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Greaves MD, Novelli L, Mansour L S, Zalesky A, Razi A. Structurally informed models of directed brain connectivity. Nat Rev Neurosci 2025; 26:23-41. [PMID: 39663407 DOI: 10.1038/s41583-024-00881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2024] [Indexed: 12/13/2024]
Abstract
Understanding how one brain region exerts influence over another in vivo is profoundly constrained by models used to infer or predict directed connectivity. Although such neural interactions rely on the anatomy of the brain, it remains unclear whether, at the macroscale, structural (or anatomical) connectivity provides useful constraints on models of directed connectivity. Here, we review the current state of research on this question, highlighting a key distinction between inference-based effective connectivity and prediction-based directed functional connectivity. We explore the methods via which structural connectivity has been integrated into directed connectivity models: through prior distributions, fixed parameters in state-space models and inputs to structure learning algorithms. Although the evidence suggests that integrating structural connectivity substantially improves directed connectivity models, assessments of reliability and out-of-sample validity are lacking. We conclude this Review with a strategy for future research that addresses current challenges and identifies opportunities for advancing the integration of structural and directed connectivity to ultimately improve understanding of the brain in health and disease.
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Affiliation(s)
- Matthew D Greaves
- School of Psychological Sciences, Monash University, Clayton, Victoria, Australia.
- Monash Biomedical Imaging, Monash University, Clayton, Victoria, Australia.
| | - Leonardo Novelli
- School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Monash Biomedical Imaging, Monash University, Clayton, Victoria, Australia
| | - Sina Mansour L
- Centre for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Zalesky
- Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia
| | - Adeel Razi
- School of Psychological Sciences, Monash University, Clayton, Victoria, Australia.
- Monash Biomedical Imaging, Monash University, Clayton, Victoria, Australia.
- Wellcome Centre for Human Neuroimaging, University College London, London, UK.
- CIFAR Azrieli Global Scholars Program, CIFAR, Toronto, Ontario, Canada.
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Ren Y, Osborne N, Peterson CB, DeMaster DM, Ewing‐Cobbs L, Vannucci M. Bayesian varying-effects vector autoregressive models for inference of brain connectivity networks and covariate effects in pediatric traumatic brain injury. Hum Brain Mapp 2024; 45:e26763. [PMID: 38943369 PMCID: PMC11213982 DOI: 10.1002/hbm.26763] [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: 09/21/2023] [Revised: 05/01/2024] [Accepted: 06/08/2024] [Indexed: 07/01/2024] Open
Abstract
In this article, we develop an analytical approach for estimating brain connectivity networks that accounts for subject heterogeneity. More specifically, we consider a novel extension of a multi-subject Bayesian vector autoregressive model that estimates group-specific directed brain connectivity networks and accounts for the effects of covariates on the network edges. We adopt a flexible approach, allowing for (possibly) nonlinear effects of the covariates on edge strength via a novel Bayesian nonparametric prior that employs a weighted mixture of Gaussian processes. For posterior inference, we achieve computational scalability by implementing a variational Bayes scheme. Our approach enables simultaneous estimation of group-specific networks and selection of relevant covariate effects. We show improved performance over competing two-stage approaches on simulated data. We apply our method on resting-state functional magnetic resonance imaging data from children with a history of traumatic brain injury (TBI) and healthy controls to estimate the effects of age and sex on the group-level connectivities. Our results highlight differences in the distribution of parent nodes. They also suggest alteration in the relation of age, with peak edge strength in children with TBI, and differences in effective connectivity strength between males and females.
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Affiliation(s)
- Yangfan Ren
- Department of StatisticsRice UniversityHoustonTexasUSA
| | | | - Christine B. Peterson
- Department of BiostatisticsThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Dana M. DeMaster
- Department of Pediatrics, Children's Learning InstituteUniversity of Texas Health Science CenterHoustonTexasUSA
| | - Linda Ewing‐Cobbs
- Department of Pediatrics, Children's Learning InstituteUniversity of Texas Health Science CenterHoustonTexasUSA
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Dennis EL, Keleher F, Bartnik-Olson B. Neuroimaging Correlates of Functional Outcome Following Pediatric TBI. ADVANCES IN NEUROBIOLOGY 2024; 42:33-84. [PMID: 39432037 DOI: 10.1007/978-3-031-69832-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
Neuroimaging plays an important role in assessing the consequences of TBI across the postinjury period. While identifying alterations to the brain is important, associating those changes to functional, cognitive, and behavioral outcomes is an essential step to establishing the value of advanced neuroimaging for pediatric TBI. Here we highlight research that has revealed links between advanced neuroimaging and outcome after TBI and point to opportunities where neuroimaging could expand our ability to prognosticate and potentially uncover opportunities to intervene.
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Affiliation(s)
- Emily L Dennis
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Finian Keleher
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Brenda Bartnik-Olson
- Department of Radiology, School of Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA.
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Huang MX, Angeles-Quinto A, Robb-Swan A, De-la-Garza BG, Huang CW, Cheng CK, Hesselink JR, Bigler ED, Wilde EA, Vaida F, Troyer EA, Max JE. Assessing Pediatric Mild Traumatic Brain Injury and Its Recovery Using Resting-State Magnetoencephalography Source Magnitude Imaging and Machine Learning. J Neurotrauma 2023; 40:1112-1129. [PMID: 36884305 PMCID: PMC10259613 DOI: 10.1089/neu.2022.0220] [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] [Indexed: 03/09/2023] Open
Abstract
The objectives of this machine-learning (ML) resting-state magnetoencephalography (rs-MEG) study involving children with mild traumatic brain injury (mTBI) and orthopedic injury (OI) controls were to define a neural injury signature of mTBI and to delineate the pattern(s) of neural injury that determine behavioral recovery. Children ages 8-15 years with mTBI (n = 59) and OI (n = 39) from consecutive admissions to an emergency department were studied prospectively for parent-rated post-concussion symptoms (PCS) at: 1) baseline (average of 3 weeks post-injury) to measure pre-injury symptoms and also concurrent symptoms; and 2) at 3-months post-injury. rs-MEG was conducted at the baseline assessment. The ML algorithm predicted cases of mTBI versus OI with sensitivity of 95.5 ± 1.6% and specificity of 90.2 ± 2.7% at 3-weeks post-injury for the combined delta-gamma frequencies. The sensitivity and specificity were significantly better (p < 0.0001) for the combined delta-gamma frequencies compared with the delta-only and gamma-only frequencies. There were also spatial differences in rs-MEG activity between mTBI and OI groups in both delta and gamma bands in frontal and temporal lobe, as well as more widespread differences in the brain. The ML algorithm accounted for 84.5% of the variance in predicting recovery measured by PCS changes between 3 weeks and 3 months post-injury in the mTBI group, and this was significantly lower (p < 10-4) in the OI group (65.6%). Frontal lobe pole (higher) gamma activity was significantly (p < 0.001) associated with (worse) PCS recovery exclusively in the mTBI group. These findings demonstrate a neural injury signature of pediatric mTBI and patterns of mTBI-induced neural injury related to behavioral recovery.
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Affiliation(s)
- Ming-Xiong Huang
- Department of Radiology, University of California, San Diego, California, USA
- Radiology and Research Services, VA San Diego Healthcare System, San Diego, California, USA
| | - Annemarie Angeles-Quinto
- Department of Radiology, University of California, San Diego, California, USA
- Radiology and Research Services, VA San Diego Healthcare System, San Diego, California, USA
| | - Ashley Robb-Swan
- Department of Radiology, University of California, San Diego, California, USA
- Radiology and Research Services, VA San Diego Healthcare System, San Diego, California, USA
| | | | - Charles W. Huang
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Chung-Kuan Cheng
- Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - John R. Hesselink
- Department of Radiology, University of California, San Diego, California, USA
| | - Erin D. Bigler
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | | | - Florin Vaida
- Herbert Wertheim School of Public Health, Division of Biostatistics and Bioinformatics, University of California, San Diego, California, USA
| | - Emily A. Troyer
- Department of Psychiatry, University of California, San Diego, California, USA
| | - Jeffrey E. Max
- Department of Psychiatry, University of California, San Diego, California, USA
- Department of Psychiatry, Rady Children's Hospital, San Diego, California, USA
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DeMaster D, Godlewska BR, Liang M, Vannucci M, Bockmann T, Cao B, Selvaraj S. Effective connectivity between resting-state networks in depression. J Affect Disord 2022; 307:79-86. [PMID: 35331822 DOI: 10.1016/j.jad.2022.03.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/12/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
Abstract
RATIONALE Although depression has been widely researched, findings characterizing how brain regions influence each other remains scarce, yet this is critical for research on antidepressant treatments and individual responses to particular treatments. OBJECTIVES To identify pre-treatment resting state effective connectivity (rsEC) patterns in patients with major depressive disorder (MDD) and explore their relationship with treatment response. METHODS Thirty-four drug-free MDD patients had an MRI scan and were subsequently treated for 6 weeks with an SSRI escitalopram 10 mg daily; the response was defined as ≥50% decrease in Hamilton Depression Rating Scale (HAMD) score. RESULTS rsEC networks in default mode, central executive, and salience networks were identified for patients with depression. Exploratory analyses indicated higher connectivity strength related to baseline depression severity and response to treatment. CONCLUSIONS Preliminary analyses revealed widespread dysfunction of rsEC in depression. Functional rsEC may be useful as a predictive tool for antidepressant treatment response. A primary limitation of the current study was the small size; however, the group was carefully chosen, well-characterized, and included only medication-free patients. Further research in large samples of placebo-controlled studies would be required to confirm the results.
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Affiliation(s)
- Dana DeMaster
- Children's Learning Institute, Department of Pediatrics, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA.
| | - Beata R Godlewska
- Department of Psychiatry, Medical Sciences Division, University of Oxford, United Kingdom.; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Mingrui Liang
- Department of Statistics, Rice University, Houston, TX, USA
| | | | - Taya Bockmann
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Bo Cao
- University of Alberta, Department of Psychiatry, Edmonton, Canada
| | - Sudhakar Selvaraj
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
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