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The brain atlas is essential for exploring the anatomical structure and function of the brain. Non-human primates, such as cynomolgus macaque, have received increasing attention due to their genetic similarity to humans. However, current macaque brain atlases only offer coarse sections with intervals along the coronal direction, failing to meet the needs of single-cell resolution studies in functional and multi-omics research of the macaque brain. To address this issue, we utilized fluorescence micro-optical sectioning tomography to obtain sub-micron resolution cytoarchitectonic images of the macaque brain at the sagittal plane. Based on the obtained 8000 image sequences, a reference brain atlas comprising 45 sagittal sections was created, delineating 270 brain regions other than the cortex. Additionally, a website was established to share the reference atlas corresponding image data. This study is expected to provide an essential dataset and tool for scientists studying the macaque brain. [ABSTRACT FROM AUTHOR]

Striatal hyperdopaminergia is implicated in the pathoetiology of schizophrenia, but how this relates to dopaminergic midbrain activity is unclear. Neuromelanin (NM)-sensitive magnetic resonance imaging provides a marker of long-term dopamine function. We examined whether midbrain NM-sensitive magnetic resonance imaging contrast-to-noise ratio (NM-CNR) was higher in people with schizophrenia than in healthy control (HC) participants and whether this correlated with dopamine synthesis capacity. One hundred fifty-four participants (schizophrenia group: n = 74, HC group: n = 80) underwent NM-sensitive magnetic resonance imaging of the substantia nigra and ventral tegmental area (SN-VTA). A subset of the schizophrenia group (n = 38) also received [18F]-DOPA positron emission tomography to measure dopamine synthesis capacity (K i cer) in the SN-VTA and striatum. SN-VTA NM-CNR was significantly higher in patients with schizophrenia than in HC participants (effect size = 0.38, p =.019). This effect was greatest for voxels in the medial and ventral SN-VTA. In patients, SN-VTA K i cer positively correlated with SN-VTA NM-CNR (r = 0.44, p =.005) and striatal K i cer (r = 0.71, p <.001). Voxelwise analysis demonstrated that SN-VTA NM-CNR was positively associated with striatal K i cer (r = 0.53, p =.005) and that this relationship seemed strongest between the ventral SN-VTA and associative striatum in schizophrenia. Our results suggest that NM levels are higher in patients with schizophrenia than in HC individuals, particularly in midbrain regions that project to parts of the striatum that receive innervation from the limbic and association cortices. The direct relationship between measures of NM and dopamine synthesis suggests that these aspects of schizophrenia pathophysiology are linked. Our findings highlight specific mesostriatal circuits as the loci of dopamine dysfunction in schizophrenia and thus as potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Humans exhibit complex mathematical skills attributed to the exceptional enlargement of neocortical regions throughout evolution. In the current work, we initiated a novel exploration of the ancient subcortical neural network essential for mathematical cognition. Using a neuropsychological approach, we report that degeneration of two subcortical structures, the cerebellum and basal ganglia, impairs performance in symbolic arithmetic. We identify distinct computational impairments in male and female participants with cerebellar degeneration (CD) or Parkinson's disease (PD). The CD group exhibited a disproportionate cost when the arithmetic sum increased, suggesting that the cerebellum is critical for iterative procedures required for calculations. The PD group showed a disproportionate cost for equations with increasing addends, suggesting that the basal ganglia are critical for chaining multiple operations. In Experiment 2, the two patient groups exhibited intact practice gains for repeated equations at odds with an alternative hypothesis that these impairments were related to memory retrieval. Notably, we discuss how the counting and chaining operations relate to cerebellar and basal ganglia function in other task domains (e.g., motor processes). Overall, we provide a novel perspective on how the cerebellum and basal ganglia contribute to symbolic arithmetic. Our studies demonstrate the constraints on the computational role of two subcortical regions in higher cognition. [ABSTRACT FROM AUTHOR]

Comorbidity has been frequently observed between generalized anxiety disorder (GAD) and major depressive disorder (MDD), however, common and distinguishable alterations in the topological organization of functional brain networks remain poorly understood. We sought to determine a robust and sensitive functional connectivity marker for diagnostic classification and symptom severity prediction. Multi-layered dynamic functional connectivity including whole brain, network-node and node-node layers via graph theory and gradient analyses were applied to functional MRI resting-state data obtained from 31 unmedicated GAD and 34 unmedicated MDD patients as well as 33 age and education matched healthy controls (HC). GAD and MDD symptoms were assessed using Penn State Worry Questionnaire and Beck Depression Inventory II, respectively. Three network measures including global properties (i.e., global efficiency, characteristic path length), regional nodal property (i.e., degree) and connectivity gradients were computed. Results showed that both patient groups exhibited abnormal dynamic cortico-subcortical topological organization compared to healthy controls, with MDD > GAD > HC in degree of randomization. Furthermore, our multi-layered dynamic functional connectivity network model reached 77% diagnostic accuracy between GAD and MDD and was highly predictive of symptom severity, respectively. Gradients of functional connectivity for superior frontal cortex-subcortical regions, middle temporal gyrus-subcortical regions and amygdala-cortical regions contributed more in this model compared to other gradients. We found shared and distinct cortico-subcortical connectivity features in dynamic functional brain networks between GAD and MDD, which together can promote the understanding of common and disorder-specific topological organization dysregulations and facilitate early neuroimaging-based diagnosis. • Both MDD and GAD showed abnormal multi-layered dynamic cortico-subcortical FC. • The degree of topological randomization demonstrated MDD > GAD > HC. • The SVM model with cortico-subcortical dFC metrics yielded the highest accuracy. • Abnormal dFC metrics significantly predicted the symptom severity of MDD and GAD. [ABSTRACT FROM AUTHOR]

A recent study by Peysakhovich and colleagues reveals how the superior colliculus (SC), a deep brain structure commonly associated with spatial orienting and motor control, causally contributes to the abstraction of visual categories. This highlights how subcortical areas with motor-control labels may have central roles in high-level visual cognition and opens avenues for investigation. [ABSTRACT FROM AUTHOR]

fMRI of the human brain reveals spatiotemporal patterns of functional connectivity (FC), forming distinct cortical networks. Lately, subcortical contributions to these configurations are receiving renewed interest, but investigations rarely focus explicitly on their effects on cortico-cortical FC. Here, we employ a straightforward multivariable approach and graph-theoretic tools to assess subcortical impact on topological features of cortical networks. Given recent evidence showing that structures like the thalamus and basal ganglia integrate input from multiple networks, we expect increased segregation between cortical networks after removal of subcortical effects on their FC patterns. We analyze resting state data of young and healthy participants (male and female; N = 100) from the human connectome project. We find that overall, the cortical network architecture becomes less segregated, and more integrated, when subcortical influences are accounted for. Underlying these global effects are the following trends: ‘Transmodal’ systems become more integrated with the rest of the network, while ‘unimodal’ networks show the opposite effect. For single nodes this hierarchical organization is reflected by a close correspondence with the spatial layout of the principal gradient of FC (Margulies et al., 2016). Lastly, we show that the limbic system is significantly less coherent with subcortical influences removed. The findings are validated in a (split-sample) replication dataset. Our results provide new insight regarding the interplay between subcortex and cortical networks, by putting the integrative impact of subcortex in the context of macroscale patterns of cortical organization.

Abstract Background There is emerging evidence that the neuroanatomy of autism forms a spectrum which extends into the general population. However, whilst several studies have identified cortical morphology correlates of autistic traits, it is not established whether morphological differences are present in the subcortical structures of the brain. Additionally, it is not clear to what extent previously reported structural associations may be confounded by co-occurring psychopathology. To address these questions, we utilised neuroimaging data from the Adolescent Brain Cognitive Development Study to assess whether a measure of autistic traits was associated with differences in child subcortical morphology, and if any observed differences persisted after adjustment for child internalising and externalising symptoms. Methods Our analyses included data from 7005 children aged 9–10 years (female: 47.19%) participating in the Adolescent Brain Cognitive Development Study. Autistic traits were assessed using scores from the Social Responsiveness Scale (SRS). Volumes of subcortical regions of interest were derived from structural magnetic resonance imaging data. Results Overall, we did not find strong evidence for an association of autistic traits with differences in subcortical morphology in this sample of school-aged children. Whilst lower absolute volumes of the nucleus accumbens and putamen were associated with higher scores of autistic traits, these differences did not persist once a global measure of brain size was accounted for. Limitations It is important to note that autistic traits were assessed using the SRS, of which higher scores are associated with general behavioural problems, and therefore may not be wholly indicative of autism-specific symptoms. In addition, individuals with a moderate or severe autism diagnosis were excluded from the ABCD study, and thus, the average level of autistic traits will be lower than in the general population which may bias findings towards the null. Conclusions These findings from our well-powered study suggest that other metrics of brain morphology, such as cortical morphology or shape-based phenotypes, may be stronger candidates to prioritise when attempting to identify robust neuromarkers of autistic traits.

Researchers often attribute higher cognition to the enlargement of cortical regions throughout evolution, reflecting the belief that humans sit at the top of the cognitive pyramid. Implicitly, this approach assumes that the subcortex is of secondary importance for higher-order cognition. While it is now recognized that subcortical regions can be involved in various cognitive domains, it remains unclear how they contribute to computations essential for higher-level cognitive processes such as endogenous attention and numerical cognition. Herein, we identify three models of subcortical–cortical relations in these cognitive processes: (i) subcortical regions are not involved in higher cognition; (ii) subcortical computations support elemental forms of higher cognition mainly in species without a developed cortex; and (iii) higher cognition depends on a whole-brain dynamic network, requiring integrated cortical and subcortical computations. Based on evolutionary theories and recent data, we propose the SEED hypothesis: the Subcortex is Essential for the Early Development of higher cognition. According to the five principles of the SEED hypothesis, subcortical computations are essential for the emergence of cognitive abilities that enable organisms to adapt to an ever-changing environment. We examine the implications of the SEED hypothesis from a multidisciplinary perspective to understand how the subcortex contributes to various forms of higher cognition. [ABSTRACT FROM AUTHOR]

Neuromodulatory nuclei that are part of the ascending arousal system (AAS) play a crucial role in regulating cortical state and optimizing task performance. Pupil diameter, under constant luminance conditions, is increasingly used as an index of activity of these AAS nuclei. Indeed, task-based functional imaging studies in humans have begun to provide evidence of stimulus-driven pupil-AAS coupling. However, whether there is such a tight pupil-AAS coupling during rest is not clear. To address this question, we examined simultaneously acquired resting-state fMRI and pupil-size data from 74 participants, focusing on six AAS nuclei: the locus coeruleus, ventral tegmental area, substantia nigra, dorsal and median raphe nuclei, and cholinergic basal forebrain. Activation in all six AAS nuclei was optimally correlated with pupil size at 0–2 s lags, suggesting that spontaneous pupil changes were almost immediately followed by corresponding BOLD-signal changes in the AAS. These results suggest that spontaneous changes in pupil size that occur during states of rest can be used as a noninvasive general index of activity in AAS nuclei. Importantly, the nature of pupil-AAS coupling during rest appears to be vastly different from the relatively slow canonical hemodynamic response function that has been used to characterize task-related pupil-AAS coupling.

Background: There is emerging evidence that the neuroanatomy of autism forms a spectrum which extends into the general population. However, whilst several studies have identified cortical morphology correlates of autistic traits, it is not established whether morphological differences are present in the subcortical structures of the brain. Additionally, it is not clear to what extent previously reported structural associations may be confounded by co-occurring psychopathology. To address these questions, we utilised neuroimaging data from the Adolescent Brain Cognitive Development Study to assess whether a measure of autistic traits was associated with differences in child subcortical morphology, and if any observed differences persisted after adjustment for child internalising and externalising symptoms. Methods: Our analyses included data from 7005 children aged 9–10 years (female: 47.19%) participating in the Adolescent Brain Cognitive Development Study. Autistic traits were assessed using scores from the Social Responsiveness Scale (SRS). Volumes of subcortical regions of interest were derived from structural magnetic resonance imaging data. Results: Overall, we did not find strong evidence for an association of autistic traits with differences in subcortical morphology in this sample of school-aged children. Whilst lower absolute volumes of the nucleus accumbens and putamen were associated with higher scores of autistic traits, these differences did not persist once a global measure of brain size was accounted for. Limitations: It is important to note that autistic traits were assessed using the SRS, of which higher scores are associated with general behavioural problems, and therefore may not be wholly indicative of autism-specific symptoms. In addition, individuals with a moderate or severe autism diagnosis were excluded from the ABCD study, and thus, the average level of autistic traits will be lower than in the general population which may bias findings towards the null. Conclusions: These findings from our well-powered study suggest that other metrics of brain morphology, such as cortical morphology or shape-based phenotypes, may be stronger candidates to prioritise when attempting to identify robust neuromarkers of autistic traits. [ABSTRACT FROM AUTHOR]

Background: We previously observed that patients with stroke complained of rhinitis symptoms that developed following the occurrence of stroke. Objectives: To investigate the relationship between chronic rhinitis (CR) and stroke. Methods: This retrospective study analyzed the medical records and questionnaires of patients with stroke who visited our outpatient clinic from June to December 2020. Stroke lesions were mainly classified as supratentorial, infratentorial, and supra/infratentorial lesions. Supratentorial lesions were further divided into cortex, subcortex, and mixed. Participants were screened for CR and were subsequently divided into the CR and non-CR groups. The Sino-Nasal Outcome Test questionnaire and a questionnaire on autonomic nervous system symptoms were administered to all patients. Results: Clinically evaluated indicators were not significantly different between the two groups. The number of patients with lesions in both the cortex and subcortex was significantly higher in the CR group than in the non-CR group. The risk of CR was higher in male patients with stroke than their female counterparts; additionally, the risk of CR was higher in patients with stroke who had both cortical and subcortical lesions, as well as autonomic dysfunction. Conclusions: Individuals with subcortical stroke damage had a greater probability of developing CR. The risk was increased in men, as compared with that in women, when autonomic symptoms were present. [ABSTRACT FROM AUTHOR]

Background and Motivation: Functional gradients have been used to study differences in connectivity between healthy and diseased brain states, however this work has largely focused on the cortex. Because the subcortex plays a key role in seizure initiation in temporal lobe epilepsy (TLE), subcortical functional-connectivity gradients may help further elucidate differences between healthy brains and TLE, as well as differences between left (L)-TLE and right (R)-TLE. Methods: In this work, we calculated subcortical functional-connectivity gradients (SFGs) from resting-state functional MRI (rs-fMRI) by measuring the similarity in connectivity profiles of subcortical voxels to cortical gray matter voxels. We performed this analysis in 24 R-TLE patients and 31 L-TLE patients (who were otherwise matched for age, gender, disease specific characteristics, and other clinical variables), and 16 controls. To measure differences in SFGs between L-TLE and R-TLE, we quantified deviations in the average functional gradient distributions, as well as their variance, across subcortical structures. Results: We found an expansion, measured by increased variance, in the principal SFG of TLE relative to controls. When comparing the gradient across subcortical structures between L-TLE and R-TLE, we found that abnormalities in the ipsilateral hippocampal gradient distributions were significantly different between L-TLE and R-TLE. Conclusion: Our results suggest that expansion of the SFG is characteristic of TLE. Subcortical functional gradient differences exist between left and right TLE and are driven by connectivity changes in the hippocampus ipsilateral to the seizure onset zone.

Recent progress in quantitative susceptibility mapping (QSM) has enabled the accurate delineation of submillimeter-scale subcortical brain structures in humans. However, the simultaneous visualization of cortical, subcortical, and white matter structure remains challenging, utilizing QSM data solely. Here we present TQ-SILiCON, a fusion method that enhances the contrast of cortex and subcortical structures and provides an excellent white matter delineation by combining QSM and conventional T1-weighted (T1w) images. In this study, we first applied QSM in the macaque monkey to map iron-rich subcortical structures. Implementing the same QSM acquisition and analysis methods allowed a similar accurate delineation of subcortical structures in humans. However, the QSM contrast of white and cortical gray matter was not sufficient for appropriate segmentation. Applying automatic brain tissue segmentation to TQ-SILiCON images of the macaque improved the classification of subcortical brain structures as compared to the single T1 contrast by maintaining an excellent white to cortical gray matter contrast. Furthermore, we validated our dual-contrast fusion approach in humans and similarly demonstrated improvements in automated segmentation of the cortex and subcortical structures. We believe the proposed contrast will facilitate translational studies in nonhuman primates to investigate the pathophysiology of neurodegenerative diseases that affect subcortical structures such as the basal ganglia in humans.

Quantitative MRI (qMRI) acquired at the ultra-high field of 7 Tesla has been used in visualizing and analyzing subcortical structures. qMRI relies on the acquisition of multiple images with different scan settings, leading to extended scanning times. Data redundancy and prior information from the relaxometry model can be exploited by deep learning to accelerate the imaging process. We propose the quantitative Recurrent Inference Machine (qRIM), with a unified forward model for joint reconstruction and R2*-mapping from sparse data, embedded in a Recurrent Inference Machine (RIM), an iterative inverse problem-solving network. To study the dependency of the proposed extension of the unified forward model to network architecture, we implemented and compared a quantitative End-to-End Variational Network (qE2EVN). Experiments were performed with high-resolution multi-echo gradient echo data of the brain at 7T of a cohort study covering the entire adult life span. The error in reconstructed R2* from undersampled data relative to reference data significantly decreased for the unified model compared to sequential image reconstruction and parameter fitting using the RIM. With increasing acceleration factor, an increasing reduction in the reconstruction error was observed, pointing to a larger benefit for sparser data. Qualitatively, this was following an observed reduction of image blurriness in R2*-maps. In contrast, when using the U-Net as network architecture, a negative bias in R2* in selected regions of interest was observed. Compressed Sensing rendered accurate, but less precise estimates of R2*. The qE2EVN showed slightly inferior reconstruction quality compared to the qRIM but better quality than the U-Net and Compressed Sensing. Subcortical maturation over age measured by a linearly increasing interquartile range of R2* in the striatum was preserved up to an acceleration factor of 9. With the integrated prior of the unified forward model, the proposed qRIM can exploit the redundancy among repeated measurements and shared information between tasks, facilitating relaxometry in accelerated MRI.

This paper reviews almost three decades of work on atlasing and segmentation methods for subcortical structures in human brain MRI. In writing this survey, we have three distinct aims. First, to document the evolution of digital subcortical atlases of the human brain, from the early MRI templates published in the nineties, to the complex multi-modal atlases at the subregion level that are available today. Second, to provide a detailed record of related efforts in the automated segmentation front, from earlier atlas-based methods to modern machine learning approaches. And third, to present a perspective on the future of high-resolution atlasing and segmentation of subcortical structures in in vivo human brain MRI, including open challenges and opportunities created by recent developments in machine learning.

Functional neuroimaging has become a widely used tool in obesity and eating disorder research to explore the alterations in neurobiology that underlie overeating and binge eating behaviors. Current and traditional neurobiological models underscore the importance of impairments in brain systems supporting reward, cognitive control, attention, and emotion regulation as primary drivers for overeating. Due to the technical limitations of standard field strength functional magnetic resonance imaging (fMRI) scanners, human neuroimaging research to date has focused largely on cortical and basal ganglia effects on appetitive behaviors. The present review draws on animal and human research to highlight how neural signaling encoding energy regulation, reward-learning, and habit formation converge on hypothalamic, brainstem, thalamic, and striatal regions to contribute to overeating in humans. We also consider the role of regions such as the mediodorsal thalamus, ventral striatum, lateral hypothalamus and locus coeruleus in supporting habit formation, inhibitory control of food craving, and attentional biases. Through these discussions, we present proposals on how the neurobiology underlying these processes could be examined using functional neuroimaging and highlight how ultra-high field 7-Tesla (7 T) fMRI may be leveraged to elucidate the potential functional alterations in subcortical networks. Focus is given to how interactions of these regions with peripheral endocannabinoids and neuropeptides, such as orexin, could be explored. Technical and methodological aspects regarding the use of ultra-high field 7 T fMRI to study eating behaviors are also reviewed. [ABSTRACT FROM AUTHOR]

A well‐documented amygdala‐dorsomedial prefrontal circuit is theorized to promote attention to threat ("threat vigilance"). Prior research has implicated a relationship between individual differences in trait anxiety/vigilance, engagement of this circuitry, and anxiogenic features of the environment (e.g., through threat‐of‐shock and movie‐watching). In the present study, we predicted that—for those scoring high in self‐reported anxiety and a behavioral measure of threat vigilance—this circuitry is chronically engaged, even in the absence of anxiogenic stimuli. Our analyses of resting‐state fMRI data (N = 639) did not, however, provide evidence for such a relationship. Nevertheless, in our planned exploratory analyses, we saw a relationship between threat vigilance behavior (but not self‐reported anxiety) and intrinsic amygdala‐periaqueductal gray connectivity. Here, we suggest this subcortical circuitry may be chronically engaged in hypervigilant individuals, but that amygdala‐prefrontal circuitry may only be engaged in response to anxiogenic stimuli. [ABSTRACT FROM AUTHOR]

Small world topologies are thought to provide a valuable insight into human brain organisation and consciousness. However, functional magnetic resonance imaging studies in consciousness have not yielded consistent results. Given the importance of dynamics for both consciousness and cognition, here we investigate how the diversity of small world dynamics (quantified by sample entropy; dSW-E11 dSW-E= dynamic small world entropy) scales with decreasing levels of awareness (i.e., sedation and disorders of consciousness). Paying particular attention to result reproducibility, we show that dSW-E is a consistent predictor of levels of awareness even when controlling for the underlying functional connectivity dynamics. We find that dSW-E of subcortical, and cortical areas are predictive, with the former showing higher and more robust effect sizes across analyses. We find that the network dynamics of intermodular communication in the cerebellum also have unique predictive power for levels of awareness. Consequently, we propose that the dynamic reorganisation of the functional information architecture, in particular of the subcortex, is a characteristic that emerges with awareness and has explanatory power beyond that of the complexity of dynamic functional connectivity.

Subcortical structures are a relative neurophysiological ‘terra incognita’ owing to their location within the skull. While perioperative subcortical sensing has been performed for more than 20 years, the neurophysiology of the basal ganglia in the home setting has remained almost unexplored. However, with the recent advent of implantable pulse generators (IPG) that are able to record neural activity, the opportunity to chronically record local field potentials (LFPs) directly from electrodes implanted for deep brain stimulation opens up. This allows for a breakthrough of chronic subcortical sensing into fundamental research and clinical practice. In this review an extensive overview of the current state of subcortical sensing is provided. The widespread potential of chronic subcortical sensing for investigational and clinical use is discussed. Finally, status and future perspectives of the most promising application of chronic subcortical sensing —i.e., adaptive deep brain stimulation (aDBS)— are discussed in the context of movement disorders. The development of aDBS based on both chronic subcortical and cortical sensing has the potential to dramatically change clinical practice and the life of patients with movement disorders. However, several barriers still stand in the way of clinical implementation. Advancements regarding IPG and lead technology, physiomarkers, and aDBS algorithms as well as harnessing artificial intelligence, multimodality and sensing in the naturalistic setting are needed to bring aDBS to clinical practice.

Researchers often attribute higher cognition to the enlargement of cortical regions throughout evolution, reflecting the belief that humans sit at the top of the cognitive pyramid. Implicitly, this approach assumes that the subcortex is of secondary importance for higher-order cognition. While it is now recognized that subcortical regions can be involved in various cognitive domains, it remains unclear how they contribute to computations essential for higher-level cognitive processes such as endogenous attention and numerical cognition. Herein, we identify three models of subcortical–cortical relations in these cognitive processes: (i) subcortical regions are not involved in higher cognition; (ii) subcortical computations support elemental forms of higher cognition mainly in species without a developed cortex; and (iii) higher cognition depends on a whole-brain dynamic network, requiring integrated cortical and subcortical computations. Based on evolutionary theories and recent data, we propose the SEED hypothesis: the Subcortex is Essential for the Early Development of higher cognition. According to the five principles of the SEED hypothesis, subcortical computations are essential for the emergence of cognitive abilities that enable organisms to adapt to an ever-changing environment. We examine the implications of the SEED hypothesis from a multidisciplinary perspective to understand how the subcortex contributes to various forms of higher cognition.

The promotion of recovery in patients who have entered a disorder of consciousness (DOC; e.g., coma or vegetative states) following severe brain injury remains an enduring medical challenge despite an ever-growing scientific understanding of these conditions. Indeed, recent work has consistently implicated altered cortical modulation by deep brain structures (e.g., the thalamus and the basal ganglia) following brain damage in the arising of, and recovery from, DOCs. The (re)emergence of low-intensity focused ultrasound (LIFU) neuromodulation may provide a means to selectively modulate the activity of deep brain structures noninvasively for the study and treatment of DOCs. This technique is unique in its combination of relatively high spatial precision and noninvasive implementation. Given the consistent implication of the thalamus in DOCs and prior results inducing behavioral recovery through invasive thalamic stimulation, here we applied ultrasound to the central thalamus in 11 acute DOC patients, measured behavioral responsiveness before and after sonication, and applied functional MRI during sonication. With respect to behavioral responsiveness, we observed significant recovery in the week following thalamic LIFU compared with baseline. With respect to functional imaging, we found decreased BOLD signals in the frontal cortex and basal ganglia during LIFU compared with baseline. In addition, we also found a relationship between altered connectivity of the sonicated thalamus and the degree of recovery observed post-LIFU. [ABSTRACT FROM AUTHOR]

Abstract Background There is no established pathogenesis of hemiparkinsonism-hemiatrophy syndrome (HPHA), and the varied clinical presentations have been reported in several case studies. To the best of our knowledge, the present report describes the first case of HPHA with unusual brain imaging findings. Case presentation A 20-year-old man presented with a 6-month history of weakness and clumsiness in his right limbs. He showed right-sided parkinsonism with dystonic hand posture; however, body asymmetry was not noted. Brain imaging revealed hemiatrophy of the left hemisphere subcortical structures and brainstem, and iron deposition in the left globus pallidus and substantia nigra. In addition, dopamine transporter imaging demonstrated normal presynaptic dopaminergic function. The patient was treated with levodopa, which had little to no effect. Conclusions This case demonstrates the unique imaging characteristics of HPHA associated with widespread brain hemiatrophy and iron deposition. Further studies are needed to elucidate the diagnostic criteria for this heterogeneous syndrome.

The human subcortex comprises hundreds of unique structures. Subcortical functioning is crucial for behavior, and disrupted function is observed in common neurodegenerative diseases. Despite their importance, human subcortical structures continue to be difficult to study in vivo. Here we provide a detailed account of 17 prominent subcortical structures and ventricles, describing their approximate iron and myelin contents, morphometry, and their age-related changes across the normal adult lifespan. The results provide compelling insights into the heterogeneity and intricate age-related alterations of these structures. They also show that the locations of many structures shift across the lifespan, which is of direct relevance for the use of standard magnetic resonance imaging atlases. The results further our understanding of subcortical morphometry and neuroimaging properties, and of normal aging processes which ultimately can improve our understanding of neurodegeneration.

Both cortical and subcortical regions can be functionally organized into networks. Regions of the basal ganglia are extensively interconnected with the cortex via reciprocal connections that relay and modulate cortical function. Here we employ an edge-centric approach, which computes co-fluctuations among region pairs in a network to investigate the role and interaction of subcortical regions with cortical systems. By clustering edges into communities, we show that cortical systems and subcortical regions couple via multiple edge communities, with hippocampus and amygdala having a distinct pattern from striatum and thalamus. We show that the edge community structure of cortical networks is highly similar to one obtained from cortical nodes when the subcortex is present in the network. Additionally, we show that the edge community profile of both cortical and subcortical nodes can be estimates solely from cortico-subcortical interactions. Finally, we used a motif analysis focusing on edge community triads where a subcortical region coupled to two cortical regions and found that two community triads where one community couples the subcortex to the cortex were overrepresented. In summary, our results show organized coupling of the subcortex to the cortex that may play a role in cortical organization of primary sensorimotor/attention and heteromodal systems and puts forth the motif analysis of edge community triads as a promising method for investigation of communication patterns in networks.

BackgroundCerebral microhemorrhages (CMH) are tiny deposits of blood degradation products in the brain and are pathological substrates of cerebral microbleeds. The existing CMH animal models are β-amyloid-, hypoxic brain injury-, or hypertension-induced. Recent evidence shows that CMH develop independently of hypoxic brain injury, hypertension, or amyloid deposition and CMH are associated with normal aging, sepsis, and neurodegenerative conditions. One common factor among the above pathologies is inflammation, and recent clinical studies show a link between systemic inflammation and CMH. Hence, we hypothesize that inflammation induces CMH development and thus, lipopolysaccharide (LPS)-induced CMH may be an appropriate model to study cerebral microbleeds.MethodsAdult C57BL/6 mice were injected with LPS (3 or 1 mg/kg, i.p.) or saline at 0, 6, and 24 h. At 2 or 7 days after the first injection, brains were harvested. Hematoxylin and eosin (H&E) and Prussian blue (PB) were used to stain fresh (acute) hemorrhages and hemosiderin (sub-acute) hemorrhages, respectively. Brain tissue ICAM-1, IgG, Iba1, and GFAP immunohistochemistry were used to examine endothelium activation, blood-brain barrier (BBB) disruption, and neuroinflammation. MRI and fluorescence microscopy were used to further confirm CMH development in this model.ResultsLPS-treated mice developed H&E-positive (at 2 days) and PB-positive (at 7 days) CMH. No surface and negligible H&E-positive CMH were observed in saline-treated mice (n = 12). LPS (3 mg/kg; n = 10) produced significantly higher number, size, and area of H&E-positive CMH at 2 days. LPS (1 mg/kg; n = 9) produced robust development of PB-positive CMH at 7 days, with significantly higher number and area compared with saline (n = 9)-treated mice. CMH showed the highest distribution in the cerebellum followed by the sub-cortex and cortex. LPS-induced CMH were predominantly adjacent to cerebral capillaries, and CMH load was associated with indices of brain endothelium activation, BBB disruption, and neuroinflammation. Fluorescence microscopy confirmed the extravasation of red blood cells into the brain parenchyma, and MRI demonstrated the presence of cerebral microbleeds.ConclusionsLPS produced rapid and robust development of H&E-positive (at 2 days) and PB-positive (at 7 days) CMH. The ease of development of both H&E- and PB-positive CMH makes the LPS-induced mouse model suitable to study inflammation-induced CMH.

Structural neuroimaging of humans with typical and atypical sex-chromosome complements has established the marked influence of both Yand X-/Y-chromosome dosage on total brain volume (TBV) and identified potential cortical substrates for the psychiatric phenotypes associated with sex-chromosome aneuploidy (SCA). Here, in a cohort of 354 humans with varying karyotypes (XX, XY, XXX, XXY, XYY, XXYY, XXXXY), we investigate sex and SCA effects on subcortical size and shape; focusing on the striatum, pallidum and thalamus. We find large effect-size differences in the volume and shape of all three structures as a function of sex and SCA. We correct for TBV effects with a novel allometric method harnessing normative scaling rules for subcortical size and shape in humans, which we derive here for the first time. We show that all three subcortical volumes scale sublinearly with TBV among healthy humans, mirroring known relationships between subcortical volume and TBV among species. Traditional TBV correction methods assume linear scaling and can therefore invert or exaggerate sex and SCA effects on subcortical anatomy. Allometric analysis restricts sex-differences to: (1) greater pallidal volume (PV) in males, and (2) relative caudate head expansion and ventral striatum contraction in females. Allometric analysis of SCA reveals that supernumerary X- and Y-chromosomes both cause disproportionate reductions in PV, and coordinated deformations of striatopallidal shape. Our study provides a novel understanding of sex and sex-chromosome dosage effects on subcortical organization, using an allometric approach that can be generalized to other basic and clinical structural neuroimaging settings.

• Prenatal activity shapes the newborn's ability to perceive face and gaze signals. • Perception of face identity, expression and gaze is highly context specific. • Race and culture represent contexts involving experience and social categorization. • Processing of face and gaze occurs in interacting subcortical and cortical pathways. • Processing of face and gaze involves a bottom-up and top-down flow of information. This review summarizes human perception and processing of face and gaze signals. Face and gaze signals are important means of non-verbal social communication. The review highlights that: (1) some evidence is available suggesting that the perception and processing of facial information starts in the prenatal period; (2) the perception and processing of face identity, expression and gaze direction is highly context specific, the effect of race and culture being a case in point. Culture affects by means of experiential shaping and social categorization the way in which information on face and gaze is collected and perceived; (3) face and gaze processing occurs in the so-called 'social brain'. Accumulating evidence suggests that the processing of facial identity, facial emotional expression and gaze involves two parallel and interacting pathways: a fast and crude subcortical route and a slower cortical pathway. The flow of information is bi-directional and includes bottom-up and top-down processing. The cortical networks particularly include the fusiform gyrus, superior temporal sulcus (STS), intraparietal sulcus, temporoparietal junction and medial prefrontal cortex. [ABSTRACT FROM AUTHOR]

The growing interest in the human subcortex is accompanied by an increasing number of parcellation procedures to identify deep brain structures in magnetic resonance imaging (MRI) contrasts. Manual procedures continue to form the gold standard for parcellating brain structures and is used for the validation of automated approaches. Performing manual parcellations is a tedious process which requires a systematic and reproducible approach. For this purpose, we created a series of protocols for the anatomical delineation of 21 individual subcortical structures. The intelligibility of the protocols was assessed by calculating Dice similarity coefficients for ten healthy volunteers. In addition, dilated Dice coefficients showed that manual parcellations created using these protocols can provide high-quality training data for automated algorithms. Here, we share the protocols, together with three example MRI datasets and the created manual delineations. The protocols can be applied to create high-quality training data for automated parcellation procedures, as well as for further validation of existing procedures and are shared without restrictions with the research community. [ABSTRACT FROM AUTHOR]

Background: Arousal and awareness are two important components of consciousness states. Functional neuroimaging has furthered our understanding of cortical and thalamocortical mechanisms of awareness. Investigating the relationship between subcortical functional connectivity and arousal has been challenging owing to the relatively small size of brainstem structures and thalamic nuclei, and their depth in the brain.Methods: Resting state functional MRI scans of 72 healthy volunteers were acquired before, during, 1 h after, and 1 day after sevoflurane general anaesthesia. Functional connectivity of subcortical regions of interest vs whole brain and homotopic functional connectivity for assessment of left-right symmetry analyses of both cortical and subcortical regions of interest were performed. Both analyses used high resolution atlases generated from deep brain stimulation applications.Results: Functional connectivity in subcortical loci within the thalamus and of the ascending reticular activating system was sharply restricted under anaesthesia, featuring a general lateralisation of connectivity. Similarly, left-right homology was sharply reduced under anaesthesia. Subcortical bilateral functional connectivity was not fully restored after emergence from anaesthesia, although greater restoration was seen between ascending reticular activating system loci and specific thalamic nuclei thought to be involved in promoting and maintaining arousal. Functional connectivity was fully restored to baseline by the following day.Conclusions: Functional connectivity in the subcortex is sharply restricted and lateralised under general anaesthesia. This restriction may play a part in loss and return of consciousness.Clinical Trial Registration: NCT02275026. [ABSTRACT FROM AUTHOR]

Hippocampal dysfunctions are a core feature of schizophrenia, but conflicting evidence exists whether volumetric and morphological changes are present in early-stage psychosis and to what extent these deficits are related to clinical trajectories. In this study, we recruited individuals at clinical high risk for psychosis (CHR-P) (n = 108), patients with a first episode of psychosis (FEP) (n = 37), healthy controls (HC) (n = 70) as well as a psychiatric control group with substance abuse and affective disorders (CHR-N: n = 38). MRI-data at baseline were obtained and volumetric as well as vertex analyses of the hippocampus were carried out. Moreover, volumetric changes were examined in the amygdala, caudate, nucleus accumbens, pallidum, putamen and thalamus. In addition, we obtained follow-up functional and symptomatic assessments in CHR-P individuals to examine the question whether anatomical deficits at baseline predicted clinical trajectories. Our results show that the hippocampus is the only structure showing significant volumetric decrease in early-stage psychosis, with FEPs showing significantly smaller hippocampal volumes bilaterally alongside widespread shape changes in the vertex analysis. For the CHR-P group, volumetric decreases were confined to the left hippocampus. However, hippocampal alterations in the CHR-P group were not robustly associated with clinical outcomes, including the persistence of attenuated psychotic symptoms and functional trajectories. Accordingly, our findings highlight that dysfunctions in hippocampal anatomy are an important feature of early-stage psychosis which may, however, not be related to clinical outcomes in CHR-P participants.

An increasing number of studies have found that a few, specific subcortical regions are involved in creative visual divergent thinking. In addition, creative thinking is heavily reliant on the fronto-striatal dopaminergic pathways. This study aimed to explore whether spontaneous fluctuations in the subcortex, which contribute to our creative abilities, showed significant differences between individuals with different levels of creativity based on resting-state functional magnetic resonance imaging data. We calculated subcortical regions' seed-wise and dynamic functional connectivity (dFC), and then examined the differences between the high and low visual creativity groups. Furthermore, the topological properties of the subcortical network were measured, and their relationship with creative visual divergent thinking was calculated using brain–behavior correlation analyses. The results showed that functional connectivity (FC) between the putamen, pallidum, and thalamus indicated group differences within the subcortex. Whole-brain FC results showed group differences across subcortical (i.e., the thalamus and pallidum) and cerebral regions (i.e., the insula, middle frontal gyrus, and middle temporal gyrus). In addition, subcortical FC demonstrated a positive correlation with visual divergent thinking scores across the pallidum, putamen, and thalamus. Our findings provide novel insights into the relationship between visual divergent thinking and the activities of the subcortex. It is likely that not only fronto-striatal dopaminergic pathways, but also "motor" pathways, are involved in creative visual divergent thinking processing. [ABSTRACT FROM AUTHOR]

Digitized neuroanatomical atlases that can be overlaid onto functional data are crucial for localizing brain structures and analyzing functional networks identified by neuroimaging techniques. To aid in functional and structural data analysis, we have created a comprehensive parcellation of the rhesus macaque subcortex using a high-resolution ex vivo structural imaging scan. This anatomical scan and its parcellation were warped to the updated NIMH Macaque Template (NMT v2), an in vivo population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM) with 210 primary regions-of-interest (ROIs). The subcortical parcellation and nomenclature reflect those of the 4th edition of the Rhesus Monkey Brain in Stereotaxic Coordinates (Paxinos et al., in preparation), rather than proposing yet another novel atlas. The primary ROIs are organized across six spatial hierarchical scales from small, fine-grained ROIs to broader composites of multiple ROIs, making the SARM suitable for analysis at different resolutions and allowing broader labeling of functional signals when more accurate localization is not possible. As an example application of this atlas, we have included a functional localizer for the dorsal lateral geniculate (DLG) nucleus in three macaques using a visual flickering checkerboard stimulus, identifying and quantifying significant fMRI activation in this atlas region. The SARM has been made openly available to the neuroimaging community and can easily be used with common MRI data processing software, such as AFNI, where the atlas has been embedded into the software alongside cortical macaque atlases.

Functional magnetic resonance imaging (fMRI) BOLD signal is commonly localized by using neuroanatomical atlases, which can also serve for region of interest analyses. Yet, the available MRI atlases have serious limitations when it comes to imaging subcortical structures: only 7% of the 455 subcortical nuclei are captured by current atlases. This highlights the general difficulty in mapping smaller nuclei deep in the brain, which can be addressed using ultra-high field 7 Tesla (T) MRI. The ventral tegmental area (VTA) is a subcortical structure that plays a pivotal role in reward processing, learning and memory. Despite the significant interest in this nucleus in cognitive neuroscience, there are currently no available, anatomically precise VTA atlases derived from 7 T MRI data that cover the full region of the VTA. Here, we first provide a protocol for multimodal VTA imaging and delineation. We then provide a data description of a probabilistic VTA atlas based on in vivo 7 T MRI data. [ABSTRACT FROM AUTHOR]

Characterizing changing brain structure in neurodegeneration is fundamental to understanding long-term effects of pathology and ultimately providing therapeutic targets. It is well established that Huntington's disease (HD) gene carriers undergo progressive brain changes during the course of disease, yet the long-term trajectory of cortical atrophy is not well defined. Given that genetic therapies currently tested in HD are primarily expected to target the cortex, understanding atrophy across this region is essential. Capitalizing on a unique longitudinal dataset with a minimum of 3 and maximum of 7 brain scans from 49 HD gene carriers and 49 age-matched control subjects, we implemented a novel dynamical systems approach to infer patterns of regional neurodegeneration over 10 years. We use Bayesian hierarchical modeling to map participant- and group-level trajectories of atrophy spatially and temporally, additionally relating atrophy to the genetic marker of HD (CAG-repeat length) and motor and cognitive symptoms. We show, for the first time, that neurodegenerative changes exhibit complex temporal dynamics with substantial regional variation around the point of clinical diagnosis. Although widespread group differences were seen across the cortex, the occipital and parietal regions undergo the greatest rate of cortical atrophy. We have established links between atrophy and genetic markers of HD while demonstrating that specific cortical changes predict decline in motor and cognitive performance. HD gene carriers display regional variability in the spatial pattern of cortical atrophy, which relates to genetic factors and motor and cognitive symptoms. Our findings indicate a complex pattern of neuronal loss, which enables greater characterization of HD progression. [ABSTRACT FROM AUTHOR]

Background: There is no established pathogenesis of hemiparkinsonism-hemiatrophy syndrome (HPHA), and the varied clinical presentations have been reported in several case studies. To the best of our knowledge, the present report describes the first case of HPHA with unusual brain imaging findings.Case Presentation: A 20-year-old man presented with a 6-month history of weakness and clumsiness in his right limbs. He showed right-sided parkinsonism with dystonic hand posture; however, body asymmetry was not noted. Brain imaging revealed hemiatrophy of the left hemisphere subcortical structures and brainstem, and iron deposition in the left globus pallidus and substantia nigra. In addition, dopamine transporter imaging demonstrated normal presynaptic dopaminergic function. The patient was treated with levodopa, which had little to no effect.Conclusions: This case demonstrates the unique imaging characteristics of HPHA associated with widespread brain hemiatrophy and iron deposition. Further studies are needed to elucidate the diagnostic criteria for this heterogeneous syndrome. [ABSTRACT FROM AUTHOR]

Background: The pathology of Parkinson's disease leads to morphological changes in brain structure. Currently, the progressive changes in gray matter volume that occur with time and are specific to patients with Parkinson's disease, compared to healthy controls, remain unclear. High-tesla magnetic resonance imaging might be useful in differentiating neurological disorders by brain cortical changes. Purpose: We aimed to investigate patterns in gray matter changes in patients with Parkinson's disease by using an automated segmentation method with 7-tesla magnetic resonance imaging. Material and Methods: High-resolution T1-weighted 7 tesla magnetic resonance imaging volumes of 24 hemispheres were acquired from 12 Parkinson's disease patients and 12 age- and sex-matched healthy controls with median ages of 64.5 (range, 41–82) years and 60.5 (range, 25–74) years, respectively. Subgroup analysis was performed according to whether axial motor symptoms were present in the Parkinson's disease patients. Cortical volume, cortical thickness, and subcortical volume were measured using a high-resolution image processing technique based on the Desikan-Killiany-Tourville atlas and an automated segmentation method (FreeSurfer version 6.0). Results: After cortical reconstruction, in 7 tesla magnetic resonance imaging volume segmental analysis, compared with the healthy controls, the Parkinson's disease patients showed global cortical atrophy, mostly in the prefrontal area (rostral middle frontal, superior frontal, inferior parietal lobule, medial orbitofrontal, rostral anterior cingulate area), and subcortical volume atrophy in limbic/paralimbic areas (fusiform, hippocampus, amygdala). Conclusion: We first demonstrated that 7 tesla magnetic resonance imaging detects structural abnormalities in Parkinson's disease patients compared to healthy controls using an automated segmentation method. Compared with the healthy controls, the Parkinson's disease patients showed global prefrontal cortical atrophy and hippocampal area atrophy. [ABSTRACT FROM AUTHOR]

The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain. Due to their small size and close proximity, up until now only 7% have been depicted in standard MRI atlases. Thus, the human subcortex can largely be considered as terra incognita. Here, we present a new open-source parcellation algorithm to automatically map the subcortex. The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla. It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset. In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.

Normative databases allow testing of novel hypotheses without the costly collection of magnetic resonance imaging (MRI) data. Here we present the Amsterdam Ultra-high field adult lifespan database (AHEAD). The AHEAD consists of 105 7 Tesla (T) whole-brain structural MRI scans tailored specifically to imaging of the human subcortex, including both male and female participants and covering the entire adult life span (18–80 yrs). We used these data to create probability maps for the subthalamic nucleus, substantia nigra, internal and external segment of the globus pallidus, and the red nucleus. Data was acquired at a submillimeter resolution using a multi-echo (ME) extension of the second gradient-echo image of the MP2RAGE sequence (MP2RAGEME) sequence, resulting in complete anatomical alignment of quantitative, R1-maps, R2*-maps, T1-maps, T1-weighted images, T2*-maps, and quantitative susceptibility mapping (QSM). Quantitative MRI maps, and derived probability maps of basal ganglia structures are freely available for further analyses.

Most fundamental cognitive processes rely on brain networks that include both cortical and subcortical structures. Studying such networks using functional magnetic resonance imaging (fMRI) requires a data acquisition protocol that provides blood-oxygenation-level dependent (BOLD) sensitivity across the entire brain. However, when using standard single echo, echo planar imaging protocols, researchers face a tradeoff between BOLD-sensitivity in cortex and in subcortical areas. Multi echo protocols avoid this tradeoff and can be used to optimize BOLD-sensitivity across the entire brain, at the cost of an increased repetition time. Here, we empirically compare the BOLD-sensitivity of a single echo protocol to a multi echo protocol. Both protocols were designed to meet the specific requirements for studying small, iron rich subcortical structures (including a relatively high spatial resolution and short echo times), while retaining coverage and BOLD-sensitivity in cortical areas. The results indicate that both sequences lead to similar BOLD-sensitivity across the brain at 7 ​T.

Objective: To identify the novel projections received by the cerebrospinal fluid (CSF)-contacting nucleus from the subcortex and limbic system to understand the biological functions of the nucleus.Methods: The cholera toxin subunit B (CB), a retrograde tracer, was injected into the CSF-contacting nucleus in Sprague–Dawley rats. After 7–10 days, the surviving rats were perfused, and the whole brain and spinal cord were sliced for CB immunofluorescence detection. The CB-positive neurons in the subcortex and limbic system were observed under a fluorescence microscope, followed by 3D reconstructed with the imaris software.Results: CB-positive neurons were found in the basal forebrain, septum, periventricular organs, preoptic area, and amygdaloid structures. Five functional areas including 46 sub-regions sent projections to the CSF-contacting nucleus. However, the projections had different densities, ranging from sparse to moderate, to dense.Conclusions: According to the projections from the subcortex and limbic system, we hypothesize that the CSF-contacting nucleus participates in emotion, cognition, homeostasis regulation, visceral activity, pain, and addiction. In this study, we illustrate the novel projections from the subcortex and limbic system to the CSF-contacting nucleus, which underlies the diverse and complicated circuits of the nucleus in body regulations.

The promotion of recovery in patients who have entered a disorder of consciousness (DOC; e.g., coma or vegetative states) following severe brain injury remains an enduring medical challenge despite an ever-growing scientific understanding of these conditions. Indeed, recent work has consistently implicated altered cortical modulation by deep brain structures (e.g., the thalamus and the basal ganglia) following brain damage in the arising of, and recovery from, DOCs. The (re)emergence of low-intensity focused ultrasound (LIFU) neuromodulation may provide a means to selectively modulate the activity of deep brain structures noninvasively for the study and treatment of DOCs. This technique is unique in its combination of relatively high spatial precision and noninvasive implementation. Given the consistent implication of the thalamus in DOCs and prior results inducing behavioral recovery through invasive thalamic stimulation, here we applied ultrasound to the central thalamus in 11 acute DOC patients, measured behavioral responsiveness before and after sonication, and applied functional MRI during sonication. With respect to behavioral responsiveness, we observed significant recovery in the week following thalamic LIFU compared with baseline. With respect to functional imaging, we found decreased BOLD signals in the frontal cortex and basal ganglia during LIFU compared with baseline. In addition, we also found a relationship between altered connectivity of the sonicated thalamus and the degree of recovery observed post-LIFU.

Understanding the similarity of cortico-subcortical networks topologies between humans and nonhuman primate species is critical to study the origin of network alternations underlying human neurologic and neuropsychiatric diseases. The New World common marmoset (Callithrix jacchus) has become popular as a nonhuman primate model for human brain function. Most marmoset connectomic research, however, has exclusively focused on cortical areas, with connectivity to subcortical networks less extensively explored. Here, we aimed to first isolate patterns of subcortical connectivity with cortical resting-state networks in awake marmosets using resting-state fMRI, then to compare these networks with those in humans using connectivity fingerprinting. In this study, we used 5 marmosets (4 males, 1 female). While we could match several marmoset and human resting-state networks based on their functional fingerprints, we also found a few striking differences, for example, strong functional connectivity of the default mode network with the superior colliculus in marmosets that was much weaker in humans. Together, these findings demonstrate that many of the core cortico-subcortical networks in humans are also present in marmosets, but that small, potentially functionally relevant differences exist. [ABSTRACT FROM AUTHOR]

Fast saccades are rapid automatic oculomotor responses to salient and ecologically important visual stimuli such as animals and faces. Discriminating the number of friends, foe, or prey may also have an evolutionary advantage. In this study, participants were asked to saccade rapidly towards the more numerous of two arrays. Participants could discriminate numerosities with high accuracy and great speed, as fast as 190 ms. Intermediate numerosities were more likely to elicit fast saccades than very low or very high numerosities. Reaction-times for vocal responses (collected in a separate experiment) were slower, did not depend on numerical range, and correlated only with the slow not the fast saccades, pointing to different systems. The short saccadic reaction-times we observe are surprising given that discrimination using numerosity estimation is thought to require a relatively complex neural circuit, with several relays of information through the parietal and prefrontal cortex. Our results suggest that fast numerosity-driven saccades may be generated on a single feed-forward pass of information recruiting a primitive system that cuts through the cortical hierarchy and rapidly transforms the numerosity information into a saccade command. [ABSTRACT FROM AUTHOR]

Most of the studies employing neuroimaging have focused on cortical and subcortical signals individually to obtain neurophysiological signatures of cognitive functions. However, understanding the dynamic communication between the cortex and subcortical structures is essential for unraveling the neural correlates of cognition. In this quest, magnetoencephalography (MEG) and electroencephalography (EEG) are the methods of choice because they are noninvasive electrophysiological recording techniques with high temporal resolution. Sophisticated MEG/EEG source estimation techniques and network analysis methods, developed recently, can provide a more comprehensive understanding of the neurophysiological mechanisms of fundamental cognitive processes. Used together with noninvasive modulation of cortical–subcortical communication, these approaches may open up new possibilities for expanding the repertoire of noninvasive cognitive neurotechnology. Advances in neuroimaging methods, combined with new brain magnetic sensors and neuromodulatory technology, open important new avenues for future research. Recent studies in brain electrophysiological imaging offer compelling evidence that, under favorable circumstances, localizing brain signals is possible, even from deep brain structures. Methodological and technological developments have opened new possibilities for comprehensive investigation of cortical–subcortical temporal dynamics. A cortical–subcortical integrative approach is essential for understanding human cognition and the mind–brain relationship. [ABSTRACT FROM AUTHOR]

Multimodal evidence suggests that brain regions accumulate information over timescales that vary according to anatomical hierarchy. Thus, these experimentally defined “temporal receptive windows” are longest in cortical regions that are distant from sensory input. Interestingly, spontaneous activity in these regions also plays out over relatively slow timescales (i.e., exhibits slower temporal autocorrelation decay). These findings raise the possibility that hierarchical timescales represent an intrinsic organizing principle of brain function. Here, using resting-state functional MRI, we show that the timescale of ongoing dynamics follows hierarchical spatial gradients throughout human cerebral cortex. These intrinsic timescale gradients give rise to systematic frequency differences among large-scale cortical networks and predict individual-specific features of functional connectivity. Whole-brain coverage permitted us to further investigate the large-scale organization of subcortical dynamics. We show that cortical timescale gradients are topographically mirrored in striatum, thalamus, and cerebellum. Finally, timescales in the hippocampus followed a posterior-to-anterior gradient, corresponding to the longitudinal axis of increasing representational scale. Thus, hierarchical dynamics emerge as a global organizing principle of mammalian brains. [ABSTRACT FROM AUTHOR]

Objective : To identify the novel projections received by the cerebrospinal fluid (CSF)-contacting nucleus from the subcortex and limbic system to understand the biological functions of the nucleus. Methods : The cholera toxin subunit B (CB), a retrograde tracer, was injected into the CSF-contacting nucleus in Sprague–Dawley rats. After 7–10 days, the surviving rats were perfused, and the whole brain and spinal cord were sliced for CB immunofluorescence detection. The CB-positive neurons in the subcortex and limbic system were observed under a fluorescence microscope, followed by 3D reconstructed with the imaris software. Results : CB-positive neurons were found in the basal forebrain, septum, periventricular organs, preoptic area, and amygdaloid structures. Five functional areas including 46 sub-regions sent projections to the CSF-contacting nucleus. However, the projections had different densities, ranging from sparse to moderate, to dense. Conclusions : According to the projections from the subcortex and limbic system, we hypothesize that the CSF-contacting nucleus participates in emotion, cognition, homeostasis regulation, visceral activity, pain, and addiction. In this study, we illustrate the novel projections from the subcortex and limbic system to the CSF-contacting nucleus, which underlies the diverse and complicated circuits of the nucleus in body regulations. [ABSTRACT FROM AUTHOR]

Autism spectrum disorder (ASD) is a common neurodevelopmental condition, and infant siblings of children with ASD are at a higher risk of developing autistic traits or an ASD diagnosis, when compared to those with typically developing siblings. Reports of differences in brain anatomy and function in high‐risk infants which predict later autistic behaviors are emerging, but although cerebellar and subcortical brain regions have been frequently implicated in ASD, no high‐risk study has examined these regions. Therefore, in this study, we compared regional MRI volumes across the whole brain in 4–6‐month‐old infants with (high‐risk, n = 24) and without (low‐risk, n = 26) a sibling with ASD. Within the high‐risk group, we also examined whether any regional differences observed were associated with autistic behaviors at 36 months. We found that high‐risk infants had significantly larger cerebellar and subcortical volumes at 4–6‐months of age, relative to low‐risk infants; and that larger volumes in high‐risk infants were linked to more repetitive behaviors at 36 months. Our preliminary observations require replication in longitudinal studies of larger samples. If correct, they suggest that the early subcortex and cerebellum volumes may be predictive biomarkers for childhood repetitive behaviors. Autism Res 2019, 12: 614–627. © 2019 The Authors. Autism Research published by International Society for Autism Research published byWiley Periodicals, Inc. Lay Summary: Individuals with a family history of autism spectrum disorder (ASD) are at risk of ASD and related developmental difficulties. This study revealed that 4–6‐month‐old infants at high‐risk of ASD have larger cerebellum and subcortical volumes than low‐risk infants, and that larger volumes in high‐risk infants are associated with more repetitive behaviors in childhood. [ABSTRACT FROM AUTHOR]

• Precise statistical control for subcortical effects on cortical connectivity. • Removal of subcortex significantly changes cortical network architecture. • Cortical topology becomes less segregated and more integrated overall. • Topography of change mirrors hierarchical organization of cortex. • Accounting for subcortical effects reduces integrity of the limbic system. fMRI of the human brain reveals spatiotemporal patterns of functional connectivity (FC), forming distinct cortical networks. Lately, subcortical contributions to these configurations are receiving renewed interest, but investigations rarely focus explicitly on their effects on cortico-cortical FC. Here, we employ a straightforward multivariable approach and graph-theoretic tools to assess subcortical impact on topological features of cortical networks. Given recent evidence showing that structures like the thalamus and basal ganglia integrate input from multiple networks, we expect increased segregation between cortical networks after removal of subcortical effects on their FC patterns. We analyze resting state data of young and healthy participants (male and female; N = 100) from the human connectome project. We find that overall, the cortical network architecture becomes less segregated, and more integrated, when subcortical influences are accounted for. Underlying these global effects are the following trends: 'Transmodal' systems become more integrated with the rest of the network, while 'unimodal' networks show the opposite effect. For single nodes this hierarchical organization is reflected by a close correspondence with the spatial layout of the principal gradient of FC (Margulies et al., 2016). Lastly, we show that the limbic system is significantly less coherent with subcortical influences removed. The findings are validated in a (split-sample) replication dataset. Our results provide new insight regarding the interplay between subcortex and cortical networks, by putting the integrative impact of subcortex in the context of macroscale patterns of cortical organization. [ABSTRACT FROM AUTHOR]