scholarly journals Desikan-Killiany-Tourville Atlas Compatible Version of M-CRIB Neonatal Parcellated Whole Brain Atlas: The M-CRIB 2.0

2018 ◽  
Author(s):  
Bonnie Alexander ◽  
Wai Yen Loh ◽  
Lillian G. Matthews ◽  
Andrea L. Murray ◽  
Chris Adamson ◽  
...  
Keyword(s):  
Brain Regions ◽  
Brain Atlas ◽  
Whole Brain ◽  
Brain Structure And Function ◽  
Postmenstrual Age ◽  
Mri Scans ◽  
Subcortical Regions ◽  
Cortical Regions ◽  
And Function ◽  
Ventral Diencephalon

AbstractOur recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: a) compatibility with this adult cortical atlas, b) greater labelling accuracy due to clearer landmarks, and c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for ten healthy neonates (postmenstrual age at MRI 40-43 weeks, 4 female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and ‘Banks STS’, and modification of boundaries of many other regions. Changes to subcortical regions included the addition of ‘ventral diencephalon’, and deletion of ‘subcortical matter’ labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labelled cortical data and FreeSurfer-labelled subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.

scholarly journals Cortex-wide neural interfacing via transparent polymer skulls

2018 ◽  
Author(s):  
Leila Ghanbari ◽  
Russell E. Carter ◽  
Matthew L. Rynes ◽  
Judith Dominguez ◽  
Gang Chen ◽  
...  
Keyword(s):  
Neural Activity ◽  
Brain Regions ◽  
Two Photon ◽  
Neural Activities ◽  
Neural Computations ◽  
Brain Structure And Function ◽  
Cortical Regions ◽  
And Function ◽  
Subcellular Resolution

ABSTRACTNeural computations occurring simultaneously in multiple cerebral cortical regions are critical for mediating cognition, perception and sensorimotor behaviors. Enormous progress has been made in understanding how neural activity in specific cortical regions contributes to behavior. However, there is a lack of tools that allow simultaneous monitoring and perturbing neural activity from multiple cortical regions. To fill this need, we have engineered “See-Shells” – digitally designed, morphologically realistic, transparent polymer skulls that allow long-term (>200 days) optical access to 45 mm2 of the dorsal cerebral cortex in the mouse. We demonstrate the ability to perform mesoscopic imaging, as well as cellular and subcellular resolution two-photon imaging of neural structures up to 600 µm through the See-Shells. See-Shells implanted on transgenic mice expressing genetically encoded calcium (Ca2+) indicators allow tracking of neural activities from multiple, non-contiguous regions spread across millimeters of the cortex. Further, neural probes can access the brain through perforated See-Shells, either for perturbing or recording neural activity from localized brain regions simultaneously with whole cortex imaging. As See-Shells can be constructed using readily available desktop fabrication tools and modified to fit a range of skull geometries, they provide a powerful tool for investigating brain structure and function.

scholarly journals Fronto-striatal atrophy correlates of neuropsychiatric dysfunction in frontotemporal dementia (FTD) and Alzheimer's disease (AD)

2013 ◽  
Vol 7 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Dong Seok Yi ◽  
Maxime Bertoux ◽  
Eneida Mioshi ◽  
John R. Hodges ◽  
Michael Hornberger
Keyword(s):  
Frontotemporal Dementia ◽  
Rating Scale ◽  
Brain Regions ◽  
Abnormal Behaviour ◽  
Behavioural Symptoms ◽  
Visual Rating ◽  
Prefrontal Cortical ◽  
Mri Scans ◽  
Visual Rating Scale ◽  
Cortical Regions

ABSTRACT Behavioural disturbances in frontotemporal dementia (FTD) are thought to reflect mainly atrophy of cortical regions. Recent studies suggest that subcortical brain regions, in particular the striatum, are also significantly affected and this pathology might play a role in the generation of behavioural symptoms. Objective: To investigate prefrontal cortical and striatal atrophy contributions to behavioural symptoms in FTD. Methods: One hundred and eighty-two participants (87 FTD patients, 39 AD patients and 56 controls) were included. Behavioural profiles were established using the Cambridge Behavioural Inventory Revised (CBI-R) and Frontal System Behaviour Scale (FrSBe). Atrophy in prefrontal (VMPFC, DLPFC) and striatal (caudate, putamen) regions was established via a 5-point visual rating scale of the MRI scans. Behavioural scores were correlated with atrophy rating scores. Results: Behavioural and atrophy ratings demonstrated that patients were significantly impaired compared to controls, with bvFTD being most severely affected. Behavioural-anatomical correlations revealed that VMPFC atrophy was closely related to abnormal behaviour and motivation disturbances. Stereotypical behaviours were associated with both VMPFC and striatal atrophy. By contrast, disturbance of eating was found to be related to striatal atrophy only. Conclusion: Frontal and striatal atrophy contributed to the behavioural disturbances seen in FTD, with some behaviours related to frontal, striatal or combined fronto-striatal pathology. Consideration of striatal contributions to the generation of behavioural disturbances should be taken into account when assessing patients with potential FTD.

Olfactory Loss and Regain: Lessons for Neuroplasticity

2017 ◽  
Vol 24 (1) ◽  
pp. 22-35 ◽  
Author(s):  
Johanna L. Reichert ◽  
Veronika Schöpf
Keyword(s):  
Structural Changes ◽  
Brain Regions ◽  
Sensory Loss ◽  
Trigeminal System ◽  
Olfactory Loss ◽  
Brain Structure And Function ◽  
Olfactory Sense ◽  
Neuronal Reorganization ◽  
Functional Neuroplasticity ◽  
And Function

For the visual and auditory senses, an array of studies has reported on neuronal reorganization processes after sensory loss. In contrast to this, neuroplasticity has been investigated only scarcely after loss of the olfactory sense. The present review focuses on the current extent of literature on structural and functional neuroplasticity effects after loss, with a focus on magnetic resonance imaging–based studies. We also include findings on the regain of the olfactory sense, for example after successful olfactory training. Existing studies indicate that widespread structural changes beyond the level of the olfactory bulb occur in the brain after loss of the olfactory sense. Moreover, on a functional level, loss of olfactory input not only entails changes in olfaction-related brain regions but also in the trigeminal system. Existing evidence should be strengthened by future longitudinal studies, a more thorough investigation of the neuronal consequences of congenital anosmia, and the application of state-of-the-art neuroimaging methods, such as connectivity analyses and joint analyses of brain structure and function.

scholarly journals Whole-brain connectivity atlas of glutamatergic and GABAergic neurons in the mouse dorsal and median raphe nuclei

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Zhengchao Xu ◽  
Zhao Feng ◽  
Mengting Zhao ◽  
Qingtao Sun ◽  
Lei Deng ◽  
...  
Keyword(s):  
Brain Regions ◽  
Gabaergic Neurons ◽  
Raphe Nucleus ◽  
Raphe Nuclei ◽  
Brain Atlas ◽  
Median Raphe ◽  
Whole Brain ◽  
Lateral Habenula ◽  
Raphé Nuclei ◽  
Median Raphé

The dorsal raphe nucleus (DR) and median raphe nucleus (MR) contain populations of glutamatergic and GABAergic neurons that regulate diverse behavioral functions. However, their whole-brain input-output circuits remain incompletely elucidated. We used viral tracing combined with fluorescence micro-optical sectioning tomography to generate a comprehensive whole-brain atlas of inputs and outputs of glutamatergic and GABAergic neurons in the DR and MR. We found that these neurons received inputs from similar upstream brain regions. The glutamatergic and GABAergic neurons in the same raphe nucleus had divergent projection patterns with differences in critical brain regions. Specifically, MR glutamatergic neurons projected to the lateral habenula through multiple pathways. Correlation and cluster analysis revealed that glutamatergic and GABAergic neurons in the same raphe nucleus received heterogeneous inputs and sent different collateral projections. This connectivity atlas further elucidates the anatomical architecture of the raphe nuclei, which could facilitate better understanding of their behavioral functions.

scholarly journals Statistical testing and annotation of gene transcriptomic-neuroimaging associations

2021 ◽  
Author(s):  
Yongbin Wei ◽  
Siemon C. de Lange ◽  
Rory Pijnenburg ◽  
Lianne H. Scholtens ◽  
Dirk Jan Ardesch ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Null Model ◽  
Brain Regions ◽  
Null Models ◽  
Statistical Testing ◽  
Web Based ◽  
Transcriptomic Data ◽  
Brain Structure And Function ◽  
Health And Disease ◽  
And Function

AbstractMultiscale integration of neuroimaging and gene transcriptome is becoming a widely used approach for exploring the molecular pathways of brain structure and function, in health and disease. Statistical testing of associations between spatial patterns of imaging-based phenotypic and transcriptomic data is key in these explorations, in particular establishing that observed associations exceed ‘chance level’ of random, non-specific observations. We discuss options for such statistical evaluations, including commonly applied linear regression, null model based on randomized brain regions that maintain spatial relationships, and null models built upon random effects that occur from other genes. Using examples and simulations of analyses as commonly performed in literature, we explain the caveats of these statistical models and provide guidelines for using proper models to evaluate both spatial and gene specificity. The null models are presented in a web-based application called GAMBA (“Gene Annotation using Macroscale Brain-imaging Association”) that is designed for exploring transcriptomic-neuroimaging associations.

Neurocircuitry of Affective, Cognitive, and Regulatory Systems

2018 ◽  
Author(s):  
Annmarie MacNamara ◽  
K. Luan Phan
Keyword(s):  
Cognitive Processes ◽  
Brain Regions ◽  
Cognition And Emotion ◽  
Functional Perspective ◽  
Regulatory Systems ◽  
Affect And Cognition ◽  
Subcortical Regions ◽  
Response Output ◽  
And Function ◽  
Regulatory Functions

This chapter provides a review and synthesis of the neurocircuitry involved in affect and cognition and their interactions as it relates to regulatory functions. Cognition and emotion are considered together taking a more integrated, functional perspective. The chapter first gives an overview regarding structure and function of key brain regions, that is, prefrontal and cingulate regions, insula, and subcortical regions, as well as other temporal-parietal-occipital regions. Following this overview, the chapter proceeds with summarizing key neuroscientific findings as organized by cognitive processes and their relevance for emotion. The choice of processes reflects the key stages involved in responding to a stimulus, from the time of sensory input to behavioral response/output, namely perception, learning and memory central executive functions, cognitive appraisal, and reappraisal. The overall aim of the chapter is to provide a better understanding of cognitive-emotional interactions at the neurocircuit level.

scholarly journals Gradients of structure–function tethering across neocortex

2019 ◽  
Vol 116 (42) ◽  
pp. 21219-21227 ◽  
Author(s):  
Bertha Vázquez-Rodríguez ◽  
Laura E. Suárez ◽  
Ross D. Markello ◽  
Golia Shafiei ◽  
Casey Paquola ◽  
...  
Keyword(s):  
Structure Function ◽  
Present Report ◽  
Brain Regions ◽  
Structure And Function ◽  
Spatial Proximity ◽  
Functional Networks ◽  
Functional Connection ◽  
Brain Structure And Function ◽  
And Function ◽  
The Brain

The white matter architecture of the brain imparts a distinct signature on neuronal coactivation patterns. Interregional projections promote synchrony among distant neuronal populations, giving rise to richly patterned functional networks. A variety of statistical, communication, and biophysical models have been proposed to study the relationship between brain structure and function, but the link is not yet known. In the present report we seek to relate the structural and functional connection profiles of individual brain areas. We apply a simple multilinear model that incorporates information about spatial proximity, routing, and diffusion between brain regions to predict their functional connectivity. We find that structure–function relationships vary markedly across the neocortex. Structure and function correspond closely in unimodal, primary sensory, and motor regions, but diverge in transmodal cortex, particularly the default mode and salience networks. The divergence between structure and function systematically follows functional and cytoarchitectonic hierarchies. Altogether, the present results demonstrate that structural and functional networks do not align uniformly across the brain, but gradually uncouple in higher-order polysensory areas.

The Application of the Rorschach Inkblot Test in the Study of Neural and Cognitive Aging

2020 ◽  
Vol 41 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Eamonn Arble ◽  
Steven W. Steinert ◽  
Ana M. Daugherty
Keyword(s):  
Cognitive Function ◽  
Cognitive Aging ◽  
Mirror Neuron ◽  
Present Review ◽  
Age Related ◽  
Brain Structure And Function ◽  
Rorschach Inkblot Test ◽  
Cortical Regions ◽  
Inkblot Test ◽  
And Function

Abstract. The Rorschach Inkblot test has been adopted and adapted by many researchers to assess and predict different aspects of human experience and cognitive performance. The present review examines research that incorporates the Rorschach to evaluate neural and cognitive aging as well as decline in age-related disease. Specifically, differences in amygdala and cortical regions, as well as mirror neuron and asymmetrical hemisphere activity that correlate with specific responses to Rorschach stimuli are discussed in the context of typical changes in brain structure and function in the course of aging. In addition, the present review provides a proposed framework for expanding the use of the Rorschach to evaluate other domains of neural and cognitive function. The authors conclude that, despite a need for increased research, the Rorschach is a viable measure to evaluate certain aspects of cognitive function and decline throughout the lifespan.

scholarly journals Current understanding of cortical structure and function in migraine

Cephalalgia ◽  
2019 ◽  
Vol 39 (13) ◽  
pp. 1683-1699 ◽  
Author(s):  
Else A Tolner ◽  
Shih-Pin Chen ◽  
Katharina Eikermann-Haerter
Keyword(s):  
Structure And Function ◽  
Dynamic Interactions ◽  
Therapeutic Implications ◽  
Functional Changes ◽  
Cortical Structure ◽  
Modifying Factors ◽  
Subcortical Regions ◽  
Underlying Mechanisms ◽  
Cortical Regions ◽  
And Function

Objective To review and discuss the literature on the role of cortical structure and function in migraine. Discussion Structural and functional findings suggest that changes in cortical morphology and function contribute to migraine susceptibility by modulating dynamic interactions across cortical and subcortical networks. The involvement of the cortex in migraine is well established for the aura phase with the underlying phenomenon of cortical spreading depolarization, while increasing evidence suggests an important role for the cortex in perception of head pain and associated sensations. As part of trigeminovascular pain and sensory processing networks, cortical dysfunction is likely to also affect initiation of attacks. Conclusion Morphological and functional changes identified across cortical regions are likely to contribute to initiation, cyclic recurrence and chronification of migraine. Future studies are needed to address underlying mechanisms, including interactions between cortical and subcortical regions and effects of internal (e.g. genetics, gender) and external (e.g. sensory inputs, stress) modifying factors, as well as possible clinical and therapeutic implications.

scholarly journals Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ben D. Fulcher ◽  
Aurina Arnatkeviciute ◽  
Alex Fornito
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Brain Atlas ◽  
Positive Bias ◽  
Spatially Resolved ◽  
Brain Structure And Function ◽  
And Function ◽  
Gene Category

AbstractTranscriptomic atlases have improved our understanding of the correlations between gene-expression patterns and spatially varying properties of brain structure and function. Gene-category enrichment analysis (GCEA) is a common method to identify functional gene categories that drive these associations, using gene-to-category annotation systems like the Gene Ontology (GO). Here, we show that applying standard GCEA methodology to spatial transcriptomic data is affected by substantial false-positive bias, with GO categories displaying an over 500-fold average inflation of false-positive associations with random neural phenotypes in mouse and human. The estimated false-positive rate of a GO category is associated with its rate of being reported as significantly enriched in the literature, suggesting that published reports are affected by this false-positive bias. We show that within-category gene–gene coexpression and spatial autocorrelation are key drivers of the false-positive bias and introduce flexible ensemble-based null models that can account for these effects, made available as a software toolbox.

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