neuromaps: structural and functional interpretation of brain maps

Nature Methods, Год журнала: 2022, Номер 19(11), С. 1472 - 1479

Опубликована: Окт. 6, 2022

Abstract Imaging technologies are increasingly used to generate high-resolution reference maps of brain structure and function. Comparing experimentally generated these facilitates cross-disciplinary scientific discovery. Although recent data sharing initiatives increase the accessibility maps, often shared in disparate coordinate systems, precluding systematic accurate comparisons. Here we introduce neuromaps, a toolbox for accessing, transforming analyzing structural functional annotations. We implement functionalities generating high-quality transformations between four standard systems. The includes curated biological ontologies human brain, such as molecular, microstructural, electrophysiological, developmental ontologies. Robust quantitative assessment map-to-map similarity is enabled via suite spatial autocorrelation-preserving null models. neuromaps combines open-access with transparent functionality standardizing comparing providing workflow comprehensive annotation enrichment analysis brain.

Язык: Английский

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BrainStat: A toolbox for brain-wide statistics and multimodal feature associations

NeuroImage, Год журнала: 2022, Номер 266, С. 119807 - 119807

Опубликована: Дек. 10, 2022

Analysis and interpretation of neuroimaging datasets has become a multidisciplinary endeavor, relying not only on statistical methods, but increasingly associations with respect to other brain-derived features such as gene expression, histological data, functional well cognitive architectures. Here, we introduce BrainStat - toolbox for (i) univariate multivariate linear models in volumetric surface-based brain imaging datasets, (ii) multidomain feature association results spatial maps post-mortem expression histology, task-based fMRI meta-analysis, resting-state motifs across several common surface templates. The combination statistics into turnkey streamlines analytical processes accelerates cross-modal research. is implemented both Python MATLAB, two widely used programming languages the neuroinformatics communities. openly available complemented by an expandable documentation.

Язык: Английский

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Local molecular and global connectomic contributions to cross-disorder cortical abnormalities

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Авг. 10, 2022

Abstract Numerous brain disorders demonstrate structural abnormalities, which are thought to arise from molecular perturbations or connectome miswiring. The unique and shared contributions of these connectomic vulnerabilities remain unknown, has yet be studied in a single multi-disorder framework. Using MRI morphometry the ENIGMA consortium, we construct maps cortical abnormalities for thirteen neurodevelopmental, neurological, psychiatric N = 21,000 participants 26,000 controls, collected using harmonised processing protocol. We systematically compare multiple micro-architectural measures, including gene expression, neurotransmitter density, metabolism, myelination (molecular vulnerability), as well global measures number connections, centrality, connection diversity (connectomic vulnerability). find relationship between vulnerability white-matter architecture that drives disorder profiles. Local attributes, particularly receptor profiles, constitute best predictors both disorder-specific morphology cross-disorder similarity. Finally, consistently subtended by small subset network epicentres bilateral sensory-motor, inferior temporal lobe, precuneus, superior parietal cortex. Collectively, our results highlight how local attributes connectivity jointly shape abnormalities.

Язык: Английский

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Robust estimation of cortical similarity networks from brain MRI

Nature Neuroscience, Год журнала: 2023, Номер 26(8), С. 1461 - 1471

Опубликована: Июль 17, 2023

Abstract Structural similarity is a growing focus for magnetic resonance imaging (MRI) of connectomes. Here we propose Morphometric INverse Divergence (MIND), new method to estimate within-subject between cortical areas based on the divergence their multivariate distributions multiple MRI features. Compared prior approach morphometric networks (MSNs) n > 11,000 scans spanning three human datasets and one macaque dataset, MIND were more reliable, consistent with cytoarchitectonics symmetry correlated tract-tracing measures axonal connectivity. derived from T1-weighted sensitive age-related changes than MSNs or by tractography diffusion-weighted MRI. Gene co-expression was strongly coupled tractography. network phenotypes also heritable, especially edges structurally differentiated areas. analysis provides biologically validated lens connectomics using readily available data.

Язык: Английский

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Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 4, 2024

Abstract Functional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate function through network science. Here, we systematically evaluate 768 data-processing pipelines for reconstruction from resting-state functional MRI, evaluating the effect of parcellation, connectivity definition, and global signal regression. Our criteria seek that minimise motion confounds spurious test-retest discrepancies topology, while being sensitive both inter-subject differences experimental effects interest. We reveal vast systematic variability across pipelines’ suitability connectomics. Inappropriate choice pipeline produce results are not only misleading, but so, with majority failing at least one criterion. However, set optimal consistently satisfy all different datasets, spanning minutes, weeks, months. provide full breakdown each pipeline’s performance inform future best practices in

Язык: Английский

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Whole-brain comparison of rodent and human brains using spatial transcriptomics

eLife, Год журнала: 2022, Номер 11

Опубликована: Ноя. 7, 2022

The ever-increasing use of mouse models in preclinical neuroscience research calls for an improvement the methods used to translate findings between and human brains. Previously, we showed that brains primates can be compared a direct quantitative manner using common reference space built from white matter tractography data (Mars et al., 2018b). Here, extend approach evaluate similarity brain regions openly accessible brain-wide transcriptomic sets. We show mouse-human homologous genes capture broad patterns neuroanatomical organization, but resolution cross-species correspondences improved novel supervised machine learning approach. Using this method, demonstrate sensorimotor subdivisions neocortex exhibit greater species, with supramodal subdivisions, isocortical separate into clusters based on their cortical regions. also find striatal are strongly conserved, caudoputamen exhibiting equal degree both caudate putamen.

Язык: Английский

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Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июль 27, 2022

Abstract Epilepsy is associated with genetic risk factors and cortico-subcortical network alterations, but associations between neurobiological mechanisms macroscale connectomics remain unclear. This multisite ENIGMA-Epilepsy study examined whole-brain structural covariance networks in patients epilepsy related findings to postmortem gene expression patterns. Brain analysis included 578 adults temporal lobe (TLE), 288 idiopathic generalized (IGE), 1328 healthy controls from 18 centres worldwide. Graph theoretical of revealed increased clustering path length orbitofrontal regions TLE, suggesting a shift towards regularization. Conversely, people IGE showed decreased fronto-temporo-parietal cortices, indicating random configuration. Syndrome-specific topological alterations reflected patterns genes for hippocampal sclerosis TLE IGE. These imaging-transcriptomic signatures could potentially guide diagnosis or tailor therapeutic approaches specific syndromes.

Язык: Английский

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Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex

PLoS Biology, Год журнала: 2022, Номер 20(8), С. e3001735 - e3001735

Опубликована: Авг. 1, 2022

Whole-brain neural communication is typically estimated from statistical associations among electromagnetic or haemodynamic time-series. The relationship between functional network architectures recovered these 2 types of activity remains unknown. Here, we map networks (measured using magnetoencephalography (MEG)) to magnetic resonance imaging (fMRI)). We find that the modalities regionally heterogeneous and systematically follows cortical hierarchy, with close correspondence in unimodal cortex poor transmodal cortex. Comparison BigBrain histological atlas reveals electromagnetic-haemodynamic coupling driven by laminar differentiation neuron density, suggesting mapping can be explained cytoarchitectural variation. Importantly, connectivity cannot a single frequency band, but rather arises mixing multiple neurophysiological rhythms. Correspondence two largely MEG at beta (15 29 Hz) band. Collectively, findings demonstrate highly organized only partly overlapping patterns fMRI networks, opening fundamentally new avenues for studying microarchitecture multimodal patterns.

Язык: Английский

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Transcriptional signatures of the cortical morphometric similarity network gradient in first-episode, treatment-naive major depressive disorder

Neuropsychopharmacology, Год журнала: 2022, Номер 48(3), С. 518 - 528

Опубликована: Окт. 17, 2022

Язык: Английский

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Trips and neurotransmitters: Discovering principled patterns across 6850 hallucinogenic experiences

Science Advances, Год журнала: 2022, Номер 8(11)

Опубликована: Март 16, 2022

Psychedelics probably alter states of consciousness by disrupting how the higher association cortex governs bottom-up sensory signals. Individual hallucinogenic drugs are usually studied in participants controlled laboratory settings. Here, we have explored word usage 6850 free-form testimonials about 27 through prism 40 neurotransmitter receptor subtypes, which were then mapped to three-dimensional coordinates brain via their gene transcription levels from invasive tissue probes. Despite high interindividual variability, our pattern-learning approach delineated drug-induced changes conscious awareness linked cortex-wide anatomical distributions density proxies. Each discovered receptor-experience factor spanned between a higher-level pole and input pole, may relate previously reported collapse hierarchical order among large-scale networks. Coanalyzing many psychoactive molecules thousands natural language descriptions drug experiences, analytical framework finds underlying semantic structure maps it directly brain.

Язык: Английский

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