1
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Jahanshad N, Lenzini P, Bijsterbosch J. Current best practices and future opportunities for reproducible findings using large-scale neuroimaging in psychiatry. Neuropsychopharmacology 2024:10.1038/s41386-024-01938-8. [PMID: 39117903 DOI: 10.1038/s41386-024-01938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/05/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024]
Abstract
Research into the brain basis of psychopathology is challenging due to the heterogeneity of psychiatric disorders, extensive comorbidities, underdiagnosis or overdiagnosis, multifaceted interactions with genetics and life experiences, and the highly multivariate nature of neural correlates. Therefore, increasingly larger datasets that measure more variables in larger cohorts are needed to gain insights. In this review, we present current "best practice" approaches for using existing databases, collecting and sharing new repositories for big data analyses, and future directions for big data in neuroimaging and psychiatry with an emphasis on contributing to collaborative efforts and the challenges of multi-study data analysis.
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Affiliation(s)
- Neda Jahanshad
- Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, 90292, USA.
| | - Petra Lenzini
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Janine Bijsterbosch
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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2
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Hu F, Lucas A, Chen AA, Coleman K, Horng H, Ng RWS, Tustison NJ, Davis KA, Shou H, Li M, Shinohara RT. DeepComBat: A statistically motivated, hyperparameter-robust, deep learning approach to harmonization of neuroimaging data. Hum Brain Mapp 2024; 45:e26708. [PMID: 39056477 PMCID: PMC11273293 DOI: 10.1002/hbm.26708] [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: 02/26/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 07/28/2024] Open
Abstract
Neuroimaging data acquired using multiple scanners or protocols are increasingly available. However, such data exhibit technical artifacts across batches which introduce confounding and decrease reproducibility. This is especially true when multi-batch data are analyzed using complex downstream models which are more likely to pick up on and implicitly incorporate batch-related information. Previously proposed image harmonization methods have sought to remove these batch effects; however, batch effects remain detectable in the data after applying these methods. We present DeepComBat, a deep learning harmonization method based on a conditional variational autoencoder and the ComBat method. DeepComBat combines the strengths of statistical and deep learning methods in order to account for the multivariate relationships between features while simultaneously relaxing strong assumptions made by previous deep learning harmonization methods. As a result, DeepComBat can perform multivariate harmonization while preserving data structure and avoiding the introduction of synthetic artifacts. We apply this method to cortical thickness measurements from a cognitive-aging cohort and show DeepComBat qualitatively and quantitatively outperforms existing methods in removing batch effects while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically motivated deep learning harmonization methods.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Alfredo Lucas
- Center for Neuroengineering and Therapeutics, Department of EngineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Andrew A. Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Kyle Coleman
- Statistical Center for Single‐Cell and Spatial GenomicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Raymond W. S. Ng
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Nicholas J. Tustison
- Department of Radiology and Medical ImagingUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Kathryn A. Davis
- Center for Neuroengineering and Therapeutics, Department of EngineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of NeurologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Center for Biomedical Image Computing and Analytics (CBICA)Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Mingyao Li
- Statistical Center for Single‐Cell and Spatial GenomicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Center for Biomedical Image Computing and Analytics (CBICA)Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
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3
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Gardner M, Shinohara RT, Bethlehem RAI, Romero-Garcia R, Warrier V, Dorfschmidt L, Shanmugan S, Thompson P, Seidlitz J, Alexander-Bloch AF, Chen AA. ComBatLS: A location- and scale-preserving method for multi-site image harmonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599875. [PMID: 39131292 PMCID: PMC11312440 DOI: 10.1101/2024.06.21.599875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Recent work has leveraged massive datasets and advanced harmonization methods to construct normative models of neuroanatomical features and benchmark individuals' morphology. However, current harmonization tools do not preserve the effects of biological covariates including sex and age on features' variances; this failure may induce error in normative scores, particularly when such factors are distributed unequally across sites. Here, we introduce a new extension of the popular ComBat harmonization method, ComBatLS, that preserves biological variance in features' locations and scales. We use UK Biobank data to show that ComBatLS robustly replicates individuals' normative scores better than other ComBat methods when subjects are assigned to sex-imbalanced synthetic "sites". Additionally, we demonstrate that ComBatLS significantly reduces sex biases in normative scores compared to traditional methods. Finally, we show that ComBatLS successfully harmonizes consortium data collected across over 50 studies. R implementation of ComBatLS is available at https://github.com/andy1764/ComBatFamily.
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Affiliation(s)
- Margaret Gardner
- Brain-Gene-Development Lab, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Center for Biomedical Imaging Computing and Analytics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, USA
| | | | - Rafael Romero-Garcia
- Instituto de Biomedicina de Sevilla (IBiS) HUVR/CSIC/Universidad de Sevilla/CIBERSAM, ISCIII, Dpto. de Fisiología Médica y Biofísica, Seville, ES
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Varun Warrier
- Department of Psychology, University of Cambridge, Cambridge, UK
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Lena Dorfschmidt
- Brain-Gene-Development Lab, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sheila Shanmugan
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA
| | - Paul Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging & Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jakob Seidlitz
- Brain-Gene-Development Lab, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aaron F Alexander-Bloch
- Brain-Gene-Development Lab, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrew A Chen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
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4
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Quidé Y, Jahanshad N, Andoh J, Antoniou G, Apkarian AV, Ashar YK, Badran BW, Baird CL, Baxter L, Bell TR, Blanco-Hinojo L, Borckardt J, Cheung CL, Ciampi de Andrade D, Couto BA, Cox SR, Cruz-Almeida Y, Dannlowski U, De Martino E, de Tommaso M, Deus J, Domin M, Egorova-Brumley N, Elliott J, Fanton S, Fauchon C, Flor H, Franz CE, Gatt JM, Gerdhem P, Gilman JM, Gollub RL, Govind V, Graven-Nielsen T, Håkansson G, Hales T, Haswell C, Heukamp NJ, Hu L, Huang L, Hussain A, Jensen K, Kircher T, Kremen WS, Leehr EJ, Lindquist M, Loggia ML, Lotze M, Martucci KT, Meeker TJ, Meinert S, Millard SK, Morey RA, Murillo C, Nees F, Nenadic I, Park HRP, Peng X, Ploner M, Pujol J, Robayo LE, Salan T, Seminowicz DA, Serian A, Slater R, Stein F, Stevens J, Strauss S, Sun D, Vachon-Presseau E, Valdes-Hernandez PA, Vanneste S, Vernon M, Verriotis M, Wager TD, Widerstrom-Noga E, Woodbury A, Zeidan F, Bhatt RR, Ching CRK, Haddad E, Thomopoulos SI, Thompson PM, Gustin SM. ENIGMA-Chronic Pain: a worldwide initiative to identify brain correlates of chronic pain. Pain 2024:00006396-990000000-00664. [PMID: 39058957 DOI: 10.1097/j.pain.0000000000003317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 07/28/2024]
Affiliation(s)
- Yann Quidé
- School of Psychology, The University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Randwick, NSW, Australia
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jamila Andoh
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Georgia Antoniou
- Division of Population Health and Genomics, Medical Research Institute, University of Dundee, Dundee, Scotland, United Kingdom
| | - Apkar Vania Apkarian
- Center for Translational Pain Research, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yoni K Ashar
- Department of General Internal Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Bashar W Badran
- Department of Psychiatry and Behavioral Sciences, Neuro-X Lab, Medical University of South Carolina, Charleston, SC, United States
| | - C Lexi Baird
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
- VA Mid-Atlantic MIRECC, Durham VA Medical Center, Durham VA, Durham, NC, United States
| | - Luke Baxter
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Tyler R Bell
- Department of Psychiatry, University of California, San Diego, CA, United States
- Center for Behavior Genetics of Aging, University of California, San Diego, CA, United States
| | - Laura Blanco-Hinojo
- MRI Research Unit, Department of Radiology, Hospital del Mar, Barcelona, Spain
- IsGlobal, Barcelona, Spain
| | - Jeffrey Borckardt
- Department of Psychiatry and Behavioral Sciences, Neuro-X Lab, Medical University of South Carolina, Charleston, SC, United States
- Medical University of South Carolina, Charleston, SC, United States
- Ralph H. Johnson VAMC, Charleston, SC, United States
| | - Chloe L Cheung
- Neuroscience Graduate Program, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Daniel Ciampi de Andrade
- Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Bruno A Couto
- Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Yenisel Cruz-Almeida
- Pain Research and Intervention Center of Excellence, University of Florida, Gainesville, FL, United States
- Department of Community Dentistry and Behavioral Sciences, College of Dentistry, University of Florida, Gainesville, FL, United States
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Udo Dannlowski
- Institute of Translational Psychiatry, University of Münster, Münster, Germany
| | - Enrico De Martino
- Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Marina de Tommaso
- Neurophysiopathology Unit, DiBrain Department, Bari Aldo Moro University, Bari, Italy
| | - Joan Deus
- MRI Research Unit, Department of Radiology, Hospital del Mar, Barcelona, Spain
- Department of Clinical and Health Psychology, Autonomous University of Barcelona, Barcelona, Spain
| | - Martin Domin
- Functional Imaging Unit, Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Natalia Egorova-Brumley
- Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - James Elliott
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Northern Sydney Local Health District, Sydney, NSW, Australia
- The Kolling Institute, St Leonards, NSW, Australia
| | - Silvia Fanton
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Camille Fauchon
- Neuro-Dol, Inserm, University Hospital of Clermont-Ferrand, University of Clermont-Auvergne, Clermont-Ferrand, France
- NEUROPAIN Team, CRNL, CNRS, Inserm, University of Saint-Etienne, Saint-Etienne, France
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Heidelberg University, Mannheim, Germany
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, CA, United States
- Center for Behavior Genetics of Aging, University of California, San Diego, CA, United States
| | - Justine M Gatt
- School of Psychology, The University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
- Centre for Wellbeing, Resilience and Recovery, Neuroscience Research Australia, Randwick, NSW, Australia
- Black Dog Institute, Randwick, NSW, Australia
| | - Paul Gerdhem
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Orthopaedics and Hand Surgery, Uppsala University Hospital, Uppsala, Sweden
| | - Jodi M Gilman
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Addiction Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Randy L Gollub
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Varan Govind
- Department of Radiology, University of Miami, Miller School of Medicine, Miami, FL, United States
| | - Thomas Graven-Nielsen
- Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Gustaf Håkansson
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Tim Hales
- Consortium Against Pain Inequality, University of Dundee, Dundee, Scotland, United Kingdom
| | - Courtney Haswell
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
- VA Mid-Atlantic MIRECC, Durham VA Medical Center, Durham VA, Durham, NC, United States
| | - Nils Jannik Heukamp
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - Li Hu
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Lejian Huang
- Center for Translational Pain Research, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Ahmed Hussain
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
- VA Mid-Atlantic MIRECC, Durham VA Medical Center, Durham VA, Durham, NC, United States
| | - Karin Jensen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, CA, United States
- Center for Behavior Genetics of Aging, University of California, San Diego, CA, United States
| | - Elisabeth J Leehr
- Institute of Translational Psychiatry, University of Münster, Münster, Germany
| | - Martin Lindquist
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, United States
| | - Marco L Loggia
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Anesthesia, Clinical Care, and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Martin Lotze
- Functional Imaging Unit, Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Katherine T Martucci
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Timothy J Meeker
- Department of Biology, Morgan State University, Baltimore, MD, United States
| | - Susanne Meinert
- Institute of Translational Psychiatry, University of Münster, Münster, Germany
- Institute for Translational Neuroscience, University of Münster, Münster, Germany
| | - Samantha K Millard
- Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Rajendra A Morey
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
- VA Mid-Atlantic MIRECC, Durham VA Medical Center, Durham VA, Durham, NC, United States
| | - Carlos Murillo
- Department of General Internal Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Rehabilitation Sciences, Ghent University, Ghent, Belgium
| | - Frauke Nees
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - Igor Nenadic
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
| | - Haeme R P Park
- School of Psychology, The University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
- Centre for Wellbeing, Resilience and Recovery, Neuroscience Research Australia, Randwick, NSW, Australia
| | - Xiaolong Peng
- Department of Psychiatry and Behavioral Sciences, Neuro-X Lab, Medical University of South Carolina, Charleston, SC, United States
| | - Markus Ploner
- Department of Neurology, Center for Interdisciplinary Pain Medicine and TUM-Neuroimaging Center, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Jesus Pujol
- MRI Research Unit, Department of Radiology, Hospital del Mar, Barcelona, Spain
| | - Linda E Robayo
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Teddy Salan
- Department of Radiology, University of Miami, Miller School of Medicine, Miami, FL, United States
| | - David A Seminowicz
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Angela Serian
- Department of Neurology, University Hospital Greifswald, Greifswald, Germany
| | - Rebeccah Slater
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Frederike Stein
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
| | - Jennifer Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
- Atlanta Veterans Affairs Healthcare System, Atlanta, GA, United States
| | - Sebastian Strauss
- Department of Neurology, University Hospital Greifswald, Greifswald, Germany
| | - Delin Sun
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
- VA Mid-Atlantic MIRECC, Durham VA Medical Center, Durham VA, Durham, NC, United States
- Department of Psychiatry, School of Medicine, Duke University, Durham, NC, United States
| | - Etienne Vachon-Presseau
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
- Department of Anesthesia, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain (AECRP), McGill University, Montreal, QC, Canada
| | - Pedro A Valdes-Hernandez
- Department of Community Dentistry and Behavioral Sciences, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Sven Vanneste
- School of Psychology, Trinity College Dublin, Dublin, Ireland
- Trinity Institute for Neuroscience, Trinity College Dublin, Dublin, Ireland
- Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
| | - Mark Vernon
- Atlanta Veterans Affairs Healthcare System, Atlanta, GA, United States
| | - Madeleine Verriotis
- Developmental Neurosciences Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Anaesthesia and Pain Medicine, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Tor D Wager
- Dartmouth College, Hanover, NH, United States
| | - Eva Widerstrom-Noga
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Anna Woodbury
- Atlanta Veterans Affairs Healthcare System, Atlanta, GA, United States
- Division of Pain Medicine, Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA, United States
| | - Fadel Zeidan
- Center for Pain Medicine, Department of Anesthesiology, University of California San Diego, La Jolla, CA, United States
| | - Ravi R Bhatt
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Christopher R K Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Elizabeth Haddad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sophia I Thomopoulos
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sylvia M Gustin
- School of Psychology, The University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Randwick, NSW, Australia
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5
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Lin J, Li Z, Zeng Y, Liu X, Li L, Jahanshad N, Ge X, Zhang D, Lu M, Liu M. Harmonizing three-dimensional MRI using pseudo-warping field guided GAN. Neuroimage 2024; 295:120635. [PMID: 38729542 DOI: 10.1016/j.neuroimage.2024.120635] [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: 02/26/2024] [Revised: 04/15/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
In pursuit of cultivating automated models for magnetic resonance imaging (MRI) to aid in diagnostics, an escalating demand for extensive, multisite, and heterogeneous brain imaging datasets has emerged. This potentially introduces biased outcomes when directly applied for subsequent analysis. Researchers have endeavored to address this issue by pursuing the harmonization of MRIs. However, most existing image-based harmonization methods for MRI are tailored for 2D slices, which may introduce inter-slice variations when they are combined into a 3D volume. In this study, we aim to resolve inconsistencies between slices by introducing a pseudo-warping field. This field is created randomly and utilized to transform a slice into an artificially warped subsequent slice. The objective of this pseudo-warping field is to ensure that generators can consistently harmonize adjacent slices to another domain, without being affected by the varying content present in different slices. Furthermore, we construct unsupervised spatial and recycle loss to enhance the spatial accuracy and slice-wise consistency across the 3D images. The results demonstrate that our model effectively mitigates inter-slice variations and successfully preserves the anatomical details of the images during the harmonization process. Compared to generative harmonization models that employ 3D operators, our model exhibits greater computational efficiency and flexibility.
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Affiliation(s)
- Jiaying Lin
- Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhuoshuo Li
- Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Youbing Zeng
- Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Xiaobo Liu
- Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Liang Li
- Genuine Digital Technology Co., Ltd., Xi'an, China.
| | - Neda Jahanshad
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Xinting Ge
- School of Information Science and Engineering, Shandong Normal University, Shandong 250358, China.
| | - Dan Zhang
- School of Cyber Science and Engineering, Ningbo University of Technology, Zhejiang 315211, China.
| | - Minhua Lu
- Department of Biomedical Engineering, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China.
| | - Mengting Liu
- Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
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6
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Pinho AL, Richard H, Ponce AF, Eickenberg M, Amadon A, Dohmatob E, Denghien I, Torre JJ, Shankar S, Aggarwal H, Thual A, Chapalain T, Ginisty C, Becuwe-Desmidt S, Roger S, Lecomte Y, Berland V, Laurier L, Joly-Testault V, Médiouni-Cloarec G, Doublé C, Martins B, Varoquaux G, Dehaene S, Hertz-Pannier L, Thirion B. Individual Brain Charting dataset extension, third release for movie watching and retinotopy data. Sci Data 2024; 11:590. [PMID: 38839770 PMCID: PMC11153490 DOI: 10.1038/s41597-024-03390-1] [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] [Received: 11/21/2023] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
The Individual Brain Charting (IBC) is a multi-task functional Magnetic Resonance Imaging dataset acquired at high spatial-resolution and dedicated to the cognitive mapping of the human brain. It consists in the deep phenotyping of twelve individuals, covering a broad range of psychological domains suitable for functional-atlasing applications. Here, we present the inclusion of task data from both naturalistic stimuli and trial-based designs, to uncover structures of brain activation. We rely on the Fast Shared Response Model (FastSRM) to provide a data-driven solution for modelling naturalistic stimuli, typically containing many features. We show that data from left-out runs can be reconstructed using FastSRM, enabling the extraction of networks from the visual, auditory and language systems. We also present the topographic organization of the visual system through retinotopy. In total, six new tasks were added to IBC, wherein four trial-based retinotopic tasks contributed with a mapping of the visual field to the cortex. IBC is open access: source plus derivatives imaging data and meta-data are available in public repositories.
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Affiliation(s)
- Ana Luísa Pinho
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France.
- Department of Computer Science, Western University, London, Ontario, Canada.
- Western Centre for Brain and Mind, Western University, London, Ontario, Canada.
| | - Hugo Richard
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
- Criteo AI Labs, Paris, France
- FAIRPLAY - IA coopérative: équité, vie privée, incitations, Paris, France
| | | | - Michael Eickenberg
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
- Flatiron Institute, New York, USA
| | - Alexis Amadon
- Université Paris-Saclay, CEA, CNRS, BAOBAB, NeuroSpin, 91191, Gif-sur-Yvette, France
| | - Elvis Dohmatob
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
- Meta FAIR, Paris, France
| | - Isabelle Denghien
- Cognitive Neuroimaging Unit, INSERM, CEA, Université Paris-Saclay, NeuroSpin center, 91191, Gif-sur-Yvette, France
| | | | - Swetha Shankar
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
| | | | - Alexis Thual
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
- Cognitive Neuroimaging Unit, INSERM, CEA, Université Paris-Saclay, NeuroSpin center, 91191, Gif-sur-Yvette, France
- Collège de France, Paris, France
| | | | | | | | | | - Yann Lecomte
- CEA Saclay/DRF/IFJ/NeuroSpin/UNIACT, Paris, France
| | | | | | | | | | | | | | - Gaël Varoquaux
- Université Paris-Saclay, Inria, CEA, Palaiseau, 91120, France
| | - Stanislas Dehaene
- Cognitive Neuroimaging Unit, INSERM, CEA, Université Paris-Saclay, NeuroSpin center, 91191, Gif-sur-Yvette, France
- Collège de France, Paris, France
| | - Lucie Hertz-Pannier
- CEA Saclay/DRF/IFJ/NeuroSpin/UNIACT, Paris, France
- UMR 1141, NeuroDiderot, Université de Paris, Paris, France
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7
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Meng Z, Huang Y, Wang W, Zhou L, Zhou K. Orienting role of the putative human posterior infero-temporal area in visual attention. Cortex 2024; 175:54-65. [PMID: 38704919 DOI: 10.1016/j.cortex.2024.04.006] [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: 09/27/2023] [Revised: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
The dorsal attention network (DAN) is a network of brain regions essential for attentional orienting, which includes the lateral intraparietal area (LIP) and frontal eye field (FEF). Recently, the putative human dorsal posterior infero-temporal area (phPITd) has been identified as a new node of the DAN. However, its functional relationship with other areas of the DAN and its specific role in visual attention remained unclear. In this study, we analyzed a large publicly available neuroimaging dataset to investigate the intrinsic functional connectivities (FCs) of the phPITd with other brain areas. The results showed that the intrinsic FCs of the phPITd with the areas of the visual network and the DAN were significantly stronger than those with the ventral attention network (VAN) areas and areas of other networks. We further conducted individual difference analyses with a sample size of 295 participants and a series of attentional tasks to investigate which attentional components each phPITd-based DAN edge predicts. Our findings revealed that the intrinsic FC of the left phPITd with the LIPv could predict individual ability in attentional orienting, but not in alerting, executive control, and distractor suppression. Our results not only provide direct evidence of the phPITd's functional relationship with the LIPv, but also offer a comprehensive understanding of its specific role in visual attention.
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Affiliation(s)
- Zong Meng
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University, Beijing, 100875, China
| | - Yingjie Huang
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University, Beijing, 100875, China
| | - Wenbo Wang
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University, Beijing, 100875, China
| | - Liqin Zhou
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University, Beijing, 100875, China.
| | - Ke Zhou
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University, Beijing, 100875, China.
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8
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Zhu Y, Maikusa N, Radua J, Sämann PG, Fusar-Poli P, Agartz I, Andreassen OA, Bachman P, Baeza I, Chen X, Choi S, Corcoran CM, Ebdrup BH, Fortea A, Garani RR, Glenthøj BY, Glenthøj LB, Haas SS, Hamilton HK, Hayes RA, He Y, Heekeren K, Kasai K, Katagiri N, Kim M, Kristensen TD, Kwon JS, Lawrie SM, Lebedeva I, Lee J, Loewy RL, Mathalon DH, McGuire P, Mizrahi R, Mizuno M, Møller P, Nemoto T, Nordholm D, Omelchenko MA, Raghava JM, Røssberg JI, Rössler W, Salisbury DF, Sasabayashi D, Smigielski L, Sugranyes G, Takahashi T, Tamnes CK, Tang J, Theodoridou A, Tomyshev AS, Uhlhaas PJ, Værnes TG, van Amelsvoort TAMJ, Waltz JA, Westlye LT, Zhou JH, Thompson PM, Hernaus D, Jalbrzikowski M, Koike S. Using brain structural neuroimaging measures to predict psychosis onset for individuals at clinical high-risk. Mol Psychiatry 2024; 29:1465-1477. [PMID: 38332374 PMCID: PMC11189817 DOI: 10.1038/s41380-024-02426-7] [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: 08/16/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
Machine learning approaches using structural magnetic resonance imaging (sMRI) can be informative for disease classification, although their ability to predict psychosis is largely unknown. We created a model with individuals at CHR who developed psychosis later (CHR-PS+) from healthy controls (HCs) that can differentiate each other. We also evaluated whether we could distinguish CHR-PS+ individuals from those who did not develop psychosis later (CHR-PS-) and those with uncertain follow-up status (CHR-UNK). T1-weighted structural brain MRI scans from 1165 individuals at CHR (CHR-PS+, n = 144; CHR-PS-, n = 793; and CHR-UNK, n = 228), and 1029 HCs, were obtained from 21 sites. We used ComBat to harmonize measures of subcortical volume, cortical thickness and surface area data and corrected for non-linear effects of age and sex using a general additive model. CHR-PS+ (n = 120) and HC (n = 799) data from 20 sites served as a training dataset, which we used to build a classifier. The remaining samples were used external validation datasets to evaluate classifier performance (test, independent confirmatory, and independent group [CHR-PS- and CHR-UNK] datasets). The accuracy of the classifier on the training and independent confirmatory datasets was 85% and 73% respectively. Regional cortical surface area measures-including those from the right superior frontal, right superior temporal, and bilateral insular cortices strongly contributed to classifying CHR-PS+ from HC. CHR-PS- and CHR-UNK individuals were more likely to be classified as HC compared to CHR-PS+ (classification rate to HC: CHR-PS+, 30%; CHR-PS-, 73%; CHR-UNK, 80%). We used multisite sMRI to train a classifier to predict psychosis onset in CHR individuals, and it showed promise predicting CHR-PS+ in an independent sample. The results suggest that when considering adolescent brain development, baseline MRI scans for CHR individuals may be helpful to identify their prognosis. Future prospective studies are required about whether the classifier could be actually helpful in the clinical settings.
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Affiliation(s)
- Yinghan Zhu
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Norihide Maikusa
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Joaquim Radua
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBERSAM, Instituto de Salud Carlos III, Universitat de Barcelona, Barcelona, Spain
| | | | - Paolo Fusar-Poli
- Early Psychosis: Interventions and Clinical-detection (EPIC) Lab, Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Ingrid Agartz
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet & Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
- KG Jebsen Center for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- KG Jebsen Center for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Bachman
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA
| | - Inmaculada Baeza
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neuroscience, 2017SGR-881, Hospital Clinic Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Universitat de Barcelona, Barcelona, Spain
| | - Xiaogang Chen
- National Clinical Research Center for Mental Disorders and Department of Psychiatry, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sunah Choi
- Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
| | - Cheryl M Corcoran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Mental Illness Research, Education, and Clinical Center, James J Peters VA Medical Center, New York City, NY, USA
| | - Bjørn H Ebdrup
- Centre for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Centre Glostrup, Copenhagen University Hospital, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adriana Fortea
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neuroscience, Hospital Clinic Barcelona, Fundació Clínic Recerca Biomèdica, Universitat de Barcelona, Barcelona, Spain
| | - Ranjini Rg Garani
- Douglas Research Center; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Birte Yding Glenthøj
- Centre for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Centre Glostrup, Copenhagen University Hospital, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louise Birkedal Glenthøj
- Copenhagen Research Center for Mental Health, Mental Health Center Copenhagen, University of Copenhagen Copenhagen, Copenhagen, Denmark
| | - Shalaila S Haas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Holly K Hamilton
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Health Care System, San Francisco, CA, USA
| | - Rebecca A Hayes
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA
| | - Ying He
- National Clinical Research Center for Mental Disorders and Department of Psychiatry, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Karsten Heekeren
- Department of Psychiatry and Psychotherapy I, LVR-Hospital Cologne, Cologne, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- The University of Tokyo Institute for Diversity and Adaptation of Human Mind, The University of Tokyo, Tokyo, Japan
- The International Research Center for Neurointelligence at The University of Tokyo Institutes for Advanced Study (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Naoyuki Katagiri
- Department of Neuropsychiatry, Toho University School of Medicine, Tokyok, Japan
| | - Minah Kim
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, South Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, South Korea
| | - Tina D Kristensen
- Centre for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Centre Glostrup, Copenhagen University Hospital, Glostrup, Denmark
| | - Jun Soo Kwon
- Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, South Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Irina Lebedeva
- Laboratory of Neuroimaging and Multimodal Analysis, Mental Health Research Center, Moscow, Russian Federation
| | - Jimmy Lee
- Department of Psychosis, Institute of Mental Health, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Rachel L Loewy
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel H Mathalon
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Health Care System, San Francisco, CA, USA
| | - Philip McGuire
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Romina Mizrahi
- Douglas Research Center; Department of Psychiatry, McGill University, Montreal, QC, Canada
| | | | - Paul Møller
- Department for Mental Health Research and Development, Division of Mental Health and Addiction, Vestre Viken Hospital Trust, Drammen, Norway
| | - Takahiro Nemoto
- Department of Neuropsychiatry, Toho University School of Medicine, Tokyok, Japan
| | - Dorte Nordholm
- Copenhagen Research Center for Mental Health, Mental Health Center Copenhagen, University of Copenhagen Copenhagen, Copenhagen, Denmark
| | - Maria A Omelchenko
- Department of Youth Psychiatry, Mental Health Research Center, Moscow, Russian Federation
| | - Jayachandra M Raghava
- Centre for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Centre Glostrup, Copenhagen University Hospital, Glostrup, Denmark
- Department of Clinical Physiology, Nuclear Medicine and PET, Functional Imaging, University of Copenhagen Copenhagen, Copenhagen, Denmark
| | - Jan I Røssberg
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Wulf Rössler
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dean F Salisbury
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daiki Sasabayashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Lukasz Smigielski
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Child and Adolescent Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Gisela Sugranyes
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neuroscience, 2017SGR-881, Hospital Clinic Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Universitat de Barcelona, Barcelona, Spain
| | - Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Christian K Tamnes
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Jinsong Tang
- Department of Psychiatry, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, China
- Key Laboratory of Medical Neurobiology of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Anastasia Theodoridou
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alexander S Tomyshev
- Laboratory of Neuroimaging and Multimodal Analysis, Mental Health Research Center, Moscow, Russian Federation
| | - Peter J Uhlhaas
- Department of Child and Adolescent Psychiatry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, UK
| | - Tor G Værnes
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Early Intervention in Psychosis Advisory Unit for South-East Norway, TIPS Sør-Øst, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Therese A M J van Amelsvoort
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - James A Waltz
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore County, Baltimore, MD, USA
| | - Lars T Westlye
- KG Jebsen Center for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Juan H Zhou
- 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
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Dennis Hernaus
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Maria Jalbrzikowski
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Cambridge, MA, USA
| | - Shinsuke Koike
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
- The University of Tokyo Institute for Diversity and Adaptation of Human Mind, The University of Tokyo, Tokyo, Japan.
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9
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Thalhammer M, Schulz J, Scheulen F, Oubaggi MEM, Kirschner M, Kaiser S, Schmidt A, Borgwardt S, Avram M, Brandl F, Sorg C. Distinct Volume Alterations of Thalamic Nuclei Across the Schizophrenia Spectrum. Schizophr Bull 2024:sbae037. [PMID: 38577901 DOI: 10.1093/schbul/sbae037] [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: 04/06/2024]
Abstract
BACKGROUND AND HYPOTHESIS Abnormal thalamic nuclei volumes and their link to cognitive impairments have been observed in schizophrenia. However, whether and how this finding extends to the schizophrenia spectrum is unknown. We hypothesized a distinct pattern of aberrant thalamic nuclei volume across the spectrum and examined its potential associations with cognitive symptoms. STUDY DESIGN We performed a FreeSurfer-based volumetry of T1-weighted brain MRIs from 137 healthy controls, 66 at-risk mental state (ARMS) subjects, 89 first-episode psychosis (FEP) individuals, and 126 patients with schizophrenia to estimate thalamic nuclei volumes of six nuclei groups (anterior, lateral, ventral, intralaminar, medial, and pulvinar). We used linear regression models, controlling for sex, age, and estimated total intracranial volume, both to compare thalamic nuclei volumes across groups and to investigate their associations with positive, negative, and cognitive symptoms. STUDY RESULTS We observed significant volume alterations in medial and lateral thalamic nuclei. Medial nuclei displayed consistently reduced volumes across the spectrum compared to controls, while lower lateral nuclei volumes were only observed in schizophrenia. Whereas positive and negative symptoms were not associated with reduced nuclei volumes across all groups, higher cognitive scores were linked to lower volumes of medial nuclei in ARMS. In FEP, cognition was not linked to nuclei volumes. In schizophrenia, lower cognitive performance was associated with lower medial volumes. CONCLUSIONS Results demonstrate distinct thalamic nuclei volume reductions across the schizophrenia spectrum, with lower medial nuclei volumes linked to cognitive deficits in ARMS and schizophrenia. Data suggest a distinctive trajectory of thalamic nuclei abnormalities along the course of schizophrenia.
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Affiliation(s)
- Melissa Thalhammer
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Schulz
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Felicitas Scheulen
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Mohamed El Mehdi Oubaggi
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias Kirschner
- Department of Psychiatry, University Hospital of Geneva, Geneva, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital, University of Zurich, Zurich, Switzerland
| | - Stefan Kaiser
- Department of Psychiatry, University Hospital of Geneva, Geneva, Switzerland
| | - André Schmidt
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
| | - Stefan Borgwardt
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Mihai Avram
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Felix Brandl
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Sorg
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany
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10
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Svanera M, Savardi M, Signoroni A, Benini S, Muckli L. Fighting the scanner effect in brain MRI segmentation with a progressive level-of-detail network trained on multi-site data. Med Image Anal 2024; 93:103090. [PMID: 38241763 DOI: 10.1016/j.media.2024.103090] [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: 02/16/2023] [Revised: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
Many clinical and research studies of the human brain require accurate structural MRI segmentation. While traditional atlas-based methods can be applied to volumes from any acquisition site, recent deep learning algorithms ensure high accuracy only when tested on data from the same sites exploited in training (i.e., internal data). Performance degradation experienced on external data (i.e., unseen volumes from unseen sites) is due to the inter-site variability in intensity distributions, and to unique artefacts caused by different MR scanner models and acquisition parameters. To mitigate this site-dependency, often referred to as the scanner effect, we propose LOD-Brain, a 3D convolutional neural network with progressive levels-of-detail (LOD), able to segment brain data from any site. Coarser network levels are responsible for learning a robust anatomical prior helpful in identifying brain structures and their locations, while finer levels refine the model to handle site-specific intensity distributions and anatomical variations. We ensure robustness across sites by training the model on an unprecedentedly rich dataset aggregating data from open repositories: almost 27,000 T1w volumes from around 160 acquisition sites, at 1.5 - 3T, from a population spanning from 8 to 90 years old. Extensive tests demonstrate that LOD-Brain produces state-of-the-art results, with no significant difference in performance between internal and external sites, and robust to challenging anatomical variations. Its portability paves the way for large-scale applications across different healthcare institutions, patient populations, and imaging technology manufacturers. Code, model, and demo are available on the project website.
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Affiliation(s)
- Michele Svanera
- Center for Cognitive Neuroimaging at the School of Psychology & Neuroscience, University of Glasgow, UK.
| | - Mattia Savardi
- Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy
| | - Alberto Signoroni
- Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy
| | - Sergio Benini
- Department of Information Engineering, University of Brescia, Italy
| | - Lars Muckli
- Center for Cognitive Neuroimaging at the School of Psychology & Neuroscience, University of Glasgow, UK
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11
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Thiel K, Lemke H, Winter A, Flinkenflügel K, Waltemate L, Bonnekoh L, Grotegerd D, Dohm K, Hahn T, Förster K, Kanske P, Repple J, Opel N, Redlich R, David F, Forstner AJ, Stein F, Brosch K, Thomas-Odenthal F, Usemann P, Teutenberg L, Straube B, Alexander N, Jamalabadi H, Jansen A, Witt SH, Andlauer TFM, Pfennig A, Bauer M, Nenadić I, Kircher T, Meinert S, Dannlowski U. White and gray matter alterations in bipolar I and bipolar II disorder subtypes compared with healthy controls - exploring associations with disease course and polygenic risk. Neuropsychopharmacology 2024; 49:814-823. [PMID: 38332015 PMCID: PMC10948847 DOI: 10.1038/s41386-024-01812-7] [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: 10/19/2023] [Revised: 12/28/2023] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
Patients with bipolar disorder (BD) show alterations in both gray matter volume (GMV) and white matter (WM) integrity compared with healthy controls (HC). However, it remains unclear whether the phenotypically distinct BD subtypes (BD-I and BD-II) also exhibit brain structural differences. This study investigated GMV and WM differences between HC, BD-I, and BD-II, along with clinical and genetic associations. N = 73 BD-I, n = 63 BD-II patients and n = 136 matched HC were included. Using voxel-based morphometry and tract-based spatial statistics, main effects of group in GMV and fractional anisotropy (FA) were analyzed. Associations between clinical and genetic features and GMV or FA were calculated using regression models. For FA but not GMV, we found significant differences between groups. BD-I patients showed lower FA compared with BD-II patients (ptfce-FWE = 0.006), primarily in the anterior corpus callosum. Compared with HC, BD-I patients exhibited lower FA in widespread clusters (ptfce-FWE < 0.001), including almost all major projection, association, and commissural fiber tracts. BD-II patients also demonstrated lower FA compared with HC, although less pronounced (ptfce-FWE = 0.049). The results remained unchanged after controlling for clinical and genetic features, for which no independent associations with FA or GMV emerged. Our findings suggest that, at a neurobiological level, BD subtypes may reflect distinct degrees of disease expression, with increasing WM microstructure disruption from BD-II to BD-I. This differential magnitude of microstructural alterations was not clearly linked to clinical and genetic variables. These findings should be considered when discussing the classification of BD subtypes within the spectrum of affective disorders.
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Affiliation(s)
- Katharina Thiel
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Hannah Lemke
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Alexandra Winter
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Kira Flinkenflügel
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Lena Waltemate
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- Translational Psychotherapy, Institute of Psychology, University of Göttingen, Göttingen, Germany
| | - Linda Bonnekoh
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Dominik Grotegerd
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Katharina Dohm
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Tim Hahn
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Katharina Förster
- Clinical Psychology and Behavioral Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Philipp Kanske
- Clinical Psychology and Behavioral Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Jonathan Repple
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- Department for Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Nils Opel
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- German Center for Mental Health (DZPG), Halle-Jena-Magdeburg, Germany
| | - Ronny Redlich
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- German Center for Mental Health (DZPG), Halle-Jena-Magdeburg, Germany
- Department of Psychology, University of Halle, Halle, Germany
- Center for Intervention and Research on adaptive and maladaptive brain circuits underlying mental health (C-I-R-C), Jena-Magdeburg-Halle, Halle, Germany
| | - Friederike David
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
| | - Frederike Stein
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Katharina Brosch
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Florian Thomas-Odenthal
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Paula Usemann
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Lea Teutenberg
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Benjamin Straube
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Nina Alexander
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Hamidreza Jamalabadi
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Andreas Jansen
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
- Core-Facility Brainimaging, Faculty of Medicine, University of Marburg, Marburg, Germany
| | - Stephanie H Witt
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Till F M Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andrea Pfennig
- Department of Psychiatry and Psychotherapy, Faculty of Medicine, TU Dresden University of Technology, Dresden, Germany
| | - Michael Bauer
- Department of Psychiatry and Psychotherapy, Faculty of Medicine, TU Dresden University of Technology, Dresden, Germany
| | - Igor Nenadić
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg, Marburg, Germany
| | - Susanne Meinert
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- Institute of Translational Neuroscience, University of Münster, Münster, Germany
| | - Udo Dannlowski
- Institute for Translational Psychiatry, University of Münster, Münster, Germany.
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12
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Ching CRK, Kang MJY, Thompson PM. Large-Scale Neuroimaging of Mental Illness. Curr Top Behav Neurosci 2024. [PMID: 38554248 DOI: 10.1007/7854_2024_462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
Neuroimaging has provided important insights into the brain variations related to mental illness. Inconsistencies in prior studies, however, call for methods that lead to more replicable and generalizable brain markers that can reliably predict illness severity, treatment course, and prognosis. A paradigm shift is underway with large-scale international research teams actively pooling data and resources to drive consensus findings and test emerging methods aimed at achieving the goals of precision psychiatry. In parallel with large-scale psychiatric genomics studies, international consortia combining neuroimaging data are mapping the transdiagnostic brain signatures of mental illness on an unprecedented scale. This chapter discusses the major challenges, recent findings, and a roadmap for developing better neuroimaging-based tools and markers for mental illness.
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Affiliation(s)
- Christopher R K Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Melody J Y Kang
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
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13
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Zhu AH, Nir TM, Javid S, Villalon-Reina JE, Rodrigue AL, Strike LT, de Zubicaray GI, McMahon KL, Wright MJ, Medland SE, Blangero J, Glahn DC, Kochunov P, Håberg AK, Thompson PM, Jahanshad N. Lifespan reference curves for harmonizing multi-site regional brain white matter metrics from diffusion MRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581646. [PMID: 38463962 PMCID: PMC10925090 DOI: 10.1101/2024.02.22.581646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Age-related white matter (WM) microstructure maturation and decline occur throughout the human lifespan, complementing the process of gray matter development and degeneration. Here, we create normative lifespan reference curves for global and regional WM microstructure by harmonizing diffusion MRI (dMRI)-derived data from ten public datasets (N = 40,898 subjects; age: 3-95 years; 47.6% male). We tested three harmonization methods on regional diffusion tensor imaging (DTI) based fractional anisotropy (FA), a metric of WM microstructure, extracted using the ENIGMA-DTI pipeline. ComBat-GAM harmonization provided multi-study trajectories most consistent with known WM maturation peaks. Lifespan FA reference curves were validated with test-retest data and used to assess the effect of the ApoE4 risk factor for dementia in WM across the lifespan. We found significant associations between ApoE4 and FA in WM regions associated with neurodegenerative disease even in healthy individuals across the lifespan, with regional age-by-genotype interactions. Our lifespan reference curves and tools to harmonize new dMRI data to the curves are publicly available as eHarmonize (https://github.com/ahzhu/eharmonize).
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Affiliation(s)
- Alyssa H Zhu
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
- Department of Biomedical Engineering, USC Viterbi School of Engineering, Los Angeles, CA, USA
| | - Talia M Nir
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Shayan Javid
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
- Department of Biomedical Engineering, USC Viterbi School of Engineering, Los Angeles, CA, USA
| | - Julio E Villalon-Reina
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Amanda L Rodrigue
- Department of Psychiatry and Behavioral Science, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lachlan T Strike
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
| | | | - Katie L McMahon
- Queensland University of Technology, Brisbane, QLD, Australia
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
- School of Psychology, `, Brisbane, QLD, Australia
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - David C Glahn
- Department of Psychiatry and Behavioral Science, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
| | - Peter Kochunov
- Faillace Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Asta K Håberg
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of MiDtT National Research Center, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Paul M Thompson
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
- Department of Biomedical Engineering, USC Viterbi School of Engineering, Los Angeles, CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
- Department of Biomedical Engineering, USC Viterbi School of Engineering, Los Angeles, CA, USA
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14
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Kim ME, Gao C, Cai LY, Yang Q, Newlin NR, Ramadass K, Jefferson A, Archer D, Shashikumar N, Pechman KR, Gifford KA, Hohman TJ, Beason-Held LL, Resnick SM, Winzeck S, Schilling KG, Zhang P, Moyer D, Landman BA. Empirical assessment of the assumptions of ComBat with diffusion tensor imaging. J Med Imaging (Bellingham) 2024; 11:024011. [PMID: 38655188 PMCID: PMC11034156 DOI: 10.1117/1.jmi.11.2.024011] [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: 10/05/2023] [Revised: 02/28/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Purpose Diffusion tensor imaging (DTI) is a magnetic resonance imaging technique that provides unique information about white matter microstructure in the brain but is susceptible to confounding effects introduced by scanner or acquisition differences. ComBat is a leading approach for addressing these site biases. However, despite its frequent use for harmonization, ComBat's robustness toward site dissimilarities and overall cohort size have not yet been evaluated in terms of DTI. Approach As a baseline, we match N = 358 participants from two sites to create a "silver standard" that simulates a cohort for multi-site harmonization. Across sites, we harmonize mean fractional anisotropy and mean diffusivity, calculated using participant DTI data, for the regions of interest defined by the JHU EVE-Type III atlas. We bootstrap 10 iterations at 19 levels of total sample size, 10 levels of sample size imbalance between sites, and 6 levels of mean age difference between sites to quantify (i) β AGE , the linear regression coefficient of the relationship between FA and age; (ii) γ ^ s f * , the ComBat-estimated site-shift; and (iii) δ ^ s f * , the ComBat-estimated site-scaling. We characterize the reliability of ComBat by evaluating the root mean squared error in these three metrics and examine if there is a correlation between the reliability of ComBat and a violation of assumptions. Results ComBat remains well behaved for β AGE when N > 162 and when the mean age difference is less than 4 years. The assumptions of the ComBat model regarding the normality of residual distributions are not violated as the model becomes unstable. Conclusion Prior to harmonization of DTI data with ComBat, the input cohort should be examined for size and covariate distributions of each site. Direct assessment of residual distributions is less informative on stability than bootstrap analysis. We caution use ComBat of in situations that do not conform to the above thresholds.
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Affiliation(s)
- Michael E. Kim
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Chenyu Gao
- Vanderbilt University, Department of Electrical Engineering, Nashville, Tennessee, United States
| | - Leon Y. Cai
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
- Vanderbilt University, Medical Scientist Training Program, Nashville, Tennessee, United States
| | - Qi Yang
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Nancy R. Newlin
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Karthik Ramadass
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Department of Electrical Engineering, Nashville, Tennessee, United States
| | - Angela Jefferson
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Department of Medicine, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Department of Neurology, Nashville, Tennessee, United States
| | - Derek Archer
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, Tennessee, United States
| | - Niranjana Shashikumar
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
| | - Kimberly R. Pechman
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
| | - Katherine A. Gifford
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
| | - Timothy J. Hohman
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, Tennessee, United States
| | - Lori L. Beason-Held
- National Institutes of Health, National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, Maryland, United States
| | - Susan M. Resnick
- National Institutes of Health, National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, Maryland, United States
| | - Stefan Winzeck
- Imperial College London, Department of Computing, BioMedIA Group, London, United Kingdom
| | - Kurt G. Schilling
- Vanderbilt University Medical Center, Department of Radiology, Nashville, Tennessee, United States
| | - Panpan Zhang
- Vanderbilt University Medical Center, Vanderbilt Memory and Alzheimer’s Center, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Department of Biostatistics, Nashville, Tennessee, United States
| | - Daniel Moyer
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Bennett A. Landman
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Department of Electrical Engineering, Nashville, Tennessee, United States
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Department of Biostatistics, Nashville, Tennessee, United States
- Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
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15
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Cetin-Karayumak S, Zhang F, Zurrin R, Billah T, Zekelman L, Makris N, Pieper S, O'Donnell LJ, Rathi Y. Harmonized diffusion MRI data and white matter measures from the Adolescent Brain Cognitive Development Study. Sci Data 2024; 11:249. [PMID: 38413633 PMCID: PMC10899197 DOI: 10.1038/s41597-024-03058-w] [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: 05/25/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
The Adolescent Brain Cognitive Development (ABCD) Study® has collected data from over 10,000 children across 21 sites, providing insights into adolescent brain development. However, site-specific scanner variability has made it challenging to use diffusion MRI (dMRI) data from this study. To address this, a dataset of harmonized and processed ABCD dMRI data (from release 3) has been created, comprising quality-controlled imaging data from 9,345 subjects, focusing exclusively on the baseline session, i.e., the first time point of the study. This resource required substantial computational time (approx. 50,000 CPU hours) for harmonization, whole-brain tractography, and white matter parcellation. The dataset includes harmonized dMRI data, 800 white matter clusters, 73 anatomically labeled white matter tracts in full and low resolution, and 804 different dMRI-derived measures per subject (72.3 TB total size). Accessible via the NIMH Data Archive, it offers a large-scale dMRI dataset for studying structural connectivity in child and adolescent neurodevelopment. Additionally, several post-harmonization experiments were conducted to demonstrate the success of the harmonization process on the ABCD dataset.
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Affiliation(s)
- Suheyla Cetin-Karayumak
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| | - Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryan Zurrin
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tashrif Billah
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Leo Zekelman
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Speech and Hearing Bioscience and Technology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Nikos Makris
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| | - Yogesh Rathi
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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16
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Coffman C, Feczko E, Larsen B, Tervo-Clemmens B, Conan G, Lundquist JT, Houghton A, Moore LA, Weldon K, McCollum R, Perrone AJ, Fayzullobekova B, Madison TJ, Earl E, Dominguez OM, Fair DA, Basu S. Heritability estimation of subcortical volumes in a multi-ethnic multi-site cohort study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575231. [PMID: 38260520 PMCID: PMC10802572 DOI: 10.1101/2024.01.11.575231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Heritability of regional subcortical brain volumes (rSBVs) describes the role of genetics in middle and inner brain development. rSBVs are highly heritable in adults but are not characterized well in adolescents. The Adolescent Brain Cognitive Development study (ABCD), taken over 22 US sites, provides data to characterize the heritability of subcortical structures in adolescence. In ABCD, site-specific effects co-occur with genetic effects which can bias heritability estimates. Existing methods adjusting for site effects require additional steps to adjust for site effects and can lead to inconsistent estimation. We propose a random-effect model-based method of moments approach that is a single step estimator and is a theoretically consistent estimator even when sites are imbalanced and performs well under simulations. We compare methods on rSBVs from ABCD. The proposed approach yielded heritability estimates similar to previous results derived from single-site studies. The cerebellum cortex and hippocampus were the most heritable regions (> 50%).
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Affiliation(s)
- Christian Coffman
- Division of Biostatistics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
| | - Eric Feczko
- Department of Pediatrics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Bart Larsen
- Department of Pediatrics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Brenden Tervo-Clemmens
- Department of Psychiatry & Behavioral Sciences, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Gregory Conan
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Jacob T. Lundquist
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Audrey Houghton
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Lucille A. Moore
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Kimberly Weldon
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Rae McCollum
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Anders J. Perrone
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Begim Fayzullobekova
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Thomas J. Madison
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Eric Earl
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Oscar Miranda Dominguez
- Department of Pediatrics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Damien A. Fair
- Department of Pediatrics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
| | - Saonli Basu
- Division of Biostatistics, University of Minnesota, 100 Church Street SE, Minneapolis, 55455-0213, MN, USA
- Masonic Institue for the Devloping Brain, University of Minnesota, 2025 East River Parkway, Minneapolis, 55414, MN, USA
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17
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Ottino-González J, Cupertino RB, Cao Z, Hahn S, Pancholi D, Albaugh MD, Brumback T, Baker FC, Brown SA, Clark DB, de Zambotti M, Goldston DB, Luna B, Nagel BJ, Nooner KB, Pohl KM, Tapert SF, Thompson WK, Jernigan TL, Conrod P, Mackey S, Garavan H. Brain structural covariance network features are robust markers of early heavy alcohol use. Addiction 2024; 119:113-124. [PMID: 37724052 PMCID: PMC10872365 DOI: 10.1111/add.16330] [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: 03/28/2023] [Accepted: 07/27/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND AND AIMS Recently, we demonstrated that a distinct pattern of structural covariance networks (SCN) from magnetic resonance imaging (MRI)-derived measurements of brain cortical thickness characterized young adults with alcohol use disorder (AUD) and predicted current and future problematic drinking in adolescents relative to controls. Here, we establish the robustness and value of SCN for identifying heavy alcohol users in three additional independent studies. DESIGN AND SETTING Cross-sectional and longitudinal studies using data from the Pediatric Imaging, Neurocognition and Genetics (PING) study (n = 400, age range = 14-22 years), the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) (n = 272, age range = 17-22 years) and the Human Connectome Project (HCP) (n = 375, age range = 22-37 years). CASES Cases were defined based on heavy alcohol use patterns or former alcohol use disorder (AUD) diagnoses: 50, 68 and 61 cases were identified. Controls had none or low alcohol use or absence of AUD: 350, 204 and 314 controls were selected. MEASUREMENTS Graph theory metrics of segregation and integration were used to summarize SCN. FINDINGS Mirroring our prior findings, and across the three data sets, cases had a lower clustering coefficient [area under the curve (AUC) = -0.029, P = 0.002], lower modularity (AUC = -0.14, P = 0.004), lower average shortest path length (AUC = -0.078, P = 0.017) and higher global efficiency (AUC = 0.007, P = 0.010). Local efficiency differences were marginal (AUC = -0.017, P = 0.052). That is, cases exhibited lower network segregation and higher integration, suggesting that adjacent nodes (i.e. brain regions) were less similar in thickness whereas spatially distant nodes were more similar. CONCLUSION Structural covariance network (SCN) differences in the brain appear to constitute an early marker of heavy alcohol use in three new data sets and, more generally, demonstrate the utility of SCN-derived metrics to detect brain-related psychopathology.
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Affiliation(s)
- Jonatan Ottino-González
- Division of Endocrinology, The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Renata B. Cupertino
- Department of Genetics, University of California San Diego, San Diego, CA, USA
| | - Zhipeng Cao
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Sage Hahn
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Devarshi Pancholi
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Matthew D. Albaugh
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Ty Brumback
- Department of Psychological Science, Northern Kentucky University, Highland Heights, KY, USA
| | - Fiona C. Baker
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | - Sandra A. Brown
- Departments of Psychology and Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Duncan B. Clark
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - David B. Goldston
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Beatriz Luna
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bonnie J. Nagel
- Departments of Psychiatry and Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Kate B. Nooner
- Department of Psychology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Kilian M. Pohl
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Susan F. Tapert
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Wesley K. Thompson
- Department of Radiology, University of California San Diego, San Diego, CA, USA
| | - Terry L. Jernigan
- Center for Human Development, University of California, San Diego, CA, USA
| | - Patricia Conrod
- Department of Psychiatry, Université de Montreal, CHU Ste Justine Hospital, Montreal, Québec, Canada
| | - Scott Mackey
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Hugh Garavan
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
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Schindler LS, Subramaniapillai S, Ambikairajah A, Barth C, Crestol A, Voldsbekk I, Beck D, Gurholt TP, Topiwala A, Suri S, Ebmeier KP, Andreassen OA, Draganski B, Westlye LT, de Lange AMG. Cardiometabolic health across menopausal years is linked to white matter hyperintensities up to a decade later. Front Glob Womens Health 2023; 4:1320640. [PMID: 38213741 PMCID: PMC10783171 DOI: 10.3389/fgwh.2023.1320640] [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: 10/12/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024] Open
Abstract
Introduction The menopause transition is associated with several cardiometabolic risk factors. Poor cardiometabolic health is further linked to microvascular brain lesions, which can be detected as white matter hyperintensities (WMHs) using T2-FLAIR magnetic resonance imaging (MRI) scans. Females show higher risk for WMHs post-menopause, but it remains unclear whether changes in cardiometabolic risk factors underlie menopause-related increase in brain pathology. Methods In this study, we assessed whether cross-sectional measures of cardiometabolic health, including body mass index (BMI) and waist-to-hip ratio (WHR), blood lipids, blood pressure, and long-term blood glucose (HbA1c), as well as longitudinal changes in BMI and WHR, differed according to menopausal status at baseline in 9,882 UK Biobank females (age range 40-70 years, n premenopausal = 3,529, n postmenopausal = 6,353). Furthermore, we examined whether these cardiometabolic factors were associated with WMH outcomes at the follow-up assessment, on average 8.78 years after baseline. Results Postmenopausal females showed higher levels of baseline blood lipids (HDL β = 0.14, p < 0.001, LDL β = 0.20, p < 0.001, triglycerides β = 0.12, p < 0.001) and HbA1c (β = 0.24, p < 0.001) compared to premenopausal women, beyond the effects of age. Over time, BMI increased more in the premenopausal compared to the postmenopausal group (β = -0.08, p < 0.001), while WHR increased to a similar extent in both groups (β = -0.03, p = 0.102). The change in WHR was however driven by increased waist circumference only in the premenopausal group. While the group level changes in BMI and WHR were in general small, these findings point to distinct anthropometric changes in pre- and postmenopausal females over time. Higher baseline measures of BMI, WHR, triglycerides, blood pressure, and HbA1c, as well as longitudinal increases in BMI and WHR, were associated with larger WMH volumes (β range = 0.03-0.13, p ≤ 0.002). HDL showed a significant inverse relationship with WMH volume (β = -0.27, p < 0.001). Discussion Our findings emphasise the importance of monitoring cardiometabolic risk factors in females from midlife through the menopause transition and into the postmenopausal phase, to ensure improved cerebrovascular outcomes in later years.
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Affiliation(s)
- Louise S. Schindler
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Sivaniya Subramaniapillai
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Ananthan Ambikairajah
- Discipline of Psychology, Faculty of Health, University of Canberra, Canberra, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - Claudia Barth
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arielle Crestol
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Irene Voldsbekk
- Department of Psychology, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dani Beck
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tiril P. Gurholt
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anya Topiwala
- Nuffield Department Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Sana Suri
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom
| | - Klaus P. Ebmeier
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Ole A. Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Bogdan Draganski
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Lars T. Westlye
- Department of Psychology, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ann-Marie G. de Lange
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
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19
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O'Connell S, Cannon DM, Broin PÓ. Predictive modelling of brain disorders with magnetic resonance imaging: A systematic review of modelling practices, transparency, and interpretability in the use of convolutional neural networks. Hum Brain Mapp 2023; 44:6561-6574. [PMID: 37909364 PMCID: PMC10681646 DOI: 10.1002/hbm.26521] [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: 03/17/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Brain disorders comprise several psychiatric and neurological disorders which can be characterized by impaired cognition, mood alteration, psychosis, depressive episodes, and neurodegeneration. Clinical diagnoses primarily rely on a combination of life history information and questionnaires, with a distinct lack of discriminative biomarkers in use for psychiatric disorders. Symptoms across brain conditions are associated with functional alterations of cognitive and emotional processes, which can correlate with anatomical variation; structural magnetic resonance imaging (MRI) data of the brain are therefore an important focus of research, particularly for predictive modelling. With the advent of large MRI data consortia (such as the Alzheimer's Disease Neuroimaging Initiative) facilitating a greater number of MRI-based classification studies, convolutional neural networks (CNNs)-deep learning models well suited to image processing tasks-have become increasingly popular for research into brain conditions. This has resulted in a myriad of studies reporting impressive predictive performances, demonstrating the potential clinical value of deep learning systems. However, methodologies can vary widely across studies, making them difficult to compare and/or reproduce, potentially limiting their clinical application. Here, we conduct a qualitative systematic literature review of 55 studies carrying out CNN-based predictive modelling of brain disorders using MRI data and evaluate them based on three principles-modelling practices, transparency, and interpretability. We propose several recommendations to enhance the potential for the integration of CNNs into clinical care.
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Affiliation(s)
- Shane O'Connell
- School of Mathematical and Statistical Sciences, College of Science and EngineeringUniversity of GalwayGalwayIreland
| | - Dara M. Cannon
- Clinical Neuroimaging Laboratory, Galway Neuroscience Centre, College of MedicineNursing and Health SciencesUniversity of GalwayGalwayIreland
| | - Pilib Ó. Broin
- School of Mathematical and Statistical Sciences, College of Science and EngineeringUniversity of GalwayGalwayIreland
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20
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Chan YH, Yew WC, Chew QH, Sim K, Rajapakse JC. Elucidating salient site-specific functional connectivity features and site-invariant biomarkers in schizophrenia via deep neural networks. Sci Rep 2023; 13:21047. [PMID: 38030699 PMCID: PMC10687079 DOI: 10.1038/s41598-023-48548-w] [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: 08/04/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Schizophrenia is a highly heterogeneous disorder and salient functional connectivity (FC) features have been observed to vary across study sites, warranting the need for methods that can differentiate between site-invariant FC biomarkers and site-specific salient FC features. We propose a technique named Semi-supervised learning with data HaRmonisation via Encoder-Decoder-classifier (SHRED) to examine these features from resting state functional magnetic resonance imaging scans gathered from four sites. Our approach involves an encoder-decoder-classifier architecture that simultaneously performs data harmonisation and semi-supervised learning (SSL) to deal with site differences and labelling inconsistencies across sites respectively. The minimisation of reconstruction loss from SSL was shown to improve model performance even within small datasets whilst data harmonisation often led to lower model generalisability, which was unaffected using the SHRED technique. We show that our proposed model produces site-invariant biomarkers, most notably the connection between transverse temporal gyrus and paracentral lobule. Site-specific salient FC features were also elucidated, especially implicating the paracentral lobule for our local dataset. Our examination of these salient FC features demonstrates how site-specific features and site-invariant biomarkers can be differentiated, which can deepen our understanding of the neurobiology of schizophrenia.
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Affiliation(s)
- Yi Hao Chan
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Wei Chee Yew
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Qian Hui Chew
- Research Division, Institute of Mental Health (IMH), Singapore, Singapore
| | - Kang Sim
- Research Division, Institute of Mental Health (IMH), Singapore, Singapore
- West Region, Institute of Mental Health (IMH), Singapore, Singapore
| | - Jagath C Rajapakse
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
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21
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Priya S, Dhruba DD, Sorensen E, Aher PY, Narayanasamy S, Nagpal P, Jacob M, Carter KD. ComBat Harmonization of Myocardial Radiomic Features Sensitive to Cardiac MRI Acquisition Parameters. Radiol Cardiothorac Imaging 2023; 5:e220312. [PMID: 37693205 PMCID: PMC10483256 DOI: 10.1148/ryct.220312] [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: 12/16/2022] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 09/12/2023]
Abstract
Purpose To investigate the effect of ComBat harmonization methods on the robustness of cardiac MRI-derived radiomic features to variations in imaging parameters. Materials and Methods This Health Insurance Portability and Accountability Act-compliant retrospective study used a publicly available data set of 11 healthy controls (mean age, 33 years ± 16 [SD]; six men) and five patients (mean age, 52 years ± 16; four men). A single midventricular short-axis section was acquired with 3-T MRI using cine balanced steady-state free precision, T1-weighted, T2-weighted, T1 mapping, and T2 mapping imaging sequences. Each sequence was acquired using baseline parameters and after variations in flip angle, spatial resolution, section thickness, and parallel imaging. Image registration was performed for all sequences at a per-individual level. Manual myocardial contouring was performed, and 1652 radiomic features per sequence were extracted using baseline and variations in imaging parameters. Radiomic feature stability to change in imaging parameters was assessed using Cohen d sensitivity. The stability of radiomic features was assessed both without and after ComBat harmonization of radiomic features. Three ComBat methods were studied: parametric, nonparametric, and Gaussian mixture model (GMM). Results For all sequences combined, 51.4% of features were robust to changes in imaging parameters when no ComBat method was applied. ComBat harmonization substantially increased the number of stable features to 95.1% (95% CI: 94.9, 95.3) when parametric ComBat was used and 90.9% (95% CI: 90.6, 91.2) when nonparametric ComBat was used. GMM combat resulted in only 52.6% stable features. Conclusion ComBat harmonization improved the stability of radiomic features to changes in imaging parameters across all cardiac MRI sequences.Keywords: Cardiac MRI, Radiomics, ComBat, Harmonization Supplemental material is available for this article. © RSNA, 2023.
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Affiliation(s)
| | | | - Eldon Sorensen
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
| | - Pritish Y. Aher
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
| | - Sabarish Narayanasamy
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
| | - Prashant Nagpal
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
| | - Mathews Jacob
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
| | - Knute D. Carter
- From the Department of Radiology, University of Iowa Carver College
of Medicine, 200 Hawkins Dr, Iowa City, IA 52242 (S.P., S.N.); Department of
Electrical and Computer Engineering (D.D.D., M.J.) and Department of
Biostatistics (E.S., K.D.C.), University of Iowa, Iowa City, Iowa; Department of
Radiology, University of Miami, Miller School of Medicine, Miami, Fla (P.Y.A.);
and Department of Radiology, University of Wisconsin School of Medicine and
Public Health, Madison, Wis (P.N.)
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22
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Botvinik-Nezer R, Wager TD. Reproducibility in Neuroimaging Analysis: Challenges and Solutions. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2023; 8:780-788. [PMID: 36906444 DOI: 10.1016/j.bpsc.2022.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/27/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Recent years have marked a renaissance in efforts to increase research reproducibility in psychology, neuroscience, and related fields. Reproducibility is the cornerstone of a solid foundation of fundamental research-one that will support new theories built on valid findings and technological innovation that works. The increased focus on reproducibility has made the barriers to it increasingly apparent, along with the development of new tools and practices to overcome these barriers. Here, we review challenges, solutions, and emerging best practices with a particular emphasis on neuroimaging studies. We distinguish 3 main types of reproducibility, discussing each in turn. Analytical reproducibility is the ability to reproduce findings using the same data and methods. Replicability is the ability to find an effect in new datasets, using the same or similar methods. Finally, robustness to analytical variability refers to the ability to identify a finding consistently across variation in methods. The incorporation of these tools and practices will result in more reproducible, replicable, and robust psychological and brain research and a stronger scientific foundation across fields of inquiry.
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Affiliation(s)
- Rotem Botvinik-Nezer
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire.
| | - Tor D Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire
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23
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Hu F, Chen AA, Horng H, Bashyam V, Davatzikos C, Alexander-Bloch A, Li M, Shou H, Satterthwaite TD, Yu M, Shinohara RT. Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization. Neuroimage 2023; 274:120125. [PMID: 37084926 PMCID: PMC10257347 DOI: 10.1016/j.neuroimage.2023.120125] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023] Open
Abstract
Magnetic resonance imaging and computed tomography from multiple batches (e.g. sites, scanners, datasets, etc.) are increasingly used alongside complex downstream analyses to obtain new insights into the human brain. However, significant confounding due to batch-related technical variation, called batch effects, is present in this data; direct application of downstream analyses to the data may lead to biased results. Image harmonization methods seek to remove these batch effects and enable increased generalizability and reproducibility of downstream results. In this review, we describe and categorize current approaches in statistical and deep learning harmonization methods. We also describe current evaluation metrics used to assess harmonization methods and provide a standardized framework to evaluate newly-proposed methods for effective harmonization and preservation of biological information. Finally, we provide recommendations to end-users to advocate for more effective use of current methods and to methodologists to direct future efforts and accelerate development of the field.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States.
| | - Andrew A Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Vishnu Bashyam
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, United States
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania, United States
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; The Penn Lifespan Informatics and Neuroimaging Center, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States
| | - Meichen Yu
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, United States
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
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Bilgel M. Probabilistic estimation for across-batch compatibility enhancement for amyloid PET. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12436. [PMID: 37424963 PMCID: PMC10323321 DOI: 10.1002/dad2.12436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/20/2023] [Accepted: 04/10/2023] [Indexed: 07/11/2023]
Abstract
INTRODUCTION It is necessary to accurately account for systematic differences due to variability in scanners, radiotracers, and acquisition protocols in multisite studies combining amyloid imaging data. METHODS We propose Probabilistic Estimation for Across-batch Compatibility Enhancement (PEACE), a fully Bayesian multimodal extension of the widely used ComBat harmonization model, and we apply it to harmonize regional amyloid positron emission tomography data from two scanners. RESULTS Simulations show that PEACE recovers true harmonized values better than ComBat, even for unimodal data. PEACE harmonization of multiscanner regional amyloid imaging data yields results that agree better with longitudinal data compared to ComBat, without removing the known biological effects of age or apolipoprotein E genotype. DISCUSSION PEACE outperforms ComBat in both unimodal and bimodal contexts, is applicable to multisite amyloid imaging data, and holds promise for the harmonization of other neuroimaging data over ComBat. HIGHLIGHTS We introduce PEACE, a fully Bayesian multimodal extension of ComBat harmonization.Simulations show that PEACE recovers true harmonized values better than ComBat.PEACE accurately harmonizes multiscanner regional amyloid imaging data.
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Affiliation(s)
- Murat Bilgel
- Laboratory of Behavioral NeuroscienceNational Institute on AgingBaltimoreMarylandUSA
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Cetin-Karayumak S, Zhang F, Billah T, Zekelman L, Makris N, Pieper S, O’Donnell LJ, Rathi Y. Harmonized diffusion MRI data and white matter measures from the Adolescent Brain Cognitive Development Study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535587. [PMID: 37066186 PMCID: PMC10104063 DOI: 10.1101/2023.04.04.535587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The Adolescent Brain Cognitive Development (ABCD) study has collected data from over 10,000 children across 21 sites, providing valuable insights into adolescent brain development. However, site-specific scanner variability has made it challenging to use diffusion MRI (dMRI) data from this study. To address this, a database of harmonized and processed ABCD dMRI data has been created, comprising quality-controlled imaging data from 9345 subjects. This resource required significant computational effort, taking ~50,000 CPU hours to harmonize the data, perform white matter parcellation, and run whole brain tractography. The database includes harmonized dMRI data, 800 white matter clusters, 73 anatomically labeled white matter tracts both in full-resolution (for analysis) and low-resolution (for visualization), and 804 different dMRI-derived measures per subject. It is available via the NIMH Data Archive and offers tremendous potential for scientific discoveries in structural connectivity studies of neurodevelopment in children and adolescents. Additionally, several post-harmonization experiments were conducted to demonstrate the success of the harmonization process on the ABCD dataset.
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Affiliation(s)
- Suheyla Cetin-Karayumak
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fan Zhang
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tashrif Billah
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Leo Zekelman
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Speech and Hearing Bioscience and Technology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Nikos Makris
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Lauren J. O’Donnell
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yogesh Rathi
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Hu F, Lucas A, Chen AA, Coleman K, Horng H, Ng RW, Tustison NJ, Davis KA, Shou H, Li M, Shinohara RT. DeepComBat: A Statistically Motivated, Hyperparameter-Robust, Deep Learning Approach to Harmonization of Neuroimaging Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537396. [PMID: 37163042 PMCID: PMC10168207 DOI: 10.1101/2023.04.24.537396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neuroimaging data from multiple batches (i.e. acquisition sites, scanner manufacturer, datasets, etc.) are increasingly necessary to gain new insights into the human brain. However, multi-batch data, as well as extracted radiomic features, exhibit pronounced technical artifacts across batches. These batch effects introduce confounding into the data and can obscure biological effects of interest, decreasing the generalizability and reproducibility of findings. This is especially true when multi-batch data is used alongside complex downstream analysis models, such as machine learning methods. Image harmonization methods seeking to remove these batch effects are important for mitigating these issues; however, significant multivariate batch effects remain in the data following harmonization by current state-of-the-art statistical and deep learning methods. We present DeepCombat, a deep learning harmonization method based on a conditional variational autoencoder architecture and the ComBat harmonization model. DeepCombat learns and removes subject-level batch effects by accounting for the multivariate relationships between features. Additionally, DeepComBat relaxes a number of strong assumptions commonly made by previous deep learning harmonization methods and is empirically robust across a wide range of hyperparameter choices. We apply this method to neuroimaging data from a large cognitive-aging cohort and find that DeepCombat outperforms existing methods, as assessed by a battery of machine learning methods, in removing scanner effects from cortical thickness measurements while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically-motivated deep learning harmonization methods.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Alfredo Lucas
- Center for Neuroengineering and Therapeutics, Department of Engineering, University of Pennsylvania
| | - Andrew A. Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Kyle Coleman
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | | | | | - Kathryn A. Davis
- Center for Neuroengineering and Therapeutics, Department of Engineering, University of Pennsylvania
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine
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Zhou Z, Li H, Srinivasan D, Abdulkadir A, Nasrallah IM, Wen J, Doshi J, Erus G, Mamourian E, Bryan NR, Wolk DA, Beason-Held L, Resnick SM, Satterthwaite TD, Davatzikos C, Shou H, Fan Y. Multiscale functional connectivity patterns of the aging brain learned from harmonized rsfMRI data of the multi-cohort iSTAGING study. Neuroimage 2023; 269:119911. [PMID: 36731813 PMCID: PMC9992322 DOI: 10.1016/j.neuroimage.2023.119911] [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: 10/14/2022] [Revised: 01/06/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
To learn multiscale functional connectivity patterns of the aging brain, we built a brain age prediction model of functional connectivity measures at seven scales on a large fMRI dataset, consisting of resting-state fMRI scans of 4186 individuals with a wide age range (22 to 97 years, with an average of 63) from five cohorts. We computed multiscale functional connectivity measures of individual subjects using a personalized functional network computational method, harmonized the functional connectivity measures of subjects from multiple datasets in order to build a functional brain age model, and finally evaluated how functional brain age gap correlated with cognitive measures of individual subjects. Our study has revealed that functional connectivity measures at multiple scales were more informative than those at any single scale for the brain age prediction, the data harmonization significantly improved the brain age prediction performance, and the data harmonization in the functional connectivity measures' tangent space worked better than in their original space. Moreover, brain age gap scores of individual subjects derived from the brain age prediction model were significantly correlated with clinical and cognitive measures. Overall, these results demonstrated that multiscale functional connectivity patterns learned from a large-scale multi-site rsfMRI dataset were informative for characterizing the aging brain and the derived brain age gap was associated with cognitive and clinical measures.
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Affiliation(s)
- Zhen Zhou
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongming Li
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dhivya Srinivasan
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ahmed Abdulkadir
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ilya M Nasrallah
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhao Wen
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jimit Doshi
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guray Erus
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elizabeth Mamourian
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nick R Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Diagnostic Medicine, University of Texas at Austin, Austin, TX, 78705, USA
| | - David A Wolk
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Neurology and Penn Memory Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lori Beason-Held
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, 20892, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, 20892, USA
| | - Theodore D Satterthwaite
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn Statistic in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Psychiatry, Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Psychiatry, Brain Behavior Laboratory and Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haochang Shou
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn Statistic in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yong Fan
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Han LK, Dinga R, Leenings R, Hahn T, Cole JH, Aftanas LI, Amod AR, Besteher B, Colle R, Corruble E, Couvy-Duchesne B, Danilenko KV, Fuentes-Claramonte P, Gonul AS, Gotlib IH, Goya-Maldonado R, Groenewold NA, Hamilton P, Ichikawa N, Ipser JC, Itai E, Koopowitz SM, Li M, Okada G, Okamoto Y, Churikova OS, Osipov EA, Penninx BW, Pomarol-Clotet E, Rodríguez-Cano E, Sacchet MD, Shinzato H, Sim K, Stein DJ, Uyar-Demir A, Veltman DJ, Schmaal L. A large-scale ENIGMA multisite replication study of brain age in depression. NEUROIMAGE: REPORTS 2022. [DOI: 10.1016/j.ynirp.2022.100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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