are not well understood, which results in lack of adequate treatment. The current study examined cognitive fatigue-related functional connectivity among 26 pwMS and 14 demographically matched healthy controls (HCs). Participants underwent functional magnetic resonance imaging (fMRI) scanning while performing a working memory task (n-back), with two conditions: one with higher cognitive load (2-back) to induce fatigue and one with lower cognitive load (0-back) as a control condition. Task-independent residual functional connectivity was assessed, with seeds in brain regions previously implicated in cognitive fatigue (dorsolateral prefrontal cortex (DLPFC), ventromedial prefrontal cortex (vmPFC), dorsal anterior cingulate cortex (dACC), insula, and striatum). Cognitive fatigue was measured using the Visual Analogue Scale of Fatigue (VAS-F). Results indicated that as VAS-F scores increased, HCs showed increased residual functional connectivity between the striatum and the vmPFC (crucial in reward processing) during the 2-back condition compared to the 0-back condition. In contrast, pwMS displayed increased residual functional connectivity from interoceptive hubs—the insula and the dACC—to the striatum. In conclusion, pwMS showed a hyperconnectivity within the interoceptive network and disconnection within the reward circuitry when experiencing cognitive fatigue.

Multivariate neural signatures for health neuroscience: assessing spontaneous regulation during food choice

Establishing links between neural systems and health can be challenging since there is not a one-to-one mapping between brain regions and psychological states. Building sensitive and specific predictive models of health-relevant constructs using multivariate activation patterns of brain activation is a promising new direction. We illustrate the potential of this approach by building two 'neural signatures' of food craving regulation (CR) using multivariate machine learning and, for comparison, a univariate contrast. We applied the signatures to two large validation samples of overweight adults who completed tasks measuring CR ability and valuation during food choice. Across these samples, the machine learning signature was more reliable. This signature decoded CR from food viewing and higher signature expression was associated with less craving. During food choice, expression of the regulation signature was stronger for unhealthy foods and inversely related to subjective value, indicating that participants engaged in CR despite never being instructed to control their cravings. Neural signatures thus have the potential to measure spontaneous engagement of mental processes in the absence of explicit instruction, affording greater ecological validity. We close by discussing the opportunities and challenges of this approach, emphasizing what machine learning tools bring to the field of health neuroscience.

Mapping neural activity patterns to contextualized fearful facial expressions onto callous-unemotional (CU) traits: intersubject representational similarity analysis reveals less variation among high-CU adolescents

Callous-unemotional (CU) traits are early-emerging personality features characterized by deficits in empathy, concern for others, and remorse following social transgressions. One of the interpersonal deficits most consistently associated with CU traits is impaired behavioral and neurophysiological responsiveness to fearful facial expressions. However, the facial expression paradigms traditionally employed in neuroimaging are often ambiguous with respect to the nature of threat (i.e., is the perceiver the threat, or is something else in the environment?). In the present study, 30 adolescents with varying CU traits viewed fearful facial expressions cued to three different contexts ("afraid for you," "afraid of you," "afraid for self") while undergoing functional magnetic resonance imaging (fMRI). Univariate analyses found that mean right amygdala activity during the "afraid for self" context was negatively associated with CU traits. With the goal of disentangling idiosyncratic stimulus-driven neural responses, we employed intersubject representational similarity analysis to link intersubject similarities in multivoxel neural response patterns to contextualized fearful expressions with differential intersubject models of CU traits. Among low-CU adolescents, neural response patterns while viewing fearful faces were most consistently similar early in the visual processing stream and among regions implicated in affective responding, but were more idiosyncratic as emotional face information moved up the cortical processing hierarchy. By contrast, high-CU adolescents' neural response patterns consistently aligned along the entire cortical hierarchy (but diverged among low-CU youths). Observed patterns varied across contexts, suggesting that interpretations of fearful expressions depend to an extent on neural response patterns and are further shaped by levels of CU traits.

Exploring the hormonal and neural correlates of paternal protective behavior to their infants

Infant protection is an important but largely neglected aspect of parental care. Available theory and research suggest that endocrine levels and neural responses might be biological correlates of protective behavior. However, no research to date examined associations between these neurobiological and behavioral aspects. This study, preregistered on https://osf.io/2acxd, explored the psychobiology of paternal protection in 77 new fathers by combining neural responses to infant-threatening situations, self-reported protective behavior, behavioral observations in a newly developed experimental set-up (Auditory Startling Task), and measurements of testosterone and vasopressin. fMRI analyses validated the role of several brain networks in the processing of infant-threatening situations and indicated replicable findings with the infant-threat paradigm. We found little overlap between observed and reported protective behavior. Robust associations between endocrine levels, neural responses, and paternal protective behavior were absent.

Dimensional connectomics of anxious misery, a human connectome study related to human disease: Overview of protocol and data quality

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We present a new imaging study of 200 adults experiencing depression and anxiety.

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Quantitative measures of image quality indicate comparable quality to the HCP-YA.

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In addition, a comprehensive set of assessments measured patients’ symptom profiles.

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Data will be publicly available through the NIMH Data Archive starting fall 2020.

Disparate diagnostic categories from the Diagnostic and Statistical Manual of Mental Disorders (DSM), including generalized anxiety disorder, major depressive disorder and post-traumatic stress disorder, share common behavioral and phenomenological dysfunctions. While high levels of comorbidity and common features across these disorders suggest shared mechanisms, past research in psychopathology has largely proceeded based on the syndromal taxonomy established by the DSM rather than on a biologically-informed framework of neural, cognitive and behavioral dysfunctions. In line with the National Institute of Mental Health’s Research Domain Criteria (RDoC) framework, we present a Human Connectome Study Related to Human Disease that is intentionally designed to generate and test novel, biologically-motivated dimensions of psychopathology. The Dimensional Connectomics of Anxious Misery study is collecting neuroimaging, cognitive and behavioral data from a heterogeneous population of adults with varying degrees of depression, anxiety and trauma, as well as a set of healthy comparators (to date, n = 97 and n = 24, respectively). This sample constitutes a dataset uniquely situated to elucidate relationships between brain circuitry and dysfunctions of the Negative Valence construct of the RDoC framework. We present a comprehensive overview of the eligibility criteria, clinical procedures and neuroimaging methods of our project. After describing our protocol, we present group-level activation maps from task fMRI data and independent components maps from resting state data. Finally, using quantitative measures of neuroimaging data quality, we demonstrate excellent data quality relative to a subset of the Human Connectome Project of Young Adults (n = 97), as well as comparable profiles of cortical thickness from T1-weighted imaging and generalized fractional anisotropy from diffusion weighted imaging. This manuscript presents results from the first 121 participants of our full target 250 participant dataset, timed with the release of this data to the National Institute of Mental Health Data Archive in fall 2020, with the remaining half of the dataset to be released in 2021.

The impact of cancer and chemotherapy during pregnancy on child neurodevelopment: A multimodal neuroimaging analysis

BACKGROUND

This study applies multimodal MRI to investigate neurodevelopment in nine-year-old children born to cancer-complicated pregnancies.

METHODS

In this cohort study, children born after cancer-complicated pregnancies were recruited alongside 1:1 matched controls regarding age, sex and gestational age at birth (GA). Multimodal MRI was used to investigate whole-brain and subcortical volume, cortical structure (using surface-based morphometry), white matter microstructure (using fixel-based analysis) and functional connectivity (using resting-state blood-oxygen-level-dependant signal correlations). Graph theory probed whole-brain structural and functional organization. For each imaging outcome we conducted two group comparisons: 1) children born after cancer-complicated pregnancies versus matched controls, and 2) the subgroup of children with prenatal chemotherapy exposure versus matched controls. In both models, we used the covariate of GA and the group-by-GA interaction, using false-discovery-rate (FDR) or family-wise-error (FWE) correction for multiple comparisons. Exploratory post-hoc analyses investigated the relation between brain structure/function, neuropsychological outcome and maternal oncological/obstetrical history.

FINDINGS

Forty-two children born after cancer-complicated pregnancies were included in this study, with 30 prenatally exposed to chemotherapy. Brain organization and functional connectivity were not significantly different between groups. Both cancer and chemotherapy in pregnancy, as compared to matched controls, were associated with a lower travel depth, indicating less pronounced gyrification, in the left superior temporal gyrus (pFDR ≤ 006), with post-hoc analysis indicating platinum derivatives during pregnancy as a potential risk factor (p = .028). Both cancer and chemotherapy in pregnancy were related to a lower fibre cross-section (FCS) and lower fibre density and cross-section (FDC) in the posterior corpus callosum and its tapetal fibres, compared to controls. Higher FDC in the chemotherapy subgroup and higher FCS in the whole study group were observed in the anterior thalamic radiations. None of the psycho-behavioural parameters correlated significantly with any of the brain differences in the study group or chemotherapy subgroup.

INTERPRETATION

Prenatal exposure to maternal cancer and its treatment might affect local grey and white matter structure, but not functional connectivity or global organization. While platinum-based therapy was identified as a potential risk factor, this was not the case for chemotherapy in general.

FUNDING

This project has received funding from the European Union's Horizon 2020 research and innovation program (European Research council, grant no 647,047), the Foundation against cancer (Stichting tegen kanker, grant no. 2014-152) and the Research Foundation Flanders (FWO, grants no. 11B9919N, 12ZV420N).

The Role of Social Reward and Corticostriatal Connectivity in Substance Use

This report describes an ongoing R03 grant that explores the links between trait reward sensitivity, substance use, and neural responses to social and nonsocial reward. Although previous research has shown that trait reward sensitivity and neural responses to reward are linked to substance use, whether this relationship is impacted by how people process social stimuli remains unclear. We are investigating these questions via a neuroimaging study with college-aged participants, using individual difference measures that examine the relation between substance use, social context, and trait reward sensitivity with tasks that measure reward anticipation, strategic behavior, social reward consumption, and the influence of social context on reward processing. We predict that substance use will be tied to distinct patterns of striatal dysfunction. Specifically, reward hyposensitive individuals will exhibit blunted striatal responses to social and non-social reward and enhanced connectivity with the orbitofrontal cortex; in contrast, reward hypersensitive individuals will exhibit enhanced striatal responses to social and non-social reward and blunted connectivity with the orbitofrontal cortex. We also will examine the relation between self-reported reward sensitivity, substance use, and striatal responses to social reward and social context. We predict that individuals reporting the highest levels of substance use will show exaggerated striatal responses to social reward and social context, independent of self-reported reward sensitivity. Examining corticostriatal responses to reward processing will help characterize the relation between reward sensitivity, social context and substance use while providing a foundation for understanding risk factors and isolating neurocognitive mechanisms that may be targeted to increase the efficacy of interventions.

Challenges and future directions for representations of functional brain organization

A key principle of brain organization is the functional integration of brain regions into interconnected networks. Functional MRI scans acquired at rest offer insights into functional integration via patterns of coherent fluctuations in spontaneous activity, known as functional connectivity. These patterns have been studied intensively and have been linked to cognition and disease. However, the field is fractionated. Diverging analysis approaches have segregated the community into research silos, limiting the replication and clinical translation of findings. A primary source of this fractionation is the diversity of approaches used to reduce complex brain data into a lower-dimensional set of features for analysis and interpretation, which we refer to as brain representations. In this Primer, we provide an overview of different brain representations, lay out the challenges that have led to the fractionation of the field and that continue to form obstacles for convergence, and propose concrete guidelines to unite the field.

Subjective value and decision entropy are jointly encoded by aligned gradients across the human brain

Recent work has considered the relationship between value and confidence in both behavioural and neural representation. Here we evaluated whether the brain organises value and confidence signals in a systematic fashion that reflects the overall desirability of options. If so, regions that respond to either increases or decreases in both value and confidence should be widespread. We strongly confirmed these predictions through a model-based fMRI analysis of a mixed gambles task that assessed subjective value (SV) and inverse decision entropy (iDE), which is related to confidence. Purported value areas more strongly signalled iDE than SV, underscoring how intertwined value and confidence are. A gradient tied to the desirability of actions transitioned from positive SV and iDE in ventromedial prefrontal cortex to negative SV and iDE in dorsal medial prefrontal cortex. This alignment of SV and iDE signals could support retrospective evaluation to guide learning and subsequent decisions.

Edge-centric functional network representations of human cerebral cortex reveal overlapping system-level architecture

Network neuroscience has relied on a node-centric network model in which cells, populations and regions are linked to one another via anatomical or functional connections. This model cannot account for interactions of edges with one another. In this study, we developed an edge-centric network model that generates constructs 'edge time series' and 'edge functional connectivity' (eFC). Using network analysis, we show that, at rest, eFC is consistent across datasets and reproducible within the same individual over multiple scan sessions. We demonstrate that clustering eFC yields communities of edges that naturally divide the brain into overlapping clusters, with regions in sensorimotor and attentional networks exhibiting the greatest levels of overlap. We show that eFC is systematically modulated by variation in sensory input. In future work, the edge-centric approach could be useful for identifying novel biomarkers of disease, characterizing individual variation and mapping the architecture of highly resolved neural circuits.

A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis

Mastering the "arcana of neuroimaging analysis", the obscure knowledge required to apply an appropriate combination of software tools and parameters to analyse a given neuroimaging dataset, is a time consuming process. Therefore, it is not typically feasible to invest the additional effort required generalise workflow implementations to accommodate for the various acquisition parameters, data storage conventions and computing environments in use at different research sites, limiting the reusability of published workflows. We present a novel software framework, Abstraction of Repository-Centric ANAlysis (Arcana), which enables the development of complex, "end-to-end" workflows that are adaptable to new analyses and portable to a wide range of computing infrastructures. Analysis templates for specific image types (e.g. MRI contrast) are implemented as Python classes, which define a range of potential derivatives and analysis methods. Arcana retrieves data from imaging repositories, which can be BIDS datasets, XNAT instances or plain directories, and stores selected derivatives and associated provenance back into a repository for reuse by subsequent analyses. Workflows are constructed using Nipype and can be executed on local workstations or in high performance computing environments. Generic analysis methods can be consolidated within common base classes to facilitate code-reuse and collaborative development, which can be specialised for study-specific requirements via class inheritance. Arcana provides a framework in which to develop unified neuroimaging workflows that can be reused across a wide range of research studies and sites.

Intrinsic Connectivity Changes Mediate the Beneficial Effect of Cardiovascular Exercise on Sustained Visual Attention

Cardiovascular exercise (CE) is an evidence-based healthy lifestyle strategy. Yet, little is known about its effects on brain and cognition in young adults. Furthermore, evidence supporting a causal path linking CE to human cognitive performance via neuroplasticity is currently lacking. To understand the brain networks that mediate the CE-cognition relationship, we conducted a longitudinal, controlled trial with healthy human participants to compare the effects of a 2-week CE intervention against a non-CE control group on cognitive performance. Concomitantly, we used structural and functional magnetic resonance imaging to investigate the neural mechanisms mediating between CE and cognition. On the behavioral level, we found that CE improved sustained attention, but not processing speed or short-term memory. Using graph theoretical measures and statistical mediation analysis, we found that a localized increase in eigenvector centrality in the left middle frontal gyrus, probably reflecting changes within an attention-related network, conveyed the effect of CE on cognition. Finally, we found CE-induced changes in white matter microstructure that correlated with intrinsic connectivity changes (intermodal correlation). These results suggest that CE is a promising intervention strategy to improve sustained attention via brain plasticity in young, healthy adults.

Unraveling the Consequences of Childhood Maltreatment: Deviations From Typical Functional Neurodevelopment Mediate the Relationship Between Maltreatment History and Depressive Symptoms

BACKGROUND

Childhood maltreatment is associated with lifelong psychiatric sequelae. However, our understanding of neurobiological mechanisms responsible for this association is limited. Childhood maltreatment may confer risk for psychopathology by altering neurodevelopmental trajectories during childhood and adolescence. Longitudinal research, which is essential for examining this question, has been limited.

METHODS

We investigated maltreatment-associated alterations in the development of neural circuitry. Associations between cumulative childhood maltreatment (assessed using a dimensional measure of abuse and neglect via the Childhood Trauma Questionnaire) and the longitudinal development of resting-state functional connectivity (rsFC) were examined in 130 community-residing adolescents. Functional magnetic resonance imaging data were acquired at age 16 (T1; mean ± SD age, 16.46 ± 0.52 years; 66 females) and age 19 (T2; mean follow-up period, 2.35 years; n = 90 with functional magnetic resonance imaging data at both time points).

RESULTS

We found maltreatment to be associated with widespread longitudinal increases in rsFC, primarily between default mode, dorsal attention, and frontoparietal systems. We also found sex-dependent increased maltreatment-associated rsFC in male participants in salience and limbic circuits. Cross-sectional analyses revealed a shift in maltreatment-related rsFC alterations, which were localized to subcortical and sensory circuits at T1 and to frontal circuits at T2. Finally, longitudinal increases in rsFC connectivity mediated the relationship between childhood maltreatment and increased depressive symptoms.

CONCLUSIONS

To our knowledge, this is the first study to examine longitudinal maltreatment-related alterations in rsFC in adolescents. Our findings shed light on the neurodevelopmental consequences of childhood maltreatment and provide evidence for their role in risk for depression.

Movie viewing elicits rich and reliable brain state dynamics

Adaptive brain function requires that sensory impressions of the social and natural milieu are dynamically incorporated into intrinsic brain activity. While dynamic switches between brain states have been well characterised in resting state acquisitions, the remodelling of these state transitions by engagement in naturalistic stimuli remains poorly understood. Here, we show that the temporal dynamics of brain states, as measured in fMRI, are reshaped from predominantly bistable transitions between two relatively indistinct states at rest, toward a sequence of well-defined functional states during movie viewing whose transitions are temporally aligned to specific features of the movie. The expression of these brain states covaries with different physiological states and reflects subjectively rated engagement in the movie. In sum, a data-driven decoding of brain states reveals the distinct reshaping of functional network expression and reliable state transitions that accompany the switch from resting state to perceptual immersion in an ecologically valid sensory experience.