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Poudel GR, Sharma P, Lorenzetti V, Parsons N, Cerin E. Network Representation of fMRI Data Using Visibility Graphs: The Impact of Motion and Test-Retest Reliability. Neuroinformatics 2024; 22:107-118. [PMID: 38332409 PMCID: PMC11021232 DOI: 10.1007/s12021-024-09652-y] [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: 01/02/2024] [Indexed: 02/10/2024]
Abstract
Visibility graphs provide a novel approach for analysing time-series data. Graph theoretical analysis of visibility graphs can provide new features for data mining applications in fMRI. However, visibility graphs features have not been used widely in the field of neuroscience. This is likely due to a lack of understanding of their robustness in the presence of noise (e.g., motion) and their test-retest reliability. In this study, we investigated visibility graph properties of fMRI data in the human connectome project (N = 1010) and tested their sensitivity to motion and test-retest reliability. We also characterised the strength of connectivity obtained using degree synchrony of visibility graphs. We found that strong correlation (r > 0.5) between visibility graph properties, such as the number of communities and average degrees, and motion in the fMRI data. The test-retest reliability (Intraclass correlation coefficient (ICC)) of graph theoretical features was high for the average degrees (0.74, 95% CI = [0.73, 0.75]), and moderate for clustering coefficient (0.43, 95% CI = [0.41, 0.44]) and average path length (0.41, 95% CI = [0.38, 0.44]). Functional connectivity between brain regions was measured by correlating the visibility graph degrees. However, the strength of correlation was found to be moderate to low (r < 0.35). These findings suggest that even small movement in fMRI data can strongly influence robustness and reliability of visibility graph features, thus, requiring robust motion correction strategies prior to data analysis. Further studies are necessary for better understanding of the potential application of visibility graph features in fMRI.
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Affiliation(s)
- Govinda R Poudel
- Mary Mackillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia.
- Braincast Neurotechnologies, Melbourne, Australia.
| | - Prabin Sharma
- Department of Computer Science, University of Massachusetts, Boston, MA, USA.
| | - Valentina Lorenzetti
- Neuroscience of Addiction and Mental Health Program, The Healthy Brain and Mind Research Centre, School of Behavioural and Health Sciences, Faculty of Health Sciences, Australian Catholic University, Melbourne, Australia.
| | - Nicholas Parsons
- School of Psychological Sciences, Monash University, Melbourne, Australia.
- Braincast Neurotechnologies, Melbourne, Australia.
| | - Ester Cerin
- Mary Mackillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia.
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Mellema CJ, Nguyen KP, Treacher A, Andrade AX, Pouratian N, Sharma VD, O'Suileabhain P, Montillo AA. Longitudinal prognosis of Parkinson's outcomes using causal connectivity. Neuroimage Clin 2024; 42:103571. [PMID: 38471435 PMCID: PMC10944096 DOI: 10.1016/j.nicl.2024.103571] [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: 08/25/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/14/2024]
Abstract
Despite the prevalence of Parkinson's disease (PD), there are no clinically-accepted neuroimaging biomarkers to predict the trajectory of motor or cognitive decline or differentiate Parkinson's disease from atypical progressive parkinsonian diseases. Since abnormal connectivity in the motor circuit and basal ganglia have been previously shown as early markers of neurodegeneration, we hypothesize that patterns of interregional connectivity could be useful to form patient-specific predictive models of disease state and of PD progression. We use fMRI data from subjects with Multiple System Atrophy (MSA), Progressive Supranuclear Palsy (PSP), idiopathic PD, and healthy controls to construct predictive models for motor and cognitive decline and differentiate between the four subgroups. Further, we identify the specific connections most informative for progression and diagnosis. When predicting the one-year progression in the MDS-UPDRS-III1* and Montreal Cognitive assessment (MoCA), we achieve new state-of-the-art mean absolute error performance. Additionally, the balanced accuracy we achieve in the diagnosis of PD, MSA, PSP, versus healthy controls surpasses that attained in most clinics, underscoring the relevance of the brain connectivity features. Our models reveal the connectivity between deep nuclei, motor regions, and the thalamus as the most important for prediction. Collectively these results demonstrate the potential of fMRI connectivity as a prognostic biomarker for PD and increase our understanding of this disease.
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Affiliation(s)
- Cooper J Mellema
- Lyda Hill Department of Bioinformatics, United States; Biomedical Engineering Department, United States; University of Texas Southwestern Medical Center, United States
| | - Kevin P Nguyen
- Lyda Hill Department of Bioinformatics, United States; Biomedical Engineering Department, United States; University of Texas Southwestern Medical Center, United States
| | - Alex Treacher
- Lyda Hill Department of Bioinformatics, United States; Biophysics Department, United States; University of Texas Southwestern Medical Center, United States
| | - Aixa X Andrade
- Lyda Hill Department of Bioinformatics, United States; Biomedical Engineering Department, United States; University of Texas Southwestern Medical Center, United States
| | - Nader Pouratian
- Neurosurgery Department, United States; University of Texas Southwestern Medical Center, United States
| | - Vibhash D Sharma
- Neurology Department, United States; University of Texas Southwestern Medical Center, United States
| | - Padraig O'Suileabhain
- Neurology Department, United States; University of Texas Southwestern Medical Center, United States
| | - Albert A Montillo
- Lyda Hill Department of Bioinformatics, United States; Biomedical Engineering Department, United States; Advanced Imaging Research Center, United States; Radiology Department, United States; University of Texas Southwestern Medical Center, United States.
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Voineskos AN, Hawco C, Neufeld NH, Turner JA, Ameis SH, Anticevic A, Buchanan RW, Cadenhead K, Dazzan P, Dickie EW, Gallucci J, Lahti AC, Malhotra AK, Öngür D, Lencz T, Sarpal DK, Oliver LD. Functional magnetic resonance imaging in schizophrenia: current evidence, methodological advances, limitations and future directions. World Psychiatry 2024; 23:26-51. [PMID: 38214624 PMCID: PMC10786022 DOI: 10.1002/wps.21159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Functional neuroimaging emerged with great promise and has provided fundamental insights into the neurobiology of schizophrenia. However, it has faced challenges and criticisms, most notably a lack of clinical translation. This paper provides a comprehensive review and critical summary of the literature on functional neuroimaging, in particular functional magnetic resonance imaging (fMRI), in schizophrenia. We begin by reviewing research on fMRI biomarkers in schizophrenia and the clinical high risk phase through a historical lens, moving from case-control regional brain activation to global connectivity and advanced analytical approaches, and more recent machine learning algorithms to identify predictive neuroimaging features. Findings from fMRI studies of negative symptoms as well as of neurocognitive and social cognitive deficits are then reviewed. Functional neural markers of these symptoms and deficits may represent promising treatment targets in schizophrenia. Next, we summarize fMRI research related to antipsychotic medication, psychotherapy and psychosocial interventions, and neurostimulation, including treatment response and resistance, therapeutic mechanisms, and treatment targeting. We also review the utility of fMRI and data-driven approaches to dissect the heterogeneity of schizophrenia, moving beyond case-control comparisons, as well as methodological considerations and advances, including consortia and precision fMRI. Lastly, limitations and future directions of research in the field are discussed. Our comprehensive review suggests that, in order for fMRI to be clinically useful in the care of patients with schizophrenia, research should address potentially actionable clinical decisions that are routine in schizophrenia treatment, such as which antipsychotic should be prescribed or whether a given patient is likely to have persistent functional impairment. The potential clinical utility of fMRI is influenced by and must be weighed against cost and accessibility factors. Future evaluations of the utility of fMRI in prognostic and treatment response studies may consider including a health economics analysis.
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Affiliation(s)
- Aristotle N Voineskos
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Colin Hawco
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nicholas H Neufeld
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Jessica A Turner
- Department of Psychiatry and Behavioral Health, Wexner Medical Center, Ohio State University, Columbus, OH, USA
| | - Stephanie H Ameis
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Cundill Centre for Child and Youth Depression and McCain Centre for Child, Youth and Family Mental Health, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Alan Anticevic
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Robert W Buchanan
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kristin Cadenhead
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Paola Dazzan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Erin W Dickie
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Julia Gallucci
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Adrienne C Lahti
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anil K Malhotra
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Psychiatry, Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY, USA
| | - Dost Öngür
- McLean Hospital/Harvard Medical School, Belmont, MA, USA
| | - Todd Lencz
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Psychiatry, Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY, USA
| | - Deepak K Sarpal
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsay D Oliver
- Campbell Family Mental Health Research Institute and Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
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