1
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Adkinson BD, Rosenblatt M, Dadashkarimi J, Tejavibulya L, Jiang R, Noble S, Scheinost D. Brain-phenotype predictions of language and executive function can survive across diverse real-world data: Dataset shifts in developmental populations. Dev Cogn Neurosci 2024; 70:101464. [PMID: 39447452 PMCID: PMC11538622 DOI: 10.1016/j.dcn.2024.101464] [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: 05/01/2024] [Revised: 09/09/2024] [Accepted: 10/15/2024] [Indexed: 10/26/2024] Open
Abstract
Predictive modeling potentially increases the reproducibility and generalizability of neuroimaging brain-phenotype associations. Yet, the evaluation of a model in another dataset is underutilized. Among studies that undertake external validation, there is a notable lack of attention to generalization across dataset-specific idiosyncrasies (i.e., dataset shifts). Research settings, by design, remove the between-site variations that real-world and, eventually, clinical applications demand. Here, we rigorously test the ability of a range of predictive models to generalize across three diverse, unharmonized developmental samples: the Philadelphia Neurodevelopmental Cohort (n=1291), the Healthy Brain Network (n=1110), and the Human Connectome Project in Development (n=428). These datasets have high inter-dataset heterogeneity, encompassing substantial variations in age distribution, sex, racial and ethnic minority representation, recruitment geography, clinical symptom burdens, fMRI tasks, sequences, and behavioral measures. Through advanced methodological approaches, we demonstrate that reproducible and generalizable brain-behavior associations can be realized across diverse dataset features. Results indicate the potential of functional connectome-based predictive models to be robust despite substantial inter-dataset variability. Notably, for the HCPD and HBN datasets, the best predictions were not from training and testing in the same dataset (i.e., cross-validation) but across datasets. This result suggests that training on diverse data may improve prediction in specific cases. Overall, this work provides a critical foundation for future work evaluating the generalizability of brain-phenotype associations in real-world scenarios and clinical settings.
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Affiliation(s)
- Brendan D Adkinson
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Matthew Rosenblatt
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Javid Dadashkarimi
- Department of Radiology, Athinoula. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, Boston, MA 02129, USA
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA; Department of Bioengineering, Northeastern University, Boston, MA 02120, USA; Department of Psychology, Northeastern University, Boston, MA 02115, USA
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA; Department of Statistics & Data Science, Yale University, New Haven, CT 06520, USA; Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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2
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Sun H, Mehta S, Khaitova M, Cheng B, Hao X, Spann M, Scheinost D. Brain age prediction and deviations from normative trajectories in the neonatal connectome. Nat Commun 2024; 15:10251. [PMID: 39592647 PMCID: PMC11599754 DOI: 10.1038/s41467-024-54657-5] [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: 05/15/2024] [Accepted: 11/13/2024] [Indexed: 11/28/2024] Open
Abstract
Structural and functional connectomes undergo rapid changes during the third trimester and the first month of postnatal life. Despite progress, our understanding of the developmental trajectories of the connectome in the perinatal period remains incomplete. Brain age prediction uses machine learning to estimate the brain's maturity relative to normative data. The difference between the individual's predicted and chronological age-or brain age gap (BAG)-represents the deviation from these normative trajectories. Here, we assess brain age prediction and BAGs using structural and functional connectomes for infants in the first month of life. We use resting-state fMRI and DTI data from 611 infants (174 preterm; 437 term) from the Developing Human Connectome Project (dHCP) and connectome-based predictive modeling to predict postmenstrual age (PMA). Structural and functional connectomes accurately predict PMA for term and preterm infants. Predicted ages from each modality are correlated. At the network level, nearly all canonical brain networks-even putatively later developing ones-generate accurate PMA prediction. Additionally, BAGs are associated with perinatal exposures and toddler behavioral outcomes. Overall, our results underscore the importance of normative modeling and deviations from these models during the perinatal period.
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Affiliation(s)
- Huili Sun
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| | - Saloni Mehta
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Milana Khaitova
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Bin Cheng
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xuejun Hao
- New York State Psychiatric Institute, New York, NY, USA
| | - Marisa Spann
- New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
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3
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Xu Y, Liao X, Lei T, Cao M, Zhao J, Zhang J, Zhao T, Li Q, Jeon T, Ouyang M, Chalak L, Rollins N, Huang H, He Y. Development of neonatal connectome dynamics and its prediction for cognitive and language outcomes at age 2. Cereb Cortex 2024; 34:bhae204. [PMID: 38771241 DOI: 10.1093/cercor/bhae204] [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: 12/15/2023] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The functional brain connectome is highly dynamic over time. However, how brain connectome dynamics evolves during the third trimester of pregnancy and is associated with later cognitive growth remains unknown. Here, we use resting-state functional Magnetic Resonance Imaging (MRI) data from 39 newborns aged 32 to 42 postmenstrual weeks to investigate the maturation process of connectome dynamics and its role in predicting neurocognitive outcomes at 2 years of age. Neonatal brain dynamics is assessed using a multilayer network model. Network dynamics decreases globally but increases in both modularity and diversity with development. Regionally, module switching decreases with development primarily in the lateral precentral gyrus, medial temporal lobe, and subcortical areas, with a higher growth rate in primary regions than in association regions. Support vector regression reveals that neonatal connectome dynamics is predictive of individual cognitive and language abilities at 2 years of age. Our findings highlight network-level neural substrates underlying early cognitive development.
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Affiliation(s)
- Yuehua Xu
- School of Systems Science, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Xuhong Liao
- School of Systems Science, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Tianyuan Lei
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Miao Cao
- Institution of Science and Technology for Brain-Inspired Intelligence, Fudan University, No. 220 Handan Road, Shanghai 200433, China
| | - Jianlong Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Jiaying Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Tengda Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Qiongling Li
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
| | - Tina Jeon
- Department of Radiology, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States
| | - Minhui Ouyang
- Department of Radiology, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States
- Department of Radiology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, United States
| | - Lina Chalak
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Nancy Rollins
- Department of Radiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Hao Huang
- Department of Radiology, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, United States
- Department of Radiology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, United States
| | - Yong He
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- Chinese Institute for Brain Research, No. 26 Kexueyuan Road, Beijing 102206, China
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4
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Sun H, Mehta S, Khaitova M, Cheng B, Hao X, Spann M, Scheinost D. Brain age prediction and deviations from normative trajectories in the neonatal connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590811. [PMID: 38712238 PMCID: PMC11071351 DOI: 10.1101/2024.04.23.590811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Structural and functional connectomes undergo rapid changes during the third trimester and the first month of postnatal life. Despite progress, our understanding of the developmental trajectories of the connectome in the perinatal period remains incomplete. Brain age prediction uses machine learning to estimate the brain's maturity relative to normative data. The difference between the individual's predicted and chronological age-or brain age gap (BAG)-represents the deviation from these normative trajectories. Here, we assess brain age prediction and BAGs using structural and functional connectomes for infants in the first month of life. We used resting-state fMRI and DTI data from 611 infants (174 preterm; 437 term) from the Developing Human Connectome Project (dHCP) and connectome-based predictive modeling to predict postmenstrual age (PMA). Structural and functional connectomes accurately predicted PMA for term and preterm infants. Predicted ages from each modality were correlated. At the network level, nearly all canonical brain networks-even putatively later developing ones-generated accurate PMA prediction. Additionally, BAGs were associated with perinatal exposures and toddler behavioral outcomes. Overall, our results underscore the importance of normative modeling and deviations from these models during the perinatal period.
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5
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Chen JV, Li Y, Tang F, Chaudhari G, Lew C, Lee A, Rauschecker AM, Haskell-Mendoza AP, Wu YW, Calabrese E. Automated neonatal nnU-Net brain MRI extractor trained on a large multi-institutional dataset. Sci Rep 2024; 14:4583. [PMID: 38403673 PMCID: PMC10894871 DOI: 10.1038/s41598-024-54436-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Brain extraction, or skull-stripping, is an essential data preprocessing step for machine learning approaches to brain MRI analysis. Currently, there are limited extraction algorithms for the neonatal brain. We aim to adapt an established deep learning algorithm for the automatic segmentation of neonatal brains from MRI, trained on a large multi-institutional dataset for improved generalizability across image acquisition parameters. Our model, ANUBEX (automated neonatal nnU-Net brain MRI extractor), was designed using nnU-Net and was trained on a subset of participants (N = 433) enrolled in the High-dose Erythropoietin for Asphyxia and Encephalopathy (HEAL) study. We compared the performance of our model to five publicly available models (BET, BSE, CABINET, iBEATv2, ROBEX) across conventional and machine learning methods, tested on two public datasets (NIH and dHCP). We found that our model had a significantly higher Dice score on the aggregate of both data sets and comparable or significantly higher Dice scores on the NIH (low-resolution) and dHCP (high-resolution) datasets independently. ANUBEX performs similarly when trained on sequence-agnostic or motion-degraded MRI, but slightly worse on preterm brains. In conclusion, we created an automatic deep learning-based neonatal brain extraction algorithm that demonstrates accurate performance with both high- and low-resolution MRIs with fast computation time.
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Affiliation(s)
- Joshua V Chen
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | - Yi Li
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | - Felicia Tang
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | - Gunvant Chaudhari
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Lew
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Amanda Lee
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Andreas M Rauschecker
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | | | - Yvonne W Wu
- University of California San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | - Evan Calabrese
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Center for Artificial Intelligence in Radiology (DAIR), Durham, NC, USA.
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6
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Adkinson BD, Rosenblatt M, Dadashkarimi J, Tejavibulya L, Jiang R, Noble S, Scheinost D. Brain-phenotype predictions can survive across diverse real-world data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576916. [PMID: 38328100 PMCID: PMC10849571 DOI: 10.1101/2024.01.23.576916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Recent work suggests that machine learning models predicting psychiatric treatment outcomes based on clinical data may fail when applied to unharmonized samples. Neuroimaging predictive models offer the opportunity to incorporate neurobiological information, which may be more robust to dataset shifts. Yet, among the minority of neuroimaging studies that undertake any form of external validation, there is a notable lack of attention to generalization across dataset-specific idiosyncrasies. Research settings, by design, remove the between-site variations that real-world and, eventually, clinical applications demand. Here, we rigorously test the ability of a range of predictive models to generalize across three diverse, unharmonized samples: the Philadelphia Neurodevelopmental Cohort (n=1291), the Healthy Brain Network (n=1110), and the Human Connectome Project in Development (n=428). These datasets have high inter-dataset heterogeneity, encompassing substantial variations in age distribution, sex, racial and ethnic minority representation, recruitment geography, clinical symptom burdens, fMRI tasks, sequences, and behavioral measures. We demonstrate that reproducible and generalizable brain-behavior associations can be realized across diverse dataset features with sample sizes in the hundreds. Results indicate the potential of functional connectivity-based predictive models to be robust despite substantial inter-dataset variability. Notably, for the HCPD and HBN datasets, the best predictions were not from training and testing in the same dataset (i.e., cross-validation) but across datasets. This result suggests that training on diverse data may improve prediction in specific cases. Overall, this work provides a critical foundation for future work evaluating the generalizability of neuroimaging predictive models in real-world scenarios and clinical settings.
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Affiliation(s)
- Brendan D Adkinson
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Matthew Rosenblatt
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Javid Dadashkarimi
- Department of Radiology, Athinoula. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Radiology, Harvard Medical School, Boston, MA, 02129, USA
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Bioengineering, Northeastern University, Boston, MA, 02120, USA
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA
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7
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Spann MN, Rogers C. The Infant Brain: A Critical Antecedent of Psychiatric Risk. Biol Psychiatry 2023; 93:854-857. [PMID: 37121613 DOI: 10.1016/j.biopsych.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 05/02/2023]
Affiliation(s)
- Marisa N Spann
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York; New York State Psychiatric Institute, New York, New York.
| | - Cynthia Rogers
- Departments of Psychiatry and Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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