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Kristanto D, Burkhardt M, Thiel C, Debener S, Gießing C, Hildebrandt A. The multiverse of data preprocessing and analysis in graph-based fMRI: A systematic literature review of analytical choices fed into a decision support tool for informed analysis. Neurosci Biobehav Rev 2024; 165:105846. [PMID: 39117132 DOI: 10.1016/j.neubiorev.2024.105846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
The large number of different analytical choices used by researchers is partly responsible for the challenge of replication in neuroimaging studies. For an exhaustive robustness analysis, knowledge of the full space of analytical options is essential. We conducted a systematic literature review to identify the analytical decisions in functional neuroimaging data preprocessing and analysis in the emerging field of cognitive network neuroscience. We found 61 different steps, with 17 of them having debatable parameter choices. Scrubbing, global signal regression, and spatial smoothing are among the controversial steps. There is no standardized order in which different steps are applied, and the parameter settings within several steps vary widely across studies. By aggregating the pipelines across studies, we propose three taxonomic levels to categorize analytical choices: 1) inclusion or exclusion of specific steps, 2) parameter tuning within steps, and 3) distinct sequencing of steps. We have developed a decision support application with high educational value called METEOR to facilitate access to the data in order to design well-informed robustness (multiverse) analysis.
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Affiliation(s)
- Daniel Kristanto
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany.
| | - Micha Burkhardt
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany
| | - Christiane Thiel
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany
| | - Stefan Debener
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany
| | - Carsten Gießing
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany.
| | - Andrea Hildebrandt
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany.
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Wang Z, Diedrichsen J, Saltoun K, Steele C, Arnold-Anteraper SR, Yeo BTT, Schmahmann JD, Bzdok D. Structural covariation between cerebellum and neocortex intrinsic structural covariation links cerebellum subregions to the cerebral cortex. J Neurophysiol 2024; 132:849-869. [PMID: 39052236 DOI: 10.1152/jn.00164.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
The human cerebellum is increasingly recognized to be involved in nonmotor and higher-order cognitive functions. Yet, its ties with the entire cerebral cortex have not been holistically studied in a whole brain exploration with a unified analytical framework. Here, we characterized dissociable cortical-cerebellar structural covariation patterns based on regional gray matter volume (GMV) across the brain in n = 38,527 UK Biobank participants. Our results invigorate previous observations in that important shares of cortical-cerebellar structural covariation are described as 1) a dissociation between the higher-level cognitive system and lower-level sensorimotor system and 2) an anticorrelation between the visual-attention system and advanced associative networks within the cerebellum. We also discovered a novel pattern of ipsilateral, rather than contralateral, cerebral-cerebellar associations. Furthermore, phenome-wide association assays revealed key phenotypes, including cognitive phenotypes, lifestyle, physical properties, and blood assays, associated with each decomposed covariation pattern, helping to understand their real-world implications. This systems neuroscience view paves the way for future studies to explore the implications of these structural covariations, potentially illuminating new pathways in our understanding of neurological and cognitive disorders.NEW & NOTEWORTHY Cerebellum's association with the entire cerebral cortex has not been holistically studied in a unified way. Here, we conjointly characterize the population-level cortical-cerebellar structural covariation patterns leveraging ∼40,000 UK Biobank participants whole brain structural scans and ∼1,000 phenotypes. We revitalize the previous hypothesis of an anticorrelation between the visual-attention system and advanced associative networks within the cerebellum. We also discovered a novel ipsilateral cerebral-cerebellar associations. Phenome-wide association (PheWAS) revealed real-world implications of the structural covariation patterns.
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Affiliation(s)
- Zilong Wang
- McConnell Brain Imaging Centre, Department of Biomedical Engineering, Faculty of Medicine, School of Computer Science, The Neuro-Montreal Neurological Institute (MNI), McGill University, Montreal, Quebec, Canada
- Mila-Quebec Artificial Intelligence Institute, Montreal, Quebec, Canada
| | - Jörn Diedrichsen
- Western Institute for Neuroscience, Western University, London, Ontario, Canada
- Department of Computer Science, Western University, London, Ontario, Canada
- Department of Statistical and Actuarial Sciences, Western University, London, Ontario, Canada
| | - Karin Saltoun
- McConnell Brain Imaging Centre, Department of Biomedical Engineering, Faculty of Medicine, School of Computer Science, The Neuro-Montreal Neurological Institute (MNI), McGill University, Montreal, Quebec, Canada
- Mila-Quebec Artificial Intelligence Institute, Montreal, Quebec, Canada
| | - Christopher Steele
- Department of Psychology, Concordia University, Montreal, Quebec, Canada
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Sheeba Rani Arnold-Anteraper
- Advanced Imaging Research Center, UTSW, Dallas, Texas, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States
| | - B T Thomas Yeo
- Department of Electrical & Computer Engineering, Centre for Translational MR Research, Centre for Sleep & Cognition, N.1 Institute for Health and Institute for Digital Medicine, National University of Singapore, Singapore, Singapore
| | - Jeremy D Schmahmann
- Ataxia Center, Cognitive Behavioral Neurology Unit, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - Danilo Bzdok
- McConnell Brain Imaging Centre, Department of Biomedical Engineering, Faculty of Medicine, School of Computer Science, The Neuro-Montreal Neurological Institute (MNI), McGill University, Montreal, Quebec, Canada
- Mila-Quebec Artificial Intelligence Institute, Montreal, Quebec, Canada
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Ma X, Li J, Yang Y, Qiu X, Sheng J, Han N, Wu C, Xu G, Jiang G, Tian J, Weng X, Wang J. Enhanced cerebral blood flow similarity of the somatomotor network in chronic insomnia: Transcriptomic decoding, gut microbial signatures and phenotypic roles. Neuroimage 2024; 297:120762. [PMID: 39089603 DOI: 10.1016/j.neuroimage.2024.120762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Chronic insomnia (CI) is a complex disease involving multiple factors including genetics, gut microbiota, and brain structure and function. However, there lacks a unified framework to elucidate how these factors interact in CI. By combining data of clinical assessment, sleep behavior recording, cognitive test, multimodal MRI (structural, functional, and perfusion), gene, and gut microbiota, this study demonstrated that enhanced cerebral blood flow (CBF) similarities of the somatomotor network (SMN) acted as a key mediator to link multiple factors in CI. Specifically, we first demonstrated that only CBF but not morphological or functional networks exhibited alterations in patients with CI, characterized by increases within the SMN and between the SMN and higher-order associative networks. Moreover, these findings were highly reproducible and the CBF similarity method was test-retest reliable. Further, we showed that transcriptional profiles explained 60.4 % variance of the pattern of the increased CBF similarities with the most correlated genes enriched in regulation of cellular and protein localization and material transport, and gut microbiota explained 69.7 % inter-individual variance in the increased CBF similarities with the most contributions from Negativicutes and Lactobacillales. Finally, we found that the increased CBF similarities were correlated with clinical variables, accounted for sleep behaviors and cognitive deficits, and contributed the most to the patient-control classification (accuracy = 84.4 %). Altogether, our findings have important implications for understanding the neuropathology of CI and may inform ways of developing new therapeutic strategies for the disease.
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Affiliation(s)
- Xiaofen Ma
- Department of Nuclear Medicine, Jinan University Affiliated Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Junle Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Yuping Yang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Xiaofan Qiu
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Jintao Sheng
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Ningke Han
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Changwen Wu
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Guang Xu
- Department of Neurology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Guihua Jiang
- Department of Nuclear Medicine, Jinan University Affiliated Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Junzhang Tian
- Department of Nuclear Medicine, Jinan University Affiliated Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xuchu Weng
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China; Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Center for Studies of Psychological Application, South China Normal University, Guangzhou, China; Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
| | - Jinhui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China; Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Center for Studies of Psychological Application, South China Normal University, Guangzhou, China; Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
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Desrosiers-Grégoire G, Devenyi GA, Grandjean J, Chakravarty MM. A standardized image processing and data quality platform for rodent fMRI. Nat Commun 2024; 15:6708. [PMID: 39112455 PMCID: PMC11306392 DOI: 10.1038/s41467-024-50826-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. Unlike the human community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, this software platform will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.
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Affiliation(s)
- Gabriel Desrosiers-Grégoire
- Computational Brain Anatomy Laboratory, Cerebral Imaging Center, Douglas Mental Health University Institute, Montreal, QC, Canada.
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
| | - Gabriel A Devenyi
- Computational Brain Anatomy Laboratory, Cerebral Imaging Center, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Joanes Grandjean
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Mallar Chakravarty
- Computational Brain Anatomy Laboratory, Cerebral Imaging Center, Douglas Mental Health University Institute, Montreal, QC, Canada.
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
- Department of Psychiatry, McGill University, Montreal, QC, Canada.
- Department of Biological and Biomedical Engineering, McGill University, Montreal, QC, Canada.
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Halcomb ME, Dzemidzic M, Avena-Koenigsberger A, Hile KL, Durazzo TC, Yoder KK. Greater ventral striatal functional connectivity in cigarette smokers relative to non-smokers across a spectrum of alcohol consumption. Brain Imaging Behav 2024:10.1007/s11682-024-00903-9. [PMID: 39106000 DOI: 10.1007/s11682-024-00903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2024] [Indexed: 08/07/2024]
Abstract
Cigarette smoking is associated with elevated risk of disease and mortality and contributes to heavy healthcare-related economic burdens. The nucleus accumbens is implicated in numerous reward-related behaviors, including reinforcement learning and incentive salience. The established functional connectivity of the accumbens includes regions associated with motivation, valuation, and affective processing. Although the high comorbidity of cigarette smoking with drinking behaviors may collectively affect brain activity, there could be independent effects of smoking in alcohol use disorder that impact brain function and behavior. We hypothesized that smoking status, independent of alcohol use, would be associated with aberrations of nucleus accumbens functional connectivity to brain regions that facilitate reward processing, salience attribution, and inhibitory control. Resting state functional magnetic resonance imaging data from thirty-one nonsmokers and nineteen smoking individuals were analyzed using seed-based correlations of the bilateral accumbens with all other brain voxels. Statistical models accounted for drinks consumed per week. The smoking group demonstrated significantly higher functional connectivity between the left accumbens and the bilateral insula and anterior cingulate cortex, as well as hyperconnectivity between the right accumbens and the insula. Confirmatory analyses using the insula and cingulate clusters generated from the original analysis as seed regions reproduced the hyperconnectivity in smokers between the bilateral insular regions and the accumbens. In conclusion, smoking status had distinct effects on neural activity; hyperconnectivity between the accumbens and insula in smokers may reflect enhanced encoding of the reinforcing effects of smoking and greater orientation toward smoking-associated stimuli.
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Affiliation(s)
- Meredith E Halcomb
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
| | - Mario Dzemidzic
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
- Department of Neurology, Indiana University School of Medicine, 355 W. 16th St., GH 4700, Indianapolis, IN, 46202, USA
| | - Andrea Avena-Koenigsberger
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
| | - Karen L Hile
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA
| | - Timothy C Durazzo
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Stanford, CA, 94305, USA
| | - Karmen K Yoder
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA.
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W. 16th St., GH 4100, Indianapolis, IN, 46202, USA.
- Department of Psychology, Indiana University Purdue University Indianapolis, 402 N. Blackford St, Indianapolis, IN, 46202, USA.
- Stark Neurosciences Research Institute, 320 W. 15th St., NB 414, Indianapolis, IN, 46202, USA.
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Li J, Jin S, Li Z, Zeng X, Yang Y, Luo Z, Xu X, Cui Z, Liu Y, Wang J. Morphological Brain Networks of White Matter: Mapping, Evaluation, Characterization, and Application. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400061. [PMID: 39005232 DOI: 10.1002/advs.202400061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/27/2024] [Indexed: 07/16/2024]
Abstract
Although white matter (WM) accounts for nearly half of adult brain, its wiring diagram is largely unknown. Here, an approach is developed to construct WM networks by estimating interregional morphological similarity based on structural magnetic resonance imaging. It is found that morphological WM networks showed nontrivial topology, presented good-to-excellent test-retest reliability, accounted for phenotypic interindividual differences in cognition, and are under genetic control. Through integration with multimodal and multiscale data, it is further showed that morphological WM networks are able to predict the patterns of hamodynamic coherence, metabolic synchronization, gene co-expression, and chemoarchitectonic covariance, and associated with structural connectivity. Moreover, the prediction followed WM functional connectomic hierarchy for the hamodynamic coherence, is related to genes enriched in the forebrain neuron development and differentiation for the gene co-expression, and is associated with serotonergic system-related receptors and transporters for the chemoarchitectonic covariance. Finally, applying this approach to multiple sclerosis and neuromyelitis optica spectrum disorders, it is found that both diseases exhibited morphological dysconnectivity, which are correlated with clinical variables of patients and are able to diagnose and differentiate the diseases. Altogether, these findings indicate that morphological WM networks provide a reliable and biologically meaningful means to explore WM architecture in health and disease.
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Affiliation(s)
- Junle Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Suhui Jin
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Zhen Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Xiangli Zeng
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Yuping Yang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Zhenzhen Luo
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Xiaoyu Xu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Zaixu Cui
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Yaou Liu
- Department of Radiology, Beijing Tiantan Hospital, Beijing, 100070, China
| | - Jinhui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, Guangzhou, 510631, China
- Center for Studies of Psychological Application, South China Normal University, Guangzhou, 510631, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
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Yang Y, Zhen Y, Wang X, Liu L, Zheng Y, Zheng Z, Zheng H, Tang S. Altered asymmetry of functional connectome gradients in major depressive disorder. Front Neurosci 2024; 18:1385920. [PMID: 38745933 PMCID: PMC11092381 DOI: 10.3389/fnins.2024.1385920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction Major depressive disorder (MDD) is a debilitating disease involving sensory and higher-order cognitive dysfunction. Previous work has shown altered asymmetry in MDD, including abnormal lateralized activation and disrupted hemispheric connectivity. However, it remains unclear whether and how MDD affects functional asymmetries in the context of intrinsic hierarchical organization. Methods Here, we evaluate intra- and inter-hemispheric asymmetries of the first three functional gradients, characterizing unimodal-transmodal, visual-somatosensory, and somatomotor/default mode-multiple demand hierarchies, to study MDD-related alterations in overarching system-level architecture. Results We find that, relative to the healthy controls, MDD patients exhibit alterations in both primary sensory regions (e.g., visual areas) and transmodal association regions (e.g., default mode areas). We further find these abnormalities are woven in heterogeneous alterations along multiple functional gradients, associated with cognitive terms involving mind, memory, and visual processing. Moreover, through an elastic net model, we observe that both intra- and inter-asymmetric features are predictive of depressive traits measured by BDI-II scores. Discussion Altogether, these findings highlight a broad and mixed effect of MDD on functional gradient asymmetry, contributing to a richer understanding of the neurobiological underpinnings in MDD.
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Affiliation(s)
- Yaqian Yang
- School of Mathematical Sciences, Beihang University, Beijing, China
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
| | - Yi Zhen
- School of Mathematical Sciences, Beihang University, Beijing, China
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
| | - Xin Wang
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
- Institute of Artificial Intelligence, Beihang University, Beijing, China
- Zhongguancun Laboratory, Beijing, China
- Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing, Beihang University, Beijing, China
- PengCheng Laboratory, Shenzhen, China
| | - Longzhao Liu
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
- Institute of Artificial Intelligence, Beihang University, Beijing, China
- Zhongguancun Laboratory, Beijing, China
- Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing, Beihang University, Beijing, China
- PengCheng Laboratory, Shenzhen, China
| | - Yi Zheng
- School of Mathematical Sciences, Beihang University, Beijing, China
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
| | - Zhiming Zheng
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
- Institute of Artificial Intelligence, Beihang University, Beijing, China
- Zhongguancun Laboratory, Beijing, China
- Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing, Beihang University, Beijing, China
- PengCheng Laboratory, Shenzhen, China
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, China
- State Key Lab of Software Development Environment, Beihang University, Beijing, China
| | - Hongwei Zheng
- Beijing Academy of Blockchain and Edge Computing, Beijing, China
| | - Shaoting Tang
- Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Beihang University, Beijing, China
- Institute of Artificial Intelligence, Beihang University, Beijing, China
- Zhongguancun Laboratory, Beijing, China
- Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing, Beihang University, Beijing, China
- PengCheng Laboratory, Shenzhen, China
- Institute of Medical Artificial Intelligence, Binzhou Medical University, Yantai, China
- State Key Lab of Software Development Environment, Beihang University, Beijing, China
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Lindquist MA. Sliding windows analysis can undo the effects of preprocessing when applied to fMRI data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561221. [PMID: 37873165 PMCID: PMC10592634 DOI: 10.1101/2023.10.06.561221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Resting-state fMRI (rs-fMRI) data is used to study the intrinsic functional connectivity (FC) in the human brain. In the past decade, interest has focused on studying the temporal dynamics of FC on short timescales, ranging from seconds to minutes. These studies of time-varying FC (TVFC) have enabled the classification of whole-brain dynamic FC profiles into distinct "brain states", defined as recurring whole-brain connectivity profiles reliably observed across subjects and sessions. The analysis of rs-fMRI data is complicated by the fact that the measured BOLD signal consists of changes induced by neuronal activation, as well as non-neuronal nuisance fluctuations that should be removed prior to further analysis. Thus, the data undergoes significant preprocesing prior to analysis. In previous work [24], we illustrated the potential pitfalls involved with using modular preprocessing pipelines, showing how later preprocessing steps can reintroduce correlation with signal previously removed from the data. Here we show that the problem runs deeper, and that certain statistical analysis techniques can potentially interact with preprocessing and reintroduce correlations with previously removed signal. One such technique is the popular sliding window analysis, used to compute TVFC. In this paper, we discuss the problem both theoretically and empirically in application to test-retest rs-fMRI data. Importantly, we show that we are able to obtain essentially the same brain states and state transitions when analyzing motion induced signal as we do when analyzing the preprocessed but windowed data. Our results cast doubt on whether the estimated brain states obtained using sliding window analysis are neuronal in nature, or simply reflect non-neuronal nuisance signal variation (e.g., motion).
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Morgado F, Vandewouw MM, Hammill C, Kelley E, Crosbie J, Schachar R, Ayub M, Nicolson R, Georgiades S, Arnold P, Iaboni A, Kushki A, Taylor MJ, Anagnostou E, Lerch JP. Behaviour-correlated profiles of cerebellar-cerebral functional connectivity observed in independent neurodevelopmental disorder cohorts. Transl Psychiatry 2024; 14:173. [PMID: 38570480 PMCID: PMC10991387 DOI: 10.1038/s41398-024-02857-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
The cerebellum, through its connectivity with the cerebral cortex, plays an integral role in regulating cognitive and affective processes, and its dysregulation can result in neurodevelopmental disorder (NDD)-related behavioural deficits. Identifying cerebellar-cerebral functional connectivity (FC) profiles in children with NDDs can provide insight into common connectivity profiles and their correlation to NDD-related behaviours. 479 participants from the Province of Ontario Neurodevelopmental Disorders (POND) network (typically developing = 93, Autism Spectrum Disorder = 172, Attention Deficit/Hyperactivity Disorder = 161, Obsessive-Compulsive Disorder = 53, mean age = 12.2) underwent resting-state functional magnetic resonance imaging and behaviour testing (Social Communication Questionnaire, Toronto Obsessive-Compulsive Scale, and Child Behaviour Checklist - Attentional Problems Subscale). FC components maximally correlated to behaviour were identified using canonical correlation analysis. Results were then validated by repeating the investigation in 556 participants from an independent NDD cohort provided from a separate consortium (Healthy Brain Network (HBN)). Replication of canonical components was quantified by correlating the feature vectors between the two cohorts. The two cerebellar-cerebral FC components that replicated to the greatest extent were correlated to, respectively, obsessive-compulsive behaviour (behaviour feature vectors, rPOND-HBN = -0.97; FC feature vectors, rPOND-HBN = -0.68) and social communication deficit contrasted against attention deficit behaviour (behaviour feature vectors, rPOND-HBN = -0.99; FC feature vectors, rPOND-HBN = -0.78). The statistically stable (|z| > 1.96) features of the FC feature vectors, measured via bootstrap re-sampling, predominantly comprised of correlations between cerebellar attentional and control network regions and cerebral attentional, default mode, and control network regions. In both cohorts, spectral clustering on FC loading values resulted in subject clusters mixed across diagnostic categories, but no cluster was significantly enriched for any given diagnosis as measured via chi-squared test (p > 0.05). Overall, two behaviour-correlated components of cerebellar-cerebral functional connectivity were observed in two independent cohorts. This suggests the existence of generalizable cerebellar network differences that span across NDD diagnostic boundaries.
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Affiliation(s)
- Felipe Morgado
- Dept. Medical Biophysics, University of Toronto, Toronto, Canada.
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Canada.
| | - Marlee M Vandewouw
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
| | - Christopher Hammill
- Data Science & Advanced Analytics, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | | | - Jennifer Crosbie
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Russell Schachar
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Muhammad Ayub
- Department of Psychiatry, University College London, London, UK
| | - Robert Nicolson
- Department of Psychiatry, University of Western Ontario, London, Canada
- Lawson Research Institute, London, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
- Offord Centre for Child Studies, McMaster University, Hamilton, Canada
| | - Paul Arnold
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Psychiatry, University of Calgary, Calgary, Canada
| | - Alana Iaboni
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
| | - Azadeh Kushki
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
| | - Margot J Taylor
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Canada
- Diagnostic Imaging, Hospital for Sick Children, Toronto, Canada
- Department of Medical Imaging, University of Toronto, Toronto, Canada
| | - Evdokia Anagnostou
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jason P Lerch
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
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10
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Rasero J, Betzel R, Sentis AI, Kraynak TE, Gianaros PJ, Verstynen T. Similarity in evoked responses does not imply similarity in macroscopic network states. Netw Neurosci 2024; 8:335-354. [PMID: 38711543 PMCID: PMC11073549 DOI: 10.1162/netn_a_00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/17/2023] [Indexed: 05/08/2024] Open
Abstract
It is commonplace in neuroscience to assume that if two tasks activate the same brain areas in the same way, then they are recruiting the same underlying networks. Yet computational theory has shown that the same pattern of activity can emerge from many different underlying network representations. Here we evaluated whether similarity in activation necessarily implies similarity in network architecture by comparing region-wise activation patterns and functional correlation profiles from a large sample of healthy subjects (N = 242). Participants performed two executive control tasks known to recruit nearly identical brain areas, the color-word Stroop task and the Multi-Source Interference Task (MSIT). Using a measure of instantaneous functional correlations, based on edge time series, we estimated the task-related networks that differed between incongruent and congruent conditions. We found that the two tasks were much more different in their network profiles than in their evoked activity patterns at different analytical levels, as well as for a wide range of methodological pipelines. Our results reject the notion that having the same activation patterns means two tasks engage the same underlying representations, suggesting that task representations should be independently evaluated at both node and edge (connectivity) levels.
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Affiliation(s)
- Javier Rasero
- Department of Psychology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- School of Data Science, University of Virginia, Charlottesville, VA, USA
| | - Richard Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Amy Isabella Sentis
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Thomas E. Kraynak
- Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter J. Gianaros
- Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Verstynen
- Department of Psychology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA
- Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
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11
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Jacob LPL, Bailes SM, Williams SD, Stringer C, Lewis LD. Distributed fMRI dynamics predict distinct EEG rhythms across sleep and wakefulness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577429. [PMID: 38352426 PMCID: PMC10862763 DOI: 10.1101/2024.01.29.577429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The brain exhibits rich oscillatory dynamics that vary across tasks and states, such as the EEG oscillations that define sleep. These oscillations play critical roles in cognition and arousal, but the brainwide mechanisms underlying them are not yet described. Using simultaneous EEG and fast fMRI in subjects drifting between sleep and wakefulness, we developed a machine learning approach to investigate which brainwide fMRI dynamics predict alpha (8-12 Hz) and delta (1-4 Hz) rhythms. We predicted moment-by-moment EEG power from fMRI activity in held-out subjects, and found that information about alpha power was represented by a remarkably small set of regions, segregated in two distinct networks linked to arousal and visual systems. Conversely, delta rhythms were diffusely represented on a large spatial scale across the cortex. These results identify distributed networks that predict delta and alpha rhythms, and establish a computational framework for investigating fMRI brainwide dynamics underlying EEG oscillations.
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Affiliation(s)
- Leandro P L Jacob
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sydney M Bailes
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Boston University, Boston, MA, USA
| | - Stephanie D Williams
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Boston University, Boston, MA, USA
| | | | - Laura D Lewis
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston MA USA
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12
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Butler ER, Samia N, White S, Gratton C, Nusslock R. Neuroimmune mechanisms connecting violence with internalizing symptoms: A high-dimensional multimodal mediation analysis. Hum Brain Mapp 2024; 45:e26615. [PMID: 38339956 DOI: 10.1002/hbm.26615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/27/2023] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Violence exposure is associated with worsening anxiety and depression symptoms among adolescents. Mechanistically, social defeat stress models in mice indicate that violence increases peripherally derived macrophages in threat appraisal regions of the brain, which have been causally linked to anxious behavior. In the present study, we investigate if there is a path connecting violence exposure with internalizing symptom severity through peripheral inflammation and amygdala connectivity. Two hundred and thirty-three adolescents, ages 12-15, from the Chicago area completed clinical assessments, immune assays and neuroimaging. A high-dimensional multimodal mediation model was fit, using violence exposure as the predictor, 12 immune variables as the first set of mediators and 288 amygdala connectivity variables as the second set, and internalizing symptoms as the primary outcome measure. 56.2% of the sample had been exposed to violence in their lifetime. Amygdala-hippocampus connectivity mediated the association between violence exposure and internalizing symptoms (ζ ̂ Hipp π ̂ Hipp = 0.059 $$ {\hat{\zeta}}_{\mathrm{Hipp}}{\hat{\pi}}_{\mathrm{Hipp}}=0.059 $$ ,95 % CI boot = 0.009,0.134 $$ 95\%{\mathrm{CI}}_{\mathrm{boot}}=\left[\mathrm{0.009,0.134}\right] $$ ). There was no evidence that inflammation or inflammation and amygdala connectivity in tandem mediated the association. Considering the amygdala and the hippocampus work together to encode, consolidate, and retrieve contextual fear memories, violence exposure may be associated with greater connectivity between the amygdala and the hippocampus because it could be adaptive for the amygdala and the hippocampus to be in greater communication following violence exposure to facilitate evaluation of contextual threat cues. Therefore, chronic elevations of amygdala-hippocampal connectivity may indicate persistent vigilance that leads to internalizing symptoms.
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Affiliation(s)
- Ellyn R Butler
- Department of Psychology, Northwestern University, Evanston, Illinois, USA
| | - Noelle Samia
- Department of Statistics and Data Science, Northwestern University, Evanston, Illinois, USA
| | - Stuart White
- Nebraska Children and Families Foundation, Lincoln, Nebraska, USA
| | - Caterina Gratton
- Department of Psychology, Northwestern University, Evanston, Illinois, USA
- Department of Psychology, Florida State University, Tallahassee, Florida, USA
| | - Robin Nusslock
- Department of Psychology, Northwestern University, Evanston, Illinois, USA
- Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
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13
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Chumin EJ, Cutts SA, Risacher SL, Apostolova LG, Farlow MR, McDonald BC, Wu YC, Betzel R, Saykin AJ, Sporns O. Edge time series components of functional connectivity and cognitive function in Alzheimer's disease. Brain Imaging Behav 2024; 18:243-255. [PMID: 38008852 PMCID: PMC10844434 DOI: 10.1007/s11682-023-00822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2023] [Indexed: 11/28/2023]
Abstract
Understanding the interrelationships of brain function as measured by resting-state magnetic resonance imaging and neuropsychological/behavioral measures in Alzheimer's disease is key for advancement of neuroimaging analysis methods in clinical research. The edge time-series framework recently developed in the field of network neuroscience, in combination with other network science methods, allows for investigations of brain-behavior relationships that are not possible with conventional functional connectivity methods. Data from the Indiana Alzheimer's Disease Research Center sample (53 cognitively normal control, 47 subjective cognitive decline, 32 mild cognitive impairment, and 20 Alzheimer's disease participants) were used to investigate relationships between functional connectivity components, each derived from a subset of time points based on co-fluctuation of regional signals, and measures of domain-specific neuropsychological functions. Multiple relationships were identified with the component approach that were not found with conventional functional connectivity. These involved attentional, limbic, frontoparietal, and default mode systems and their interactions, which were shown to couple with cognitive, executive, language, and attention neuropsychological domains. Additionally, overlapping results were obtained with two different statistical strategies (network contingency correlation analysis and network-based statistics correlation). Results demonstrate that connectivity components derived from edge time-series based on co-fluctuation reveal disease-relevant relationships not observed with conventional static functional connectivity.
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Affiliation(s)
- Evgeny J Chumin
- Department of Psychological and Brain Sciences, Indiana University (IU), Psychology Building 308, 1101 E 10th St, Bloomington, IN, 47405, USA.
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA.
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA.
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA.
| | - Sarah A Cutts
- Department of Psychological and Brain Sciences, Indiana University (IU), Psychology Building 308, 1101 E 10th St, Bloomington, IN, 47405, USA
- Program in Neuroscience, IU, Bloomington, IN, USA
| | - Shannon L Risacher
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
| | - Liana G Apostolova
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
- Department of Neurology, IUSM, Indianapolis, IN, USA
| | - Martin R Farlow
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Neurology, IUSM, Indianapolis, IN, USA
| | - Brenna C McDonald
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
- Department of Neurology, IUSM, Indianapolis, IN, USA
| | - Yu-Chien Wu
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
| | - Richard Betzel
- Department of Psychological and Brain Sciences, Indiana University (IU), Psychology Building 308, 1101 E 10th St, Bloomington, IN, 47405, USA
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Program in Neuroscience, IU, Bloomington, IN, USA
| | - Andrew J Saykin
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
- Department of Neurology, IUSM, Indianapolis, IN, USA
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University (IU), Psychology Building 308, 1101 E 10th St, Bloomington, IN, 47405, USA
- Indiana University Network Sciences Institute, IU, Bloomington, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, IUSM, Indianapolis, IN, USA
- Program in Neuroscience, IU, Bloomington, IN, USA
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, USA
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14
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Quek DYL, Taylor N, Gilat M, Lewis SJG, Ehgoetz Martens KA. Effect of dopamine on limbic network connectivity at rest in Parkinson's disease patients with freezing of gait. Transl Neurosci 2024; 15:20220336. [PMID: 38708096 PMCID: PMC11066616 DOI: 10.1515/tnsci-2022-0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 05/07/2024] Open
Abstract
Background Freezing of gait (FOG) in Parkinson's disease (PD) has a poorly understood pathophysiology, which hinders treatment development. Recent work showed a dysfunctional fronto-striato-limbic circuitry at rest in PD freezers compared to non-freezers in the dopamine "OFF" state. While other studies found that dopaminergic replacement therapy alters functional brain organization in PD, the specific effect of dopamine medication on fronto-striato-limbic functional connectivity in freezers remains unclear. Objective To evaluate how dopamine therapy alters resting state functional connectivity (rsFC) of the fronto-striato-limbic circuitry in PD freezers, and whether the degree of connectivity change is related to freezing severity and anxiety. Methods Twenty-three PD FOG patients underwent MRI at rest (rsfMRI) in their clinically defined "OFF" and "ON" dopaminergic medication states. A seed-to-seed based analysis was performed between a priori defined limbic circuitry ROIs. Functional connectivity was compared between OFF and ON states. A secondary correlation analyses evaluated the relationship between Hospital Anxiety and Depression Scale (HADS)-Anxiety) and FOG Questionnaire with changes in rsFC from OFF to ON. Results PD freezers' OFF compared to ON showed increased functional coupling between the right hippocampus and right caudate nucleus, and between the left putamen and left posterior parietal cortex (PPC). A negative association was found between HADS-Anxiety and the rsFC change from OFF to ON between the left amygdala and left prefrontal cortex, and left putamen and left PPC. Conclusion These findings suggest that dopaminergic medication partially modulates the frontoparietal-limbic-striatal circuitry in PD freezers, and that the influence of medication on the amygdala, may be related to clinical anxiety in freezer.
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Affiliation(s)
- Dione Y. L. Quek
- Parkinson’s Disease Research Clinic, Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Natasha Taylor
- Parkinson’s Disease Research Clinic, Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Moran Gilat
- Neurorehabilitation Research Group (eNRGy), Department of Rehabilitation Sciences, KU Leuven, Leuven, Belgium
| | - Simon J. G. Lewis
- Parkinson’s Disease Research Clinic, Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Kaylena A. Ehgoetz Martens
- Parkinson’s Disease Research Clinic, Brain and Mind Centre, University of Sydney, Sydney, Australia
- Department of Kinesiology and Health Sciences, University of Waterloo, 200 University Avenue West, WaterlooON, N2L3G1Canada
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15
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Freedberg MV. The balance of hippocampal and caudate network functional connectivity is associated with episodic memory performance and its decline across adulthood. Neuropsychologia 2023; 191:108723. [PMID: 37923122 DOI: 10.1016/j.neuropsychologia.2023.108723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The hippocampal and caudate networks interact to support episodic memory, but the relationship between hippocampal and caudate connectivity strength and episodic memory is unclear. In general, cognition is optimally supported when connectivity within a functional network dominates connectivity from other networks. For example, episodic memory may be optimally supported when the hippocampal and caudate networks express this pattern of connectivity, consistent with research showing that the two networks are organized competitively. Alternatively, episodic memory may be optimally supported when connectivity in both networks is more balanced, consistent with fMRI reports showing cooperation between networks. Using cross-sectional behavioral and resting state fMRI data from a diverse sample (N = 347; Ages 18-85), I tested the hypothesis that reduced hippocampal and caudate network dominance would be associated with reduced episodic memory across individuals and age. Consistent with this hypothesis, lower caudate network dominance in bilateral thalamic regions was associated with worse episodic memory regardless of age. Age-related differences in caudate network dominance in the pallidum and putamen were also associated with worse episodic memory performance, but through their shared variance with age. I found no evidence that network dominance was related to processing speed or executive function, or that hippocampal network dominance was relate to episodic memory performance. These results show that ongoing biological dynamics between the hippocampal and caudate networks throughout adulthood are related to episodic memory performance and support a growing literature specifying the role of the caudate network in episodic memory.
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Affiliation(s)
- Michael V Freedberg
- The University of Texas, Department of Kinesiology and Health Education, Austin, TX, 78712, USA; The University of Texas, Institute for Neuroscience, Austin, TX, 78712, USA.
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16
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Wilson JD, Gerlach AR, Karim HT, Aizenstein HJ, Andreescu C. Sex matters: acute functional connectivity changes as markers of remission in late-life depression differ by sex. Mol Psychiatry 2023; 28:5228-5236. [PMID: 37414928 PMCID: PMC10919097 DOI: 10.1038/s41380-023-02158-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023]
Abstract
The efficacy of antidepressant treatment in late-life is modest, a problem magnified by an aging population and increased prevalence of depression. Understanding the neurobiological mechanisms of treatment response in late-life depression (LLD) is imperative. Despite established sex differences in depression and neural circuits, sex differences associated with fMRI markers of antidepressant treatment response are underexplored. In this analysis, we assess the role of sex on the relationship of acute functional connectivity changes with treatment response in LLD. Resting state fMRI scans were collected at baseline and day one of SSRI/SNRI treatment for 80 LLD participants. One-day changes in functional connectivity (differential connectivity) were related to remission status after 12 weeks. Sex differences in differential connectivity profiles that distinguished remitters from non-remitters were assessed. A random forest classifier was used to predict the remission status with models containing various combinations of demographic, clinical, symptomatological, and connectivity measures. Model performance was assessed with area under the curve, and variable importance was assessed with permutation importance. The differential connectivity profile associated with remission status differed significantly by sex. We observed evidence for a difference in one-day connectivity changes between remitters and non-remitters in males but not females. Additionally, prediction of remission was significantly improved in male-only and female-only models over pooled models. Predictions of treatment outcome based on early changes in functional connectivity show marked differences between sexes and should be considered in future MR-based treatment decision-making algorithms.
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Affiliation(s)
- James D Wilson
- Department of Mathematics and Statistics, University of San Francisco, San Francisco, CA, USA
| | - Andrew R Gerlach
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Helmet T Karim
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Howard J Aizenstein
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carmen Andreescu
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
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17
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Mawla I, Huang Z, Kaplan CM, Ichesco E, Waller N, Larkin TE, Zöllner HJ, Edden RA, Harte SE, Clauw DJ, Mashour GA, Napadow V, Harris RE. Large-scale momentary brain co-activation patterns are associated with hyperalgesia and mediate focal neurochemistry and cross-network functional connectivity in fibromyalgia. Pain 2023; 164:2737-2748. [PMID: 37751539 PMCID: PMC10652715 DOI: 10.1097/j.pain.0000000000002973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 09/28/2023]
Abstract
ABSTRACT Fibromyalgia has been characterized by augmented cross-network functional communication between the brain's sensorimotor, default mode, and attentional (salience/ventral and dorsal) networks. However, the underlying mechanisms of these aberrant communication patterns are unknown. In this study, we sought to understand large-scale topographic patterns at instantaneous timepoints, known as co-activation patterns (CAPs). We found that a sustained pressure pain challenge temporally modulated the occurrence of CAPs. Using proton magnetic resonance spectroscopy, we found that greater basal excitatory over inhibitory neurotransmitter levels within the anterior insula orchestrated higher cross-network connectivity between the anterior insula and the default mode network through lower occurrence of a CAP encompassing the attentional networks during sustained pain. Moreover, we found that hyperalgesia in fibromyalgia was mediated through increased occurrence of a CAP encompassing the sensorimotor network during sustained pain. In conclusion, this study elucidates the role of momentary large-scale topographic brain patterns in shaping noxious information in patients with fibromyalgia, while laying the groundwork for using precise spatiotemporal dynamics of the brain for the potential development of therapeutics.
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Affiliation(s)
- Ishtiaq Mawla
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Zirui Huang
- Department of Anesthesiology, Center for Consciousness Science, University of Michigan, Ann Arbor, MI, United States
| | - Chelsea M. Kaplan
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Eric Ichesco
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Noah Waller
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Tony E. Larkin
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Helge J. Zöllner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States
| | - Richard A.E. Edden
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States
| | - Steven E. Harte
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Daniel J. Clauw
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
| | - George A. Mashour
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
- Department of Anesthesiology, Center for Consciousness Science, University of Michigan, Ann Arbor, MI, United States
| | - Vitaly Napadow
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Network, Harvard Medical School, Charlestown, MA, United States
| | - Richard E. Harris
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
- Department of Anesthesiology, Chronic Pain and Fatigue Research Center, University of Michigan, Ann Arbor, MI, United States
- Susan Samueli Integrative Health Institute, School of Medicine, University of California at Irvine, Irvine, CA, United States
- Department of Anesthesiology and Perioperative Care, School of Medicine, University of California at Irvine, Irvine, CA, United States
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18
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Chumin EJ, Cutts SA, Risacher SL, Apostolova LG, Farlow MR, McDonald BC, Wu YC, Betzel R, Saykin AJ, Sporns O. Edge Time Series Components of Functional Connectivity and Cognitive Function in Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.13.23289936. [PMID: 38014005 PMCID: PMC10680898 DOI: 10.1101/2023.05.13.23289936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Understanding the interrelationships of brain function as measured by resting-state magnetic resonance imaging and neuropsychological/behavioral measures in Alzheimer's disease is key for advancement of neuroimaging analysis methods in clinical research. The edge time-series framework recently developed in the field of network neuroscience, in combination with other network science methods, allows for investigations of brain-behavior relationships that are not possible with conventional functional connectivity methods. Data from the Indiana Alzheimer's Disease Research Center sample (53 cognitively normal control, 47 subjective cognitive decline, 32 mild cognitive impairment, and 20 Alzheimer's disease participants) were used to investigate relationships between functional connectivity components, each derived from a subset of time points based on co-fluctuation of regional signals, and measures of domain-specific neuropsychological functions. Multiple relationships were identified with the component approach that were not found with conventional functional connectivity. These involved attentional, limbic, frontoparietal, and default mode systems and their interactions, which were shown to couple with cognitive, executive, language, and attention neuropsychological domains. Additionally, overlapping results were obtained with two different statistical strategies (network contingency correlation analysis and network-based statistics correlation). Results demonstrate that connectivity components derived from edge time-series based on co-fluctuation reveal disease-relevant relationships not observed with conventional static functional connectivity.
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Affiliation(s)
- Evgeny J. Chumin
- Department of Psychological and Brain Sciences, Indiana University (IU), Bloomington, IN, United States
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
| | - Sarah A. Cutts
- Department of Psychological and Brain Sciences, Indiana University (IU), Bloomington, IN, United States
- Program in Neuroscience, IU, Bloomington, IN, United States
| | - Shannon L. Risacher
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
| | - Liana G. Apostolova
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
- Department of Neurology, IUSM, Indianapolis, IN, United States
| | - Martin R. Farlow
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Neurology, IUSM, Indianapolis, IN, United States
| | - Brenna C. McDonald
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
- Department of Neurology, IUSM, Indianapolis, IN, United States
| | - Yu-Chien Wu
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
| | - Richard Betzel
- Department of Psychological and Brain Sciences, Indiana University (IU), Bloomington, IN, United States
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Program in Neuroscience, IU, Bloomington, IN, United States
| | - Andrew J. Saykin
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
- Department of Neurology, IUSM, Indianapolis, IN, United States
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University (IU), Bloomington, IN, United States
- Indiana University Network Sciences Institute, IU, Bloomington, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine (IUSM), Indianapolis, IN, United States
- Indiana Alzheimer’s Disease Research Center, IUSM, Indianapolis, IN, United States
- Program in Neuroscience, IU, Bloomington, IN, United States
- Department of Radiology and Imaging Sciences, IUSM, Indianapolis, IN, United States
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19
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Hannum A, Lopez MA, Blanco SA, Betzel RF. High-accuracy machine learning techniques for functional connectome fingerprinting and cognitive state decoding. Hum Brain Mapp 2023; 44:5294-5308. [PMID: 37498048 PMCID: PMC10543109 DOI: 10.1002/hbm.26423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/26/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The human brain is a complex network comprised of functionally and anatomically interconnected brain regions. A growing number of studies have suggested that empirical estimates of brain networks may be useful for discovery of biomarkers of disease and cognitive state. A prerequisite for realizing this aim, however, is that brain networks also serve as reliable markers of an individual. Here, using Human Connectome Project data, we build upon recent studies examining brain-based fingerprints of individual subjects and cognitive states based on cognitively demanding tasks that assess, for example, working memory, theory of mind, and motor function. Our approach achieves accuracy of up to 99% for both identification of the subject of an fMRI scan, and for classification of the cognitive state of a previously unseen subject in a scan. More broadly, we explore the accuracy and reliability of five different machine learning techniques on subject fingerprinting and cognitive state decoding objectives, using functional connectivity data from fMRI scans of a high number of subjects (865) across a number of cognitive states (8). These results represent an advance on existing techniques for functional connectivity-based brain fingerprinting and state decoding. Additionally, 16 different functional connectome (FC) matrix construction pipelines are compared in order to characterize the effects of different aspects of the production of FCs on the accuracy of subject and task classification, and to identify possible confounds.
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Affiliation(s)
- Andrew Hannum
- Department of Computer ScienceUniversity of DenverDenverColoradoUSA
| | - Mario A. Lopez
- Department of Computer ScienceUniversity of DenverDenverColoradoUSA
| | - Saúl A. Blanco
- Department of Computer ScienceIndiana UniversityBloomingtonIndianaUSA
| | - Richard F. Betzel
- Department of Psychological and Brain SciencesIndiana UniversityBloomingtonIndianaUSA
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20
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Meca A, Peraza JA, Riedel MC, Hale W, Pettit JW, Musser ED, Salo T, Flannery JS, Bottenhorn KL, Dick AS, Pintos Lobo R, Ucros LM, Greaves CA, Hawes SW, Sanchez M, Gonzalez MR, Sutherland MT, Gonzalez R, Laird AR. Acculturative Orientations Among Hispanic/Latinx Caregivers in the ABCD Study: Associations With Caregiver and Youth Mental Health and Youth Brain Function. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:785-796. [PMID: 37881576 PMCID: PMC10593892 DOI: 10.1016/j.bpsgos.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/19/2023] Open
Abstract
Background Population-based neuroscience offers opportunities to examine important but understudied sociocultural factors such as acculturation. Acculturation refers to the extent to which an individual retains their cultural heritage and/or adopts the receiving society's culture and is particularly salient among Hispanic/Latinx immigrants. Specific acculturative orientations have been linked to vulnerability to substance use, depression, and suicide and are known to influence family dynamics between caregivers and their children. Methods Using data from first- and second-generation Hispanic/Latinx caregivers in the Adolescent Brain Cognitive Development (ABCD) Study (N = 1057), we examined how caregivers' acculturative orientation affects their mental health, as well as the mental health and brain function of their children. Neuroimaging analyses focused on regions associated with self- and affiliation-based social processing (ventromedial prefrontal cortex, insula, and temporoparietal junction). Results We identified 2 profiles of caregiver acculturation: bicultural (retains heritage culture while adopting U.S. culture) and detached (discards heritage culture and rejects U.S. culture). Bicultural caregivers exhibited fewer internalizing and externalizing problems than detached caregivers; furthermore, youth exhibited similar internalizing effects across caregiver profiles. In addition, youth with bicultural caregivers displayed increased resting-state brain activity (i.e., fractional amplitude of low-frequency fluctuations and regional homogeneity) in the left insula, which has been linked to psychopathology; however, differences in long-range functional connectivity were not significant. Conclusions Caregiver acculturation is an important familial factor that has been linked to significant differences in youth mental health and insula activity. Future work should examine sociocultural and neurodevelopmental changes across adolescence to assess health outcomes and determine whether localized, corticolimbic brain effects are ultimately translated into long-range connectivity differences.
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Affiliation(s)
- Alan Meca
- Department of Psychology, University of Texas San Antonio, San Antonio, Texas
| | - Julio A. Peraza
- Department of Physics, Florida International University, Miami, Florida
| | - Michael C. Riedel
- Department of Physics, Florida International University, Miami, Florida
| | - Willie Hale
- Department of Psychology, University of Texas San Antonio, San Antonio, Texas
| | - Jeremy W. Pettit
- Department of Psychology, Florida International University, Miami, Florida
| | - Erica D. Musser
- Department of Psychology, Florida International University, Miami, Florida
| | - Taylor Salo
- Department of Psychology, Florida International University, Miami, Florida
| | - Jessica S. Flannery
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, North Carolina
| | - Katherine L. Bottenhorn
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California
| | - Anthony S. Dick
- Department of Psychology, Florida International University, Miami, Florida
| | | | - Laura M. Ucros
- School of Integrated Science and Humanities, Florida International University, Miami, Florida
| | - Chelsea A. Greaves
- School of Integrated Science and Humanities, Florida International University, Miami, Florida
| | - Samuel W. Hawes
- Department of Psychology, Florida International University, Miami, Florida
| | - Mariana Sanchez
- Department of Health Promotion and Disease Prevention, Florida International University, Miami, Florida
| | | | | | - Raul Gonzalez
- Department of Psychology, Florida International University, Miami, Florida
| | - Angela R. Laird
- Department of Physics, Florida International University, Miami, Florida
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21
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Wilcox RR, Barbey AK. Connectome-based predictive modeling of fluid intelligence: evidence for a global system of functionally integrated brain networks. Cereb Cortex 2023; 33:10322-10331. [PMID: 37526284 DOI: 10.1093/cercor/bhad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 06/21/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
Cognitive neuroscience continues to advance our understanding of the neural foundations of human intelligence, with significant progress elucidating the role of the frontoparietal network in cognitive control mechanisms for flexible, intelligent behavior. Recent evidence in network neuroscience further suggests that this finding may represent the tip of the iceberg and that fluid intelligence may depend on the collective interaction of multiple brain networks. However, the global brain mechanisms underlying fluid intelligence and the nature of multi-network interactions remain to be well established. We therefore conducted a large-scale Connectome-based Predictive Modeling study, administering resting-state fMRI to 159 healthy college students and examining the contributions of seven intrinsic connectivity networks to the prediction of fluid intelligence, as measured by a state-of-the-art cognitive task (the Bochum Matrices Test). Specifically, we aimed to: (i) identify whether fluid intelligence relies on a primary brain network or instead engages multiple brain networks; and (ii) elucidate the nature of brain network interactions by assessing network allegiance (within- versus between-network connections) and network topology (strong versus weak connections) in the prediction of fluid intelligence. Our results demonstrate that whole-brain predictive models account for a large and significant proportion of variance in fluid intelligence (18%) and illustrate that the contribution of individual networks is relatively modest by comparison. In addition, we provide novel evidence that the global architecture of fluid intelligence prioritizes between-network connections and flexibility through weak ties. Our findings support a network neuroscience approach to understanding the collective role of brain networks in fluid intelligence and elucidate the system-wide network mechanisms from which flexible, adaptive behavior is constructed.
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Affiliation(s)
- Ramsey R Wilcox
- Decision Neuroscience Laboratory, University of Nebraska-Lincoln, NE 68501, United States
- Center for Brain, Biology, and Behavior, University of Nebraska-Lincoln, NE 68501, United States
- Department of Psychology, University of Nebraska-Lincoln, NE 68501, United States
- Department of Psychology, University of Illinois, Urbana, IL 61801, United States
| | - Aron K Barbey
- Decision Neuroscience Laboratory, University of Nebraska-Lincoln, NE 68501, United States
- Center for Brain, Biology, and Behavior, University of Nebraska-Lincoln, NE 68501, United States
- Department of Psychology, University of Nebraska-Lincoln, NE 68501, United States
- Department of Psychology, University of Illinois, Urbana, IL 61801, United States
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, United States
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22
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Desmidt T, Dujardin PA, Andersson F, Brizard B, Réméniéras JP, Gissot V, Arlicot N, Barantin L, Espitalier F, Belzung C, Tanti A, Robert G, Bulteau S, Gallet Q, Kazour F, Cognet S, Camus V, El-Hage W, Poupin P, Karim HT. Changes in cerebral connectivity and brain tissue pulsations with the antidepressant response to an equimolar mixture of oxygen and nitrous oxide: an MRI and ultrasound study. Mol Psychiatry 2023; 28:3900-3908. [PMID: 37592013 DOI: 10.1038/s41380-023-02217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Nitrous oxide (N2O) has recently emerged as a potential fast-acting antidepressant but the cerebral mechanisms involved in this effect remain speculative. We hypothesized that the antidepressant response to an Equimolar Mixture of Oxygen and Nitrous Oxide (EMONO) would be associated with changes in cerebral connectivity and brain tissue pulsations (BTP). Thirty participants (20 with a major depressive episode resistant to at least one antidepressant and 10 healthy controls-HC, aged 25-50, only females) were exposed to a 1-h single session of EMONO and followed for 1 week. We defined response as a reduction of at least 50% in the MADRS score 1 week after exposure. Cerebral connectivity of the Anterior Cingulate Cortex (ACC), using ROI-based resting state fMRI, and BTP, using ultrasound Tissue Pulsatility Imaging, were compared before and rapidly after exposure (as well as during exposure for BTP) among HC, non-responders and responders. We conducted analyses to compare group × time, group, and time effects. Nine (45%) depressed participants were considered responders and eleven (55%) non-responders. In responders, we observed a significant reduction in the connectivity of the subgenual ACC with the precuneus. Connectivity of the supracallosal ACC with the mid-cingulate also significantly decreased after exposure in HC and in non-responders. BTP significantly increased in the three groups between baseline and gas exposure, but the increase in BTP within the first 10 min was only significant in responders. We found that a single session of EMONO can rapidly modify the functional connectivity in the subgenual ACC-precuneus, nodes within the default mode network, in depressed participants responders to EMONO. In addition, larger increases in BTP, associated with a significant rise in cerebral blood flow, appear to promote the antidepressant response, possibly by facilitating optimal drug delivery to the brain. Our study identified potential cerebral mechanisms related to the antidepressant response of N2O, as well as potential markers for treatment response with this fast-acting antidepressant.
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Affiliation(s)
- Thomas Desmidt
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.
- CHU de Tours, Tours, France.
- CIC 1415, CHU de Tours, Inserm, Tours, France.
| | | | | | - Bruno Brizard
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | | | | | - Nicolas Arlicot
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
- CHU de Tours, Tours, France
| | | | - Fabien Espitalier
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
- CHU de Tours, Tours, France
| | | | - Arnaud Tanti
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Gabriel Robert
- Behavior and Basal Ganglia Host Team 4712, University of Rennes 1, Rennes, France Department of Psychiatry, Rennes University Hospital, Guillaume Régnier Hospital Centre, Rennes, France
| | - Samuel Bulteau
- Addictology and Liaison Psychiatry Department, CHU de Nantes, 44000, Nantes, France
| | - Quentin Gallet
- Department of Psychiatry, University Hospital, Angers, France
| | - François Kazour
- Department of Psychiatry, University Hospital, Angers, France
| | | | - Vincent Camus
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
- CHU de Tours, Tours, France
| | - Wissam El-Hage
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
- CHU de Tours, Tours, France
- CIC 1415, CHU de Tours, Inserm, Tours, France
| | | | - Helmet T Karim
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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23
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Martin S, Frieling R, Saur D, Hartwigsen G. TMS over the pre-SMA enhances semantic cognition via remote network effects on task-based activity and connectivity. Brain Stimul 2023; 16:1346-1357. [PMID: 37704032 PMCID: PMC10615837 DOI: 10.1016/j.brs.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND The continuous decline of executive abilities with age is mirrored by increased neural activity of domain-general networks during task processing. So far, it remains unclear how much domain-general networks contribute to domain-specific processes such as language when cognitive demands increase. The current neuroimaging study explored the potential of intermittent theta-burst stimulation (iTBS) over a domain-general hub to enhance executive and semantic processing in healthy middle-aged to older adults. METHODS We implemented a cross-over within-subject study design with three task-based neuroimaging sessions per participant. Using an individualized stimulation approach, each participant received once effective and once sham iTBS over the pre-supplementary motor area (pre-SMA), a region of domain-general control. Subsequently, task-specific stimulation effects were assessed in functional MRI using a semantic and a non-verbal executive task with varying cognitive demand. RESULTS Effective stimulation increased activity only during semantic processing in visual and dorsal attention networks. Further, iTBS induced increased seed-based connectivity in task-specific networks for semantic and executive conditions with high cognitive load but overall reduced whole-brain coupling between domain-general networks. Notably, stimulation-induced changes in activity and connectivity related differently to behavior: While stronger activity of the parietal dorsal attention network was linked to poorer semantic performance, its enhanced coupling with the pre-SMA was associated with more efficient semantic processing. CONCLUSIONS iTBS modulates networks in a task-dependent manner and generates effects at regions remote to the stimulation site. These neural changes are linked to more efficient semantic processing, which underlines the general potential of network stimulation approaches in cognitive aging.
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Affiliation(s)
- Sandra Martin
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, 04103, Leipzig, Germany; Language & Aphasia Laboratory, Department of Neurology, University of Leipzig Medical Center, Liebigstrasse 20, 04103, Leipzig, Germany.
| | - Regine Frieling
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, 04103, Leipzig, Germany
| | - Dorothee Saur
- Language & Aphasia Laboratory, Department of Neurology, University of Leipzig Medical Center, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Gesa Hartwigsen
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, 04103, Leipzig, Germany; Wilhelm Wundt Institute for Psychology, Leipzig University, Neumarkt 9-19, 04109, Leipzig, Germany
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24
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Li J, Wang R, Mao N, Huang M, Qiu S, Wang J. Multimodal and multiscale evidence for network-based cortical thinning in major depressive disorder. Neuroimage 2023; 277:120265. [PMID: 37414234 DOI: 10.1016/j.neuroimage.2023.120265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is associated with widespread, irregular cortical thickness (CT) reductions across the brain. However, little is known regarding mechanisms that govern spatial distribution of the reductions. METHODS We combined multimodal MRI and genetic, cytoarchitectonic and chemoarchitectonic data to examine structural covariance, functional synchronization, gene co-expression, cytoarchitectonic similarity and chemoarchitectonic covariance between regions atrophied in MDD. RESULTS Regions atrophied in MDD were associated with significantly higher structural covariance, functional synchronization, gene co-expression and chemoarchitectonic covariance. These results were robust against methodological variations in brain parcellation and null model, reproducible in patients and controls, and independent of age at onset of MDD. Despite no significant differences in the cytoarchitectonic similarity, MDD-related CT reductions were susceptible to specific cytoarchitectonic class of association cortex. Further, we found that nodal shortest path lengths to disease epicenters derived from structural (right supramarginal gyrus) and chemoarchitectonic covariance (right sulcus intermedius primus) networks of healthy brains were correlated with the extent to which a region was atrophied in MDD, supporting the transneuronal spread hypothesis that regions closer to the epicenters are more susceptible to MDD. Finally, we showed that structural covariance and functional synchronization among regions atrophied in MDD were mainly related to genes enriched in metabolic and membrane-related processes, driven by genes in excitatory neurons, and associated with specific neurotransmitter transporters and receptors. CONCLUSIONS Altogether, our findings provide empirical evidence for and genetic and molecular insights into connectivity-constrained CT thinning in MDD.
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Affiliation(s)
- Junle Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Rui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Ning Mao
- Department of Radiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Manli Huang
- Department of Psychiatry, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China
| | - Shijun Qiu
- Department of Radiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong, China
| | - Jinhui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China; Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Center for Studies of Psychological Application, South China Normal University, Guangzhou, China; Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
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25
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Hou X, Guo P, Wang P, Liu P, Lin DDM, Fan H, Li Y, Wei Z, Lin Z, Jiang D, Jin J, Kelly C, Pillai JJ, Huang J, Pinho MC, Thomas BP, Welch BG, Park DC, Patel VM, Hillis AE, Lu H. Deep-learning-enabled brain hemodynamic mapping using resting-state fMRI. NPJ Digit Med 2023; 6:116. [PMID: 37344684 PMCID: PMC10284915 DOI: 10.1038/s41746-023-00859-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/09/2023] [Indexed: 06/23/2023] Open
Abstract
Cerebrovascular disease is a leading cause of death globally. Prevention and early intervention are known to be the most effective forms of its management. Non-invasive imaging methods hold great promises for early stratification, but at present lack the sensitivity for personalized prognosis. Resting-state functional magnetic resonance imaging (rs-fMRI), a powerful tool previously used for mapping neural activity, is available in most hospitals. Here we show that rs-fMRI can be used to map cerebral hemodynamic function and delineate impairment. By exploiting time variations in breathing pattern during rs-fMRI, deep learning enables reproducible mapping of cerebrovascular reactivity (CVR) and bolus arrival time (BAT) of the human brain using resting-state CO2 fluctuations as a natural "contrast media". The deep-learning network is trained with CVR and BAT maps obtained with a reference method of CO2-inhalation MRI, which includes data from young and older healthy subjects and patients with Moyamoya disease and brain tumors. We demonstrate the performance of deep-learning cerebrovascular mapping in the detection of vascular abnormalities, evaluation of revascularization effects, and vascular alterations in normal aging. In addition, cerebrovascular maps obtained with the proposed method exhibit excellent reproducibility in both healthy volunteers and stroke patients. Deep-learning resting-state vascular imaging has the potential to become a useful tool in clinical cerebrovascular imaging.
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Affiliation(s)
- Xirui Hou
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pengfei Guo
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Puyang Wang
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peiying Liu
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Doris D M Lin
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongli Fan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yang Li
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhiliang Wei
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Zixuan Lin
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dengrong Jiang
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin Jin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Catherine Kelly
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jay J Pillai
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Judy Huang
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marco C Pinho
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Binu P Thomas
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Babu G Welch
- Department of Neurologic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Denise C Park
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Vishal M Patel
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Argye E Hillis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanzhang Lu
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
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26
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Demeter DV, Gordon EM, Nugiel T, Garza A, Larguinho TL, Church JA. Resting-state cortical hubs in youth organize into four categories. Cell Rep 2023; 42:112521. [PMID: 37200192 PMCID: PMC10281712 DOI: 10.1016/j.celrep.2023.112521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023] Open
Abstract
During childhood, neural systems supporting high-level cognitive processes undergo periods of rapid growth and refinement, which rely on the successful coordination of activation across the brain. Some coordination occurs via cortical hubs-brain regions that coactivate with functional networks other than their own. Adult cortical hubs map into three distinct profiles, but less is known about hub categories during development, when critical improvement in cognition occurs. We identify four distinct hub categories in a large youth sample (n = 567, ages 8.5-17.2), each exhibiting more diverse connectivity profiles than adults. Youth hubs integrating control-sensory processing split into two distinct categories (visual control and auditory/motor control), whereas adult hubs unite under one. This split suggests a need for segregating sensory stimuli while functional networks are experiencing rapid development. Functional coactivation strength for youth control-processing hubs are associated with task performance, suggesting a specialized role in routing sensory information to and from the brain's control system.
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Affiliation(s)
- Damion V Demeter
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92093, USA.
| | - Evan M Gordon
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tehila Nugiel
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - AnnaCarolina Garza
- Department of Psychology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tyler L Larguinho
- Department of Psychology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jessica A Church
- Department of Psychology, The University of Texas at Austin, Austin, TX 78712, USA
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27
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Tay J, Düring M, van Leijsen EMC, Bergkamp MI, Norris DG, de Leeuw FE, Markus HS, Tuladhar AM. Network structure-function coupling and neurocognition in cerebral small vessel disease. Neuroimage Clin 2023; 38:103421. [PMID: 37141644 PMCID: PMC10176072 DOI: 10.1016/j.nicl.2023.103421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/23/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cerebral small vessel disease is a leading cause of cognitive decline and vascular dementia. Small vessel disease pathology changes structural brain networks, but its impact on functional networks remains poorly understood. Structural and functional networks are closely coupled in healthy individuals, and decoupling is associated with clinical symptoms in other neurological conditions. We tested the hypothesis that structural-functional network coupling is related to neurocognitive outcomes in 262 small vessel disease patients. METHODS Participants underwent multimodal magnetic resonance imaging and cognitive assessment in 2011 and 2015. Structural connectivity networks were reconstructed using probabilistic diffusion tractography, while functional connectivity networks were estimated from resting-state functional magnetic resonance imaging. Structural and functional networks were then correlated to calculate a measure of structural-functional network coupling for each participant. RESULTS Lower whole-brain coupling was associated with reduced processing speed and greater apathy both cross-sectionally and longitudinally. In addition, coupling within the cognitive control network was associated with all cognitive outcomes, suggesting that neurocognitive outcomes in small vessel disease may be related to the functioning of this intrinsic connectivity network. CONCLUSIONS Our work demonstrates the influence of structural-functional connectivity network decoupling in small vessel disease symptomatology. Cognitive control network function may be investigated in future studies.
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Affiliation(s)
- Jonathan Tay
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Marco Düring
- Medical Image Analysis Center (MIAC AG) and qbig, Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | | | - Mayra I Bergkamp
- Department of Neurology, Donders Center for Medical Neurosciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - David G Norris
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Frank-Erik de Leeuw
- Department of Neurology, Donders Center for Medical Neurosciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anil M Tuladhar
- Department of Neurology, Donders Center for Medical Neurosciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands.
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Phạm DĐ, McDonald DJ, Ding L, Nebel MB, Mejia AF. Less is more: balancing noise reduction and data retention in fMRI with data-driven scrubbing. Neuroimage 2023; 270:119972. [PMID: 36842522 PMCID: PMC10773988 DOI: 10.1016/j.neuroimage.2023.119972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023] Open
Abstract
Functional MRI (fMRI) data may be contaminated by artifacts arising from a myriad of sources, including subject head motion, respiration, heartbeat, scanner drift, and thermal noise. These artifacts cause deviations from common distributional assumptions, introduce spatial and temporal outliers, and reduce the signal-to-noise ratio of the data-all of which can have negative consequences for the accuracy and power of downstream statistical analysis. Scrubbing is a technique for excluding fMRI volumes thought to be contaminated by artifacts and generally comes in two flavors. Motion scrubbing based on subject head motion-derived measures is popular but suffers from a number of drawbacks, among them the need to choose a threshold, a lack of generalizability to multiband acquisitions, and high rates of censoring of individual volumes and entire subjects. Alternatively, data-driven scrubbing methods like DVARS are based on observed noise in the processed fMRI timeseries and may avoid some of these issues. Here we propose "projection scrubbing", a novel data-driven scrubbing method based on a statistical outlier detection framework and strategic dimension reduction, including independent component analysis (ICA), to isolate artifactual variation. We undertake a comprehensive comparison of motion scrubbing with data-driven projection scrubbing and DVARS. We argue that an appropriate metric for the success of scrubbing is maximal data retention subject to reasonable performance on typical benchmarks such as the validity, reliability, and identifiability of functional connectivity. We find that stringent motion scrubbing yields worsened validity, worsened reliability, and produced small improvements to fingerprinting. Meanwhile, data-driven scrubbing methods tend to yield greater improvements to fingerprinting while not generally worsening validity or reliability. Importantly, however, data-driven scrubbing excludes a fraction of the number of volumes or entire sessions compared to motion scrubbing. The ability of data-driven fMRI scrubbing to improve data retention without negatively impacting the quality of downstream analysis has major implications for sample sizes in population neuroscience research.
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Affiliation(s)
- Damon Đ Phạm
- Department of Statistics, Indiana University, Bloomington, IN, USA.
| | - Daniel J McDonald
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - Lei Ding
- Department of Statistics, Indiana University, Bloomington, IN, USA
| | - Mary Beth Nebel
- Center for Neurodevelopmental and Imaging Research, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Amanda F Mejia
- Department of Statistics, Indiana University, Bloomington, IN, USA
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de Lange SC, Helwegen K, van den Heuvel MP. Structural and functional connectivity reconstruction with CATO - A Connectivity Analysis TOolbox. Neuroimage 2023; 273:120108. [PMID: 37059156 DOI: 10.1016/j.neuroimage.2023.120108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023] Open
Abstract
We describe a Connectivity Analysis TOolbox (CATO) for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging and resting-state functional MRI data. CATO is a multimodal software package that enables researchers to run end-to-end reconstructions from MRI data to structural and functional connectome maps, customize their analyses and utilize various software packages to preprocess data. Structural and functional connectome maps can be reconstructed with respect to user-defined (sub)cortical atlases providing aligned connectivity matrices for integrative multimodal analyses. We outline the implementation and usage of the structural and functional processing pipelines in CATO. Performance was calibrated with respect to simulated diffusion weighted imaging from the ITC2015 challenge, test-retest diffusion weighted imaging data and resting-state functional MRI data from the Human Connectome Project. CATO is open-source software distributed under the MIT License and available as a MATLAB toolbox and as a stand-alone application at www.dutchconnectomelab.nl/CATO.
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Affiliation(s)
- Siemon C de Lange
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.
| | - Koen Helwegen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands; Department of Child Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam
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30
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Standage DI, Areshenkoff CN, Gale DJ, Nashed JY, Flanagan JR, Gallivan JP. Whole-brain dynamics of human sensorimotor adaptation. Cereb Cortex 2023; 33:4761-4778. [PMID: 36245212 PMCID: PMC10110437 DOI: 10.1093/cercor/bhac378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/13/2022] Open
Abstract
Humans vary greatly in their motor learning abilities, yet little is known about the neural processes that underlie this variability. We identified distinct profiles of human sensorimotor adaptation that emerged across 2 days of learning, linking these profiles to the dynamics of whole-brain functional networks early on the first day when cognitive strategies toward sensorimotor adaptation are believed to be most prominent. During early learning, greater recruitment of a network of higher-order brain regions, involving prefrontal and anterior temporal cortex, was associated with faster learning. At the same time, greater integration of this "cognitive network" with a sensorimotor network was associated with slower learning, consistent with the notion that cognitive strategies toward adaptation operate in parallel with implicit learning processes of the sensorimotor system. On the second day, greater recruitment of a network that included the hippocampus was associated with faster learning, consistent with the notion that declarative memory systems are involved with fast relearning of sensorimotor mappings. Together, these findings provide novel evidence for the role of higher-order brain systems in driving variability in adaptation.
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Affiliation(s)
- Dominic I Standage
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Corson N Areshenkoff
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
| | - Daniel J Gale
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
| | - Joseph Y Nashed
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - J Randall Flanagan
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
- Department of Psychology, Queen’s University, Humphrey Hall, 62 Arch Street, Kingston, Ontario K7L 3N6, Canada
| | - Jason P Gallivan
- Centre for Neuroscience Studies, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- Department of Psychology, Queen’s University, Humphrey Hall, 62 Arch Street, Kingston, Ontario K7L 3N6, Canada
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31
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Martin S, Williams KA, Saur D, Hartwigsen G. Age-related reorganization of functional network architecture in semantic cognition. Cereb Cortex 2023; 33:4886-4903. [PMID: 36190445 PMCID: PMC10110455 DOI: 10.1093/cercor/bhac387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/15/2022] Open
Abstract
Cognitive aging is associated with widespread neural reorganization processes in the human brain. However, the behavioral impact of such reorganization is not well understood. The current neuroimaging study investigated age differences in the functional network architecture during semantic word retrieval in young and older adults. Combining task-based functional connectivity, graph theory and cognitive measures of fluid and crystallized intelligence, our findings show age-accompanied large-scale network reorganization even when older adults have intact word retrieval abilities. In particular, functional networks of older adults were characterized by reduced decoupling between systems, reduced segregation and efficiency, and a larger number of hub regions relative to young adults. Exploring the predictive utility of these age-related changes in network topology revealed high, albeit less efficient, performance for older adults whose brain graphs showed stronger dedifferentiation and reduced distinctiveness. Our results extend theoretical accounts on neurocognitive aging by revealing the compensational potential of the commonly reported pattern of network dedifferentiation when older adults can rely on their prior knowledge for successful task processing. However, we also demonstrate the limitations of such compensatory reorganization and show that a youth-like network architecture in terms of balanced integration and segregation is associated with more economical processing.
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Affiliation(s)
- Sandra Martin
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
- Language & Aphasia Laboratory, Department of Neurology, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Kathleen A Williams
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
| | - Dorothee Saur
- Language & Aphasia Laboratory, Department of Neurology, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Gesa Hartwigsen
- Lise Meitner Research Group Cognition and Plasticity, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
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fMRIflows: A Consortium of Fully Automatic Univariate and Multivariate fMRI Processing Pipelines. Brain Topogr 2023; 36:172-191. [PMID: 36575327 PMCID: PMC10014671 DOI: 10.1007/s10548-022-00935-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022]
Abstract
How functional magnetic resonance imaging (fMRI) data are analyzed depends on the researcher and the toolbox used. It is not uncommon that the processing pipeline is rewritten for each new dataset. Consequently, code transparency, quality control and objective analysis pipelines are important for improving reproducibility in neuroimaging studies. Toolboxes, such as Nipype and fMRIPrep, have documented the need for and interest in automated pre-processing analysis pipelines. Recent developments in data-driven models combined with high resolution neuroimaging dataset have strengthened the need not only for a standardized preprocessing workflow, but also for a reliable and comparable statistical pipeline. Here, we introduce fMRIflows: a consortium of fully automatic neuroimaging pipelines for fMRI analysis, which performs standard preprocessing, as well as 1st- and 2nd-level univariate and multivariate analyses. In addition to the standardized pre-processing pipelines, fMRIflows provides flexible temporal and spatial filtering to account for datasets with increasingly high temporal resolution and to help appropriately prepare data for advanced machine learning analyses, improving signal decoding accuracy and reliability. This paper first describes fMRIflows' structure and functionality, then explains its infrastructure and access, and lastly validates the toolbox by comparing it to other neuroimaging processing pipelines such as fMRIPrep, FSL and SPM. This validation was performed on three datasets with varying temporal sampling and acquisition parameters to prove its flexibility and robustness. fMRIflows is a fully automatic fMRI processing pipeline which uniquely offers univariate and multivariate single-subject and group analyses as well as pre-processing.
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Hebart MN, Contier O, Teichmann L, Rockter AH, Zheng CY, Kidder A, Corriveau A, Vaziri-Pashkam M, Baker CI. THINGS-data, a multimodal collection of large-scale datasets for investigating object representations in human brain and behavior. eLife 2023; 12:e82580. [PMID: 36847339 PMCID: PMC10038662 DOI: 10.7554/elife.82580] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/25/2023] [Indexed: 03/01/2023] Open
Abstract
Understanding object representations requires a broad, comprehensive sampling of the objects in our visual world with dense measurements of brain activity and behavior. Here, we present THINGS-data, a multimodal collection of large-scale neuroimaging and behavioral datasets in humans, comprising densely sampled functional MRI and magnetoencephalographic recordings, as well as 4.70 million similarity judgments in response to thousands of photographic images for up to 1,854 object concepts. THINGS-data is unique in its breadth of richly annotated objects, allowing for testing countless hypotheses at scale while assessing the reproducibility of previous findings. Beyond the unique insights promised by each individual dataset, the multimodality of THINGS-data allows combining datasets for a much broader view into object processing than previously possible. Our analyses demonstrate the high quality of the datasets and provide five examples of hypothesis-driven and data-driven applications. THINGS-data constitutes the core public release of the THINGS initiative (https://things-initiative.org) for bridging the gap between disciplines and the advancement of cognitive neuroscience.
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Affiliation(s)
- Martin N Hebart
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
- Vision and Computational Cognition Group, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Department of Medicine, Justus Liebig University GiessenGiessenGermany
| | - Oliver Contier
- Vision and Computational Cognition Group, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Max Planck School of Cognition, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Lina Teichmann
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Adam H Rockter
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Charles Y Zheng
- Machine Learning Core, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Alexis Kidder
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Anna Corriveau
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Maryam Vaziri-Pashkam
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Chris I Baker
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
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34
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Al-Arfaj HK, Al-Sharydah AM, AlSuhaibani SS, Alaqeel S, Yousry T. Task-Based and Resting-State Functional MRI in Observing Eloquent Cerebral Areas Personalized for Epilepsy and Surgical Oncology Patients: A Review of the Current Evidence. J Pers Med 2023; 13:jpm13020370. [PMID: 36836604 PMCID: PMC9964201 DOI: 10.3390/jpm13020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Functional magnetic resonance imaging (fMRI) is among the newest techniques of advanced neuroimaging that offer the opportunity for neuroradiologists, neurophysiologists, neuro-oncologists, and neurosurgeons to pre-operatively plan and manage different types of brain lesions. Furthermore, it plays a fundamental role in the personalized evaluation of patients with brain tumors or patients with an epileptic focus for preoperative planning. While the implementation of task-based fMRI has increased in recent years, the existing resources and evidence related to this technique are limited. We have, therefore, conducted a comprehensive review of the available resources to compile a detailed resource for physicians who specialize in managing patients with brain tumors and seizure disorders. This review contributes to the existing literature because it highlights the lack of studies on fMRI and its precise role and applicability in observing eloquent cerebral areas in surgical oncology and epilepsy patients, which we believe is underreported. Taking these considerations into account would help to better understand the role of this advanced neuroimaging technique and, ultimately, improve patient life expectancy and quality of life.
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Affiliation(s)
| | - Abdulaziz Mohammad Al-Sharydah
- Diagnostic and Interventional Radiology Department, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia
- Correspondence: ; Fax: +966-013-8676697
| | - Sari Saleh AlSuhaibani
- Diagnostic and Interventional Radiology Department, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia
| | - Soliman Alaqeel
- Medical Imaging Department, Dammam Medical Complex, Ministry of Health, Dammam 11176, Saudi Arabia
| | - Tarek Yousry
- Division of Neuroradiology and Neurophysics, Lysholm Department of Neuroradiology, UCL IoN, UCLH, London NW1 2BU, UK
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35
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Di X, Biswal BB. A functional MRI pre-processing and quality control protocol based on statistical parametric mapping (SPM) and MATLAB. FRONTIERS IN NEUROIMAGING 2023; 1:1070151. [PMID: 37555150 PMCID: PMC10406300 DOI: 10.3389/fnimg.2022.1070151] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/19/2022] [Indexed: 08/10/2023]
Abstract
Functional MRI (fMRI) has become a popular technique to study brain functions and their alterations in psychiatric and neurological conditions. The sample sizes for fMRI studies have been increasing steadily, and growing studies are sourced from open-access brain imaging repositories. Quality control becomes critical to ensure successful data processing and valid statistical results. Here, we outline a simple protocol for fMRI data pre-processing and quality control based on statistical parametric mapping (SPM) and MATLAB. The focus of this protocol is not only to identify and remove data with artifacts and anomalies, but also to ensure the processing has been performed properly. We apply this protocol to the data from fMRI Open quality control (QC) Project, and illustrate how each quality control step can help to identify potential issues. We also show that simple steps such as skull stripping can improve coregistration between the functional and anatomical images.
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Affiliation(s)
- Xin Di
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
| | - Bharat B. Biswal
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
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36
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Henry TR, Fogleman ND, Nugiel T, Cohen JR. Effect of methylphenidate on functional controllability: a preliminary study in medication-naïve children with ADHD. Transl Psychiatry 2022; 12:518. [PMID: 36528602 PMCID: PMC9759578 DOI: 10.1038/s41398-022-02283-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Methylphenidate (MPH) is the recommended first-line treatment for attention-deficit/hyperactivity disorder (ADHD). While MPH's mechanism of action as a dopamine and noradrenaline transporter blocker is well known, how this translates to ADHD-related symptom mitigation is still unclear. As functional connectivity is reliably altered in ADHD, with recent literature indicating dysfunctional connectivity dynamics as well, one possible mechanism is through altering brain network dynamics. In a double-blind, placebo-controlled MPH crossover trial, 19 medication-naïve children with ADHD underwent two functional MRI scanning sessions (one on MPH and one on placebo) that included a resting state scan and two inhibitory control tasks; 27 typically developing (TD) children completed the same protocol without medication. Network control theory, which quantifies how brain activity reacts to system inputs based on underlying connectivity, was used to assess differences in average and modal functional controllability during rest and both tasks between TD children and children with ADHD (on and off MPH) and between children with ADHD on and off MPH. Children with ADHD on placebo exhibited higher average controllability and lower modal controllability of attention, reward, and somatomotor networks than TD children. Children with ADHD on MPH were statistically indistinguishable from TD children on almost all controllability metrics. These findings suggest that MPH may stabilize functional network dynamics in children with ADHD, both reducing reactivity of brain organization and making it easier to achieve brain states necessary for cognitively demanding tasks.
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Affiliation(s)
- Teague R Henry
- Department of Psychology and School of Data Science, University of Virginia, Charlottesville, VA, USA.
| | - Nicholas D Fogleman
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tehila Nugiel
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jessica R Cohen
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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McColgan P, Gregory S, Zeun P, Zarkali A, Johnson EB, Parker C, Fayer K, Lowe J, Nair A, Estevez-Fraga C, Papoutsi M, Zhang H, Scahill RI, Tabrizi SJ, Rees G. Neurofilament light-associated connectivity in young-adult Huntington's disease is related to neuronal genes. Brain 2022; 145:3953-3967. [PMID: 35758263 PMCID: PMC9679168 DOI: 10.1093/brain/awac227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 05/27/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Upregulation of functional network connectivity in the presence of structural degeneration is seen in the premanifest stages of Huntington's disease (preHD) 10-15 years from clinical diagnosis. However, whether widespread network connectivity changes are seen in gene carriers much further from onset has yet to be explored. We characterized functional network connectivity throughout the brain and related it to a measure of disease pathology burden (CSF neurofilament light, NfL) and measures of structural connectivity in asymptomatic gene carriers, on average 24 years from onset. We related these measurements to estimates of cortical and subcortical gene expression. We found no overall differences in functional (or structural) connectivity anywhere in the brain comparing control and preHD participants. However, increased functional connectivity, particularly between posterior cortical areas, correlated with increasing CSF NfL level in preHD participants. Using the Allen Human Brain Atlas and expression-weighted cell-type enrichment analysis, we demonstrated that this functional connectivity upregulation occurred in cortical regions associated with regional expression of genes specific to neuronal cells. This relationship was validated using single-nucleus RNAseq data from post-mortem Huntington's disease and control brains showing enrichment of neuronal-specific genes that are differentially expressed in Huntington's disease. Functional brain networks in asymptomatic preHD gene carriers very far from disease onset show evidence of upregulated connectivity correlating with increased disease burden. These changes occur among brain areas that show regional expression of genes specific to neuronal GABAergic and glutamatergic cells.
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Affiliation(s)
- Peter McColgan
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Sarah Gregory
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Paul Zeun
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Angeliki Zarkali
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Eileanoir B Johnson
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Christopher Parker
- Department of Computer Science and Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Kate Fayer
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Jessica Lowe
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Akshay Nair
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Carlos Estevez-Fraga
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Marina Papoutsi
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Hui Zhang
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Rachael I Scahill
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Sarah J Tabrizi
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Geraint Rees
- University College London Institute of Cognitive Neuroscience, University College London, London WC1N 3AZ, UK
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Cahart MS, Dell’Acqua F, Giampietro V, Cabral J, Timmers M, Streffer J, Einstein S, Zelaya F, Williams SCR, O’Daly O. Test-retest reliability of time-varying patterns of brain activity across single band and multiband resting-state functional magnetic resonance imaging in healthy older adults. Front Hum Neurosci 2022; 16:980280. [PMID: 36438643 PMCID: PMC9685802 DOI: 10.3389/fnhum.2022.980280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2023] Open
Abstract
Leading Eigenvector Dynamics Analysis (LEiDA) is an analytic approach that characterizes brain activity recorded with functional Magnetic Resonance Imaging (fMRI) as a succession of discrete phase-locking patterns, or states, that consistently recur over time across all participants. LEiDA allows for the extraction of three state-related measures which have previously been key to gaining a better understanding of brain dynamics in both healthy and clinical populations: the probability of occurrence of a given state, its lifetime and the probability of switching from one state to another. The degree to which test-retest reliability of the LEiDA measures may be affected by increasing MRI multiband (MB) factors in comparison with single band sequences is yet to be established. In this study, 24 healthy older adults were scanned over three sessions, on weeks 0, 1, and 4. On each visit, they underwent a conventional single band resting-state fMRI (rs-fMRI) scan and three different MB rs-fMRI scans, with MB factors of 4, with and without in-plane acceleration, and 6 without in-plane acceleration. We found test-retest reliability scores to be significantly higher with MB factor 4 with and without in-plane acceleration for most cortical networks. These findings will inform the choice of acquisition parameters for future studies and clinical trials.
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Affiliation(s)
- Marie-Stephanie Cahart
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Flavio Dell’Acqua
- NatBrainLab, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Vincent Giampietro
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Joana Cabral
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Maarten Timmers
- Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Johannes Streffer
- AC Immune SA, Lausanne, Switzerland
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | | | - Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Steven C. R. Williams
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Owen O’Daly
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
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Panula JM, Alho J, Lindgren M, Kieseppä T, Suvisaari J, Raij TT. State-like changes in the salience network correlate with delusion severity in first-episode psychosis patients. Neuroimage Clin 2022; 36:103234. [PMID: 36270161 PMCID: PMC9668644 DOI: 10.1016/j.nicl.2022.103234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/17/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND AND HYPOTHESIS Delusions are characteristic of psychotic disorders; however, the brain correlates of delusions remain poorly known. Imaging studies on delusions typically compare images across individuals. Related confounding of inter-individual differences beyond delusions may be avoided by comparing delusional and non-delusional states within individuals. STUDY DESIGN We studied correlations of delusions using intra-subject correlation (intra-SC) and inter-subject correlation of functional magnetic resonance imaging (fMRI) signal time series, obtained during a movie stimulus at baseline and follow-up. We included 27 control subjects and 24 first-episode psychosis patients, who were free of delusions at follow-up, to calculate intra-SC between fMRI signals obtained during the two time points. In addition, we studied changes in functional connectivity at baseline and during the one-year follow-up using regions where delusion severity correlated with intra-SC as seeds. RESULTS The intra-SC correlated negatively with the baseline delusion severity in the bilateral anterior insula. In addition, we observed a subthreshold cluster in the anterior cingulate. These three regions constitute the cortical salience network (SN). Functional connectivity between the bilateral insula and the precuneus was weaker in the patients at baseline than in patients at follow-up or in control subjects at any time point. CONCLUSIONS The results suggest that intra-SC is a powerful tool to study brain correlates of symptoms and highlight the role of the SN and internetwork dysconnectivity between the SN and the default mode network in delusions.
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Affiliation(s)
- Jonatan M Panula
- Department of Psychiatry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Neuroscience and Biomedical Engineering and Advanced Magnetic Imaging Center, Aalto University School of Science, Espoo, Finland.
| | - Jussi Alho
- Department of Neuroscience and Biomedical Engineering and Advanced Magnetic Imaging Center, Aalto University School of Science, Espoo, Finland
| | - Maija Lindgren
- Mental Health, Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tuula Kieseppä
- Department of Psychiatry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jaana Suvisaari
- Mental Health, Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tuukka T Raij
- Department of Psychiatry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Neuroscience and Biomedical Engineering and Advanced Magnetic Imaging Center, Aalto University School of Science, Espoo, Finland
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Luo L, Xiao M, Luo Y, Yi H, Dong D, Liu Y, Chen X, Li W, Chen H. Knowing what you feel: Inferior frontal gyrus-based structural and functional neural patterns underpinning adaptive body awareness. J Affect Disord 2022; 315:224-233. [PMID: 35901991 DOI: 10.1016/j.jad.2022.07.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Heightened body awareness (BA) is conducive for increasing understanding of bodily state and improves individuals' health and well-being. Although there has been cumulative research concentrating on the self-perceived tendency to focus on negatively valenced interoceptive sensations, the specific structural and functional neural patterns underlying BA and their role in the relationship between BA and individual well-being remain unclear. METHODS Voxel-based morphometry and whole brain functional connectivity analyses were conducted to examine the structural and functional neural patterns, respectively, in 686 healthy subjects. BA and subjective well-being were assessed using questionnaires. RESULTS BA was inversely related to gray matter volume of the right inferior frontal gyrus, opercular part (IFGoperc). Higher BA was correlated with enhanced IFGoperc-precuneus and IFGoperc-anterior supramarginal gyrus connectivities, and with decreased IFGoperc-lateral occipital cortex and IFGoperc-medial frontal cortex connectivities. The inferior frontal gyrus, triangular part (in the fronto-parietal task control network) acted as the hub that linked the sensory/somatomotor network, the default mode network, and the dorsal and ventral attention network. The IFGoperc-precuneus connectivity moderated the association between BA and subjective well-being. LIMITATIONS We were unable to rank all the networks by their relative importance, because the absolute weighted value in each module was not calculated. CONCLUSION Our findings demonstrated that BA was reflected by specific neural patterns mainly involved in cognitive-affective control, attentional and self-referential processing, as well as multisensory integration, which could offer some references for current therapies (e.g., mindfulness, yoga training) that are dedicated to solving health problems and improving individual well-being.
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Affiliation(s)
- Lin Luo
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Mingyue Xiao
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Yijun Luo
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Haijing Yi
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Debo Dong
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Yong Liu
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Ximei Chen
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Wei Li
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China
| | - Hong Chen
- Key Laboratory of Cognition and Personality (SWU), Ministry of Education, Chongqing, China; Department of Psychology, Southwest University, Chongqing, China.
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Alamdari SB, Sadeghi Damavandi M, Zarei M, Khosrowabadi R. Cognitive theories of autism based on the interactions between brain functional networks. Front Hum Neurosci 2022; 16:828985. [PMID: 36310850 PMCID: PMC9614840 DOI: 10.3389/fnhum.2022.828985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 08/15/2022] [Indexed: 12/03/2022] Open
Abstract
Cognitive functions are directly related to interactions between the brain's functional networks. This functional organization changes in the autism spectrum disorder (ASD). However, the heterogeneous nature of autism brings inconsistency in the findings, and specific pattern of changes based on the cognitive theories of ASD still requires to be well-understood. In this study, we hypothesized that the theory of mind (ToM), and the weak central coherence theory must follow an alteration pattern in the network level of functional interactions. The main aim is to understand this pattern by evaluating interactions between all the brain functional networks. Moreover, the association between the significantly altered interactions and cognitive dysfunctions in autism is also investigated. We used resting-state fMRI data of 106 subjects (5-14 years, 46 ASD: five female, 60 HC: 18 female) to define the brain functional networks. Functional networks were calculated by applying four parcellation masks and their interactions were estimated using Pearson's correlation between pairs of them. Subsequently, for each mask, a graph was formed based on the connectome of interactions. Then, the local and global parameters of the graph were calculated. Finally, statistical analysis was performed using a two-sample t-test to highlight the significant differences between autistic and healthy control groups. Our corrected results show significant changes in the interaction of default mode, sensorimotor, visuospatial, visual, and language networks with other functional networks that can support the main cognitive theories of autism. We hope this finding sheds light on a better understanding of the neural underpinning of autism.
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Affiliation(s)
| | | | - Mojtaba Zarei
- University of Southern Denmark, Neurology Unit, Odense, Denmark
- Institute of Medical Science and Technology, Shahid Beheshti University, Tehran, Iran
| | - Reza Khosrowabadi
- Institute for Cognitive and Brain Sciences, Shahid Beheshti University, Tehran, Iran
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42
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Folvik L, Sneve MH, Ness HT, Vidal-Piñeiro D, Raud L, Geier OM, Walhovd KB, Fjell AM. Sustained upregulation of widespread hippocampal-neocortical coupling following memory encoding. Cereb Cortex 2022; 33:4844-4858. [PMID: 36190442 PMCID: PMC10110434 DOI: 10.1093/cercor/bhac384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/14/2022] Open
Abstract
Systems consolidation of new experiences into lasting episodic memories involves hippocampal-neocortical interactions. Evidence of this process is already observed during early post-encoding rest periods, both as increased hippocampal coupling with task-relevant perceptual regions and reactivation of stimulus-specific patterns following intensive encoding tasks. We investigate the spatial and temporal characteristics of these hippocampally anchored post-encoding neocortical modulations. Eighty-nine adults participated in an experiment consisting of interleaved memory task- and resting-state periods. We observed increased post-encoding functional connectivity between hippocampus and individually localized neocortical regions responsive to stimuli encountered during memory encoding. Post-encoding modulations were manifested as a nearly system-wide upregulation in hippocampal coupling with all major functional networks. The configuration of these extensive modulations resembled hippocampal-neocortical interaction patterns estimated from active encoding operations, suggesting hippocampal post-encoding involvement exceeds perceptual aspects. Reinstatement of encoding patterns was not observed in resting-state scans collected 12 h later, nor when using other candidate seed regions. The similarity in hippocampal functional coupling between online memory encoding and offline post-encoding rest suggests reactivation in humans involves a spectrum of cognitive processes engaged during the experience of an event. There were no age effects, suggesting that upregulation of hippocampal-neocortical connectivity represents a general phenomenon seen across the adult lifespan.
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Affiliation(s)
- Line Folvik
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway
| | - Markus H Sneve
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway
| | - Hedda T Ness
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway
| | - Didac Vidal-Piñeiro
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway
| | - Liisa Raud
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway
| | - Oliver M Geier
- Department of Diagnostic Physics, Oslo University Hospital, Postbox 4950 Nydalen, OUS, Rikshospitalet, 0424 Oslo, Norway
| | - Kristine B Walhovd
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway.,Division of Radiology and Nuclear Medicine, Oslo University Hospital, Postbox 4950 Nydalen, OUS, Rikshospitalet, 0424 Oslo, Norway
| | - Anders M Fjell
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Forskningsveien 3A, 0373 Oslo, Norway.,Division of Radiology and Nuclear Medicine, Oslo University Hospital, Postbox 4950 Nydalen, OUS, Rikshospitalet, 0424 Oslo, Norway
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43
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Sclocco R, Fisher H, Staley R, Han K, Mendez A, Bolender A, Coll-Font J, Kettner NW, Nguyen C, Kuo B, Napadow V. Cine gastric MRI reveals altered Gut-Brain Axis in Functional Dyspepsia: gastric motility is linked with brainstem-cortical fMRI connectivity. Neurogastroenterol Motil 2022; 34:e14396. [PMID: 35560690 PMCID: PMC9529794 DOI: 10.1111/nmo.14396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/31/2022] [Accepted: 04/25/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Functional dyspepsia (FD) is a disorder of gut-brain interaction, and its putative pathophysiology involves dysregulation of gastric motility and central processing of gastric afference. The vagus nerve modulates gastric peristalsis and carries afferent sensory information to brainstem nuclei, specifically the nucleus tractus solitarii (NTS). Here, we combine MRI assessment of gastric kinematics with measures of NTS functional connectivity to the brain in patients with FD and healthy controls (HC), in order to elucidate how gut-brain axis communication is associated with FD pathophysiology. METHODS Functional dyspepsia and HC subjects experienced serial gastric MRI and brain fMRI following ingestion of a food-based contrast meal. Gastric function indices estimated from 4D cine MRI data were compared between FD and HC groups using repeated measure ANOVA models, controlling for ingested volume. Brain connectivity of the NTS was contrasted between groups and associated with gastric function indices. KEY RESULTS Propagation velocity of antral peristalsis was significantly lower in FD compared to HC. The brain network defined by NTS connectivity loaded most strongly onto the Default Mode Network, and more strongly onto the Frontoparietal Network in FD. FD also demonstrated higher NTS connectivity to insula, anterior cingulate and prefrontal cortices, and pre-supplementary motor area. NTS connectivity was linked to propagation velocity in HC, but not FD, whereas peristalsis frequency was linked with NTS connectivity in patients with FD. CONCLUSIONS & INFERENCES Our multi-modal MRI approach revealed lower peristaltic propagation velocity linked to altered brainstem-cortical functional connectivity in patients suffering from FD suggesting specific plasticity in gut-brain communication.
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Affiliation(s)
- Roberta Sclocco
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
- Department of Radiology, Logan University, Chesterfield, MO, USA
| | - Harrison Fisher
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
| | - Rowan Staley
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
- Department of Gastroenterology and Center for Neurointestinal Health, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyungsun Han
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
- Korean Institute of Oriental Medicine, Daejeon, Korea
| | - April Mendez
- Department of Gastroenterology and Center for Neurointestinal Health, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Bolender
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
- Department of Gastroenterology and Center for Neurointestinal Health, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaume Coll-Font
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Christopher Nguyen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Braden Kuo
- Department of Gastroenterology and Center for Neurointestinal Health, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vitaly Napadow
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Radiology, Harvard Medical School, Charlestown, MA, USA
- Department of Radiology, Logan University, Chesterfield, MO, USA
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Pitfalls and Recommended Strategies and Metrics for Suppressing Motion Artifacts in Functional MRI. Neuroinformatics 2022; 20:879-896. [PMID: 35291020 DOI: 10.1007/s12021-022-09565-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2022] [Indexed: 12/31/2022]
Abstract
In resting-state functional magnetic resonance imaging (rs-fMRI), artefactual signals arising from subject motion can dwarf and obfuscate the neuronal activity signal. Typical motion correction approaches involve the generation of nuisance regressors, which are timeseries of non-brain signals regressed out of the fMRI timeseries to yield putatively artifact-free data. Recent work suggests that concatenating all regressors into a single regression model is more effective than the sequential application of individual regressors, which may reintroduce previously removed artifacts. This work compares 18 motion correction pipelines consisting of head motion, independent components analysis, and non-neuronal physiological signal regressors in sequential or concatenated combinations. The pipelines are evaluated on a dataset of cognitively normal individuals with repeat imaging and on datasets of studies of Autism Spectrum Disorder, Major Depressive Disorder, and Parkinson's Disease. Extensive metrics of motion artifact removal are measured, including resting state network recovery, Quality Control-Functional Connectivity (QC-FC) correlation, distance-dependent artifact, network modularity, and test-retest reliability of multiple rs-fMRI analyses. The results reveal limitations in previously proposed metrics, including the QC-FC correlation and modularity quality, and identify more robust artifact removal metrics. The results also reveal limitations in the concatenated regression approach, which is outperformed by the sequential regression approach in the test-retest reliability metrics. Finally, pipelines are recommended that perform well based on quantitative and qualitative comparisons across multiple datasets and robust metrics. These new insights and recommendations help address the need for effective motion artifact correction to reduce noise and confounds in rs-fMRI.
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Lee JJ, Lee S, Lee DH, Woo CW. Functional brain reconfiguration during sustained pain. eLife 2022; 11:e74463. [PMID: 36173388 PMCID: PMC9522250 DOI: 10.7554/elife.74463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pain is constructed through complex interactions among multiple brain systems, but it remains unclear how functional brain networks are reconfigured over time while experiencing pain. Here, we investigated the time-varying changes in the functional brain networks during 20 min capsaicin-induced sustained orofacial pain. In the early stage, the orofacial areas of the primary somatomotor cortex were separated from other areas of the somatosensory cortex and integrated with subcortical and frontoparietal regions, constituting an extended brain network of sustained pain. As pain decreased over time, the subcortical and frontoparietal regions were separated from this brain network and connected to multiple cerebellar regions. Machine-learning models based on these network features showed significant predictions of changes in pain experience across two independent datasets (n = 48 and 74). This study provides new insights into how multiple brain systems dynamically interact to construct and modulate pain experience, advancing our mechanistic understanding of sustained pain.
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Affiliation(s)
- Jae-Joong Lee
- Center for Neuroscience Imaging Research, Institute for Basic ScienceSuwonRepublic of Korea
- Department of Biomedical Engineering, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Sungwoo Lee
- Center for Neuroscience Imaging Research, Institute for Basic ScienceSuwonRepublic of Korea
- Department of Biomedical Engineering, Sungkyunkwan UniversitySuwonRepublic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Dong Hee Lee
- Center for Neuroscience Imaging Research, Institute for Basic ScienceSuwonRepublic of Korea
- Department of Biomedical Engineering, Sungkyunkwan UniversitySuwonRepublic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Choong-Wan Woo
- Center for Neuroscience Imaging Research, Institute for Basic ScienceSuwonRepublic of Korea
- Department of Biomedical Engineering, Sungkyunkwan UniversitySuwonRepublic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan UniversitySuwonRepublic of Korea
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46
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The medial temporal lobe structure and function support positive affect. Neuropsychologia 2022; 176:108373. [PMID: 36167193 DOI: 10.1016/j.neuropsychologia.2022.108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022]
Abstract
Positive affect (PA) is not only associated with individuals' psychological and physical health, but also their cognitive processes. However, whether medial temporal lobe (MTL) and its subfields' volume/functional connectivity can explain individual variability in PA remains understudied. We investigated the morphological (i.e., grey matter volume; GMV) and functional characteristics (i.e., resting-state functional connectivity; rsFC) of PA with a combination of univariate and multivariate pattern analyses (MVPA) using a large sample of participants (n = 321). We simultaneously collected the T1-weighted (n = 321), high-resolution MTL T2-weighted, and resting-state functional imaging data (n = 209). The MTL and its subfields' volumes, including the CA1, CA2+3, DG, and subiculum (SUB), perirhinal cortex (PRC), and parahippocampus (PHC), were extracted using an automatic segmentation of hippocampal subfields (ASHS) software. The morphological results revealed that GMVs in the prefrontal-occipital and limbic (i.e., hippocampus, amygdala, and PHC) systems were associated with variability in PA at the whole-brain level using MVPA but not univariate analysis. Linear regression results further revealed a positive association between the MTL subfields' GMV, especially for the right PRC, and PA after controlling for several covariates. PRC-seed-based rsFC analyses further revealed that its couplings with the fronto-parietal-occipital system predicted PA in both univariate and MVPA. These findings provide novel insights into the neuroanatomical and functional substrates underlying human PA trait. Findings also suggest critical contributions of the MTL and its subfield of the perirhinal cortex, but not hippocampal subfields, as well as its functional coupling with the fronto-parietal control-system on the formation of PA.
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A cognitive neurogenetic approach to uncovering the structure of executive functions. Nat Commun 2022; 13:4588. [PMID: 35933428 PMCID: PMC9357028 DOI: 10.1038/s41467-022-32383-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/27/2022] [Indexed: 11/08/2022] Open
Abstract
One central mission of cognitive neuroscience is to understand the ontology of complex cognitive functions. We addressed this question with a cognitive neurogenetic approach using a large-scale dataset of executive functions (EFs), whole-brain resting-state functional connectivity, and genetic polymorphisms. We found that the bifactor model with common and shifting-specific components not only was parsimonious but also showed maximal dissociations among the EF components at behavioral, neural, and genetic levels. In particular, the genes with enhanced expression in the middle frontal gyrus (MFG) and the subcallosal cingulate gyrus (SCG) showed enrichment for the common and shifting-specific component, respectively. Finally, High-dimensional mediation models further revealed that the functional connectivity patterns significantly mediated the genetic effect on the common EF component. Our study not only reveals insights into the ontology of EFs and their neurogenetic basis, but also provides useful tools to uncover the structure of complex constructs of human cognition.
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Bansal IR, Ashourvan A, Bertolero M, Bassett DS, Pequito S. Model-based stationarity filtering of long-term memory data applied to resting-state blood-oxygen-level-dependent signal. PLoS One 2022; 17:e0268752. [PMID: 35895686 PMCID: PMC9328502 DOI: 10.1371/journal.pone.0268752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Resting-state blood-oxygen-level-dependent (BOLD) signal acquired through functional magnetic resonance imaging is a proxy of neural activity and a key mechanism for assessing neurological conditions. Therefore, practical tools to filter out artefacts that can compromise the assessment are required. On the one hand, a variety of tailored methods to preprocess the data to deal with identified sources of noise (e.g., head motion, heart beating, and breathing, just to mention a few) are in place. But, on the other hand, there might be unknown sources of unstructured noise present in the data. Therefore, to mitigate the effects of such unstructured noises, we propose a model-based filter that explores the statistical properties of the underlying signal (i.e., long-term memory). Specifically, we consider autoregressive fractional integrative process filters. Remarkably, we provide evidence that such processes can model the signals at different regions of interest to attain stationarity. Furthermore, we use a principled analysis where a ground-truth signal with statistical properties similar to the BOLD signal under the injection of noise is retrieved using the proposed filters. Next, we considered preprocessed (i.e., the identified sources of noise removed) resting-state BOLD data of 98 subjects from the Human Connectome Project. Our results demonstrate that the proposed filters decrease the power in the higher frequencies. However, unlike the low-pass filters, the proposed filters do not remove all high-frequency information, instead they preserve process-related higher frequency information. Additionally, we considered four different metrics (power spectrum, functional connectivity using the Pearson's correlation, coherence, and eigenbrains) to infer the impact of such filter. We provided evidence that whereas the first three keep most of the features of interest from a neuroscience perspective unchanged, the latter exhibits some variations that could be due to the sporadic activity filtered out.
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Affiliation(s)
- Ishita Rai Bansal
- Delft Centre for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Arian Ashourvan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Maxwell Bertolero
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Danielle S. Bassett
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Neurology, Hospital of the University of Pennsylvania, Pennsylvania, United States of America
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Electrical & Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Physics & Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Sérgio Pequito
- Delft Centre for Systems and Control, Delft University of Technology, Delft, Netherlands
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Van Schuerbeek P, De Wandel L, Baeken C. The optimized combination of aCompCor and ICA-AROMA to reduce motion and physiologic noise in task fMRI data. Biomed Phys Eng Express 2022; 8. [PMID: 35378526 DOI: 10.1088/2057-1976/ac63f0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/04/2022] [Indexed: 11/12/2022]
Abstract
One of the main challenges in fMRI processing is filtering the task BOLD signals from the noise. Independent component analysis with automatic removal of motion artifacts (ICA-AROMA) reduces motion artifacts by identifying ICA noise components based on their location at the brain edges and cerebrospinal fluid (CSF), high frequency content and correlation with motion regressors. In anatomical component correction (aCompCor), physiological noise regressors extracted from CSF were regressed out from the fMRI time series. In this study, we compared three methods to combine aCompCor and ICA-AROMA denoising in one denoising step. In the first analysis, we regressed the temporal signals of the ICA components identified as noise by ICA-AROMA together with the noise signals determined by aCompCor from the fMRI signals. For the second and third analyses, the correlation between the temporal signals of the ICA components and the aCompCor noise signals was used as an additional criterion to identify the noise components. In the second analysis, the temporal signals of the ICA components classified as noise were regressed from the fMRI signals. In the third analysis, the noise components were removed. To compare the denoising strategies, we examined the fractional amplitude of low-frequency fluctuations (fALFF) and the overlap between the contrast maps. Our results revealed that including the aCompCor noise signals as regressors in ICA-AROMA resulted in more correctly identified noise components, higher fALFF values, and larger activation maps. Moreover, combining the temporal signals of the noise components identified by ICA-AROMA with the aCompCor signals in a noise regression matrix resulted in deactivations. These results suggest that using the correlation between the ICA component temporal signals and the aCompCor signals as noise identification criteria in ICA-AROMA is the best approach for combining both denoising methods.
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Affiliation(s)
- P Van Schuerbeek
- Department of Radiology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - L De Wandel
- Faculty of Medicine and Health Sciences, Ghent Experimental Psychiatry (GHEP) Lab, Ghent University, Ghent, Belgium
| | - C Baeken
- Faculty of Medicine and Health Sciences, Ghent Experimental Psychiatry (GHEP) Lab, Ghent University, Ghent, Belgium.,Department of Psychiatry, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium.,Eindhoven University of Technology, Department of Electrical Engineering, The Netherlands
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Cortico-subcortical interactions in overlapping communities of edge functional connectivity. Neuroimage 2022; 250:118971. [PMID: 35131435 PMCID: PMC9903436 DOI: 10.1016/j.neuroimage.2022.118971] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 02/01/2023] Open
Abstract
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.
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