Charting brain growth and aging at high spatial precision

  1. Saige Rutherford  Is a corresponding author
  2. Charlotte Fraza
  3. Richard Dinga
  4. Seyed Mostafa Kia
  5. Thomas Wolfers
  6. Mariam Zabihi
  7. Pierre Berthet
  8. Amanda Worker
  9. Serena Verdi
  10. Derek Andrews
  11. Laura KM Han
  12. Johanna MM Bayer
  13. Paola Dazzan
  14. Phillip McGuire
  15. Roel T Mocking
  16. Aart Schene
  17. Chandra Sripada
  18. Ivy F Tso
  19. Elizabeth R Duval
  20. Soo-Eun Chang
  21. Brenda WJH Penninx
  22. Mary M Heitzeg
  23. S Alexandra Burt
  24. Luke W Hyde
  25. David Amaral
  26. Christine Wu Nordahl
  27. Ole A Andreasssen
  28. Lars T Westlye
  29. Roland Zahn
  30. Henricus G Ruhe
  31. Christian Beckmann
  32. Andre F Marquand
  1. Donders Institute for Brain, Cognition, and Behavior, Radboud University, Netherlands
  2. Department of Cognitive Neuroscience, Radboud University Medical Center, Netherlands
  3. Department of Psychiatry, University of Michigan, United States
  4. Department of Psychiatry, Utrecht University Medical Center, Netherlands
  5. Department of Psychology, University of Oslo, Norway
  6. Norwegian Center for Mental Disorders Research (NORMENT), University of Oslo, and Oslo University Hospital, Norway
  7. Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, United Kingdom
  8. Centre for Medical Image Computing, Medical Physics and Biomedical Engineering, University College London, United Kingdom
  9. Dementia Research Centre, UCL Queen Square Institute of Neurology, United Kingdom
  10. The Medical Investigation of Neurodevelopmental Disorders (MIND) Institute and Department of Psychiatry and Behavioral Sciences, UC Davis School of Medicine, University of California, Davis, United States
  11. Amsterdam UMC, Vrije Universiteit, Psychiatry, Amsterdam Public Health Research Institute, Netherlands
  12. GGZ inGeest, Amsterdam Neuroscience, Netherlands
  13. Centre for Youth Mental Health, University of Melbourne, Australia
  14. Orygen Youth Health, Australia
  15. National Institute for Health Research Mental Health Biomedical Research Centre, South London and Maudsley National Health Service Foundation Trust and King’s College London, United Kingdom
  16. Department of Psychosis Studies, Institute of Psychiatry, King’s College London, United Kingdom
  17. Department of Psychiatry, Amsterdam UMC, Location AMC, Netherlands
  18. Department of Psychiatry, Radboud University Medical Center, Netherlands
  19. Department of Psychology, Michigan State University, United States
  20. Department of Psychology, University of Michigan, United States
  21. KG Jebsen Centre for Neurodevelopmental Disorders Research, Institute of Clinical Medicine, University of Oslo, Norway
  22. Centre for Affective Disorders at the Institute of Psychiatry, King's College London, United Kingdom
  23. Centre for Functional MRI of the Brain (FMRIB), Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
4 figures, 1 video, 1 table and 4 additional files

Figures

Normative model overview.

(A) Age density distribution (x-axis) of each site (y-axis) in the full model train and test, clinical, and transfer validation set. (B) Age count distribution of the full sample (N=58,836). (C, D) …

Normative modeling in clinical cohorts.

Reference brain charts were transferred to several clinical samples (described in (A)). Patterns of extreme deviations were summarized for each clinical group and compared to matched control groups …

Figure 3 with 3 supplements
Evaluation metrics across all test sets.

The distribution of evaluation metrics in four different test sets (full, mQC, patients, and transfer, see Materials and methods) separated into left and right hemispheres and subcortical regions, …

Figure 3—figure supplement 1
Comparison of the explained variance in cortical thickness across the different test sets.

The patterns appear to be robust and consistent across the different test sets.

Figure 3—figure supplement 2
Showing the explained variance for each brain region across 10 randomized resampling of the full control test set.
Figure 3—figure supplement 3
Per site explained variance across the different test sets.
Author response image 1
Example of the online interactive visualizations created to help interpret the evaluation metrics.

This interactive figure was created for each evaluation metric (EV, MSLL, skew, and kurtosis) and all test sets (full controls, mQC controls, clinical, and transfer).

Videos

Video 1
"Demonstation of the functionality of our interactive online visualization tool (https://brainviz-app.herokuapp.com/) that is available for all evaluation metrics across all test sets.

The code for creating this website can be found on GitHub (https://github.com/saigerutherford/brainviz-app; copy archived at swh:1:rev:021fff9a48b26f2d07bbb4b3fb92cd5202418905; Rutherford, 2022b).

Tables

Table 1
Sample description and demographics.

mQC refers to the manual quality checked subset of the full sample. ‘All’ rows=Train+Test. Clinical refers to the transdiagnostic psychiatric sample (diagnostic details in Figure 2A).

N (subjects)N (sites)Sex (%F/%M)Age (Mean, S.D)
FullAll58,83682
Training set29,4188251.1/48.946.9, 24.4
 Test set29,4188250.9/49.146.9, 24.4
mQCAll24,35459
 Training set12,1775950.2/49.830.2, 24.1
Test set12,1775950.4/49.430.1, 24.2
ClinicalTest set19852438.9/61.130.5, 14.1
TransferTest set546644.5/55.524.8, 13.7

Additional files

Supplementary file 1

Full Sample Description, per site, in the train, test, and clinical validation sets.

https://cdn.elifesciences.org/articles/72904/elife-72904-supp1-v2.docx
Supplementary file 2

Manual Quality Checked (mQC) Sample Description, per site, train and test sets.

https://cdn.elifesciences.org/articles/72904/elife-72904-supp2-v2.docx
Supplementary file 3

Transfer Test Set Sample Descriptions, per site.

Data were downloaded from https://openneuro.org/ (Markiewicz et al., 2021) and are shared on GitHub along with code to transfer to demonstrate how to re-use models on new data.

https://cdn.elifesciences.org/articles/72904/elife-72904-supp3-v2.docx
Transparent reporting form
https://cdn.elifesciences.org/articles/72904/elife-72904-transrepform1-v2.pdf

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