Image processing and analysis methods for the Adolescent Brain Cognitive Development Study

Donald J Hagler Jr, SeanN Hatton, M Daniela Cornejo, Carolina Makowski, Damien A Fair, Anthony Steven Dick, Matthew T Sutherland, B J Casey, Deanna M Barch, Michael P Harms, Richard Watts, James M Bjork, Hugh P Garavan, Laura Hilmer, Christopher J Pung, Chelsea S Sicat, Joshua Kuperman, Hauke Bartsch, Feng Xue, Mary M Heitzeg, Angela R Laird, Thanh T Trinh, Raul Gonzalez, Susan F Tapert, Michael C Riedel, Lindsay M Squeglia, Luke W Hyde, Monica D Rosenberg, Eric A Earl, Katia D Howlett, Fiona C Baker, Mary Soules, Jazmin Diaz, Octavio Ruiz de Leon, Wesley K Thompson, Michael C Neale, Megan Herting, Elizabeth R Sowell, Ruben P Alvarez, Samuel W Hawes, Mariana Sanchez, Jerzy Bodurka, Florence J Breslin, Amanda Sheffield Morris, Martin P Paulus, W Kyle Simmons, Jonathan R Polimeni, Andre van der Kouwe, Andrew S Nencka, Kevin M Gray, Carlo Pierpaoli, John A Matochik, Antonio Noronha, Will M Aklin, Kevin Conway, Meyer Glantz, Elizabeth Hoffman, Roger Little, Marsha Lopez, Vani Pariyadath, Susan Rb Weiss, Dana L Wolff-Hughes, Rebecca DelCarmen-Wiggins, Sarah W Feldstein Ewing, Oscar Miranda-Dominguez, Bonnie J Nagel, Anders J Perrone, Darrick T Sturgeon, Aimee Goldstone, Adolf Pfefferbaum, Kilian M Pohl, Devin Prouty, Kristina Uban, Susan Y Bookheimer, Mirella Dapretto, Adriana Galvan, Kara Bagot, Jay Giedd, M Alejandra Infante, Joanna Jacobus, Kevin Patrick, Paul D Shilling, Rahul Desikan, Yi Li, Leo Sugrue, Marie T Banich, Naomi Friedman, John K Hewitt, Christian Hopfer, Joseph Sakai, Jody Tanabe, Linda B Cottler, Sara Jo Nixon, Linda Chang, Christine Cloak, Thomas Ernst, Gloria Reeves, David N Kennedy, Steve Heeringa, Scott Peltier, John Schulenberg, Chandra Sripada, Robert A Zucker, William G Iacono, Monica Luciana, Finnegan J Calabro, Duncan B Clark, David A Lewis, Beatriz Luna, Claudiu Schirda, Tufikameni Brima, John J Foxe, Edward G Freedman, Daniel W Mruzek, Michael J Mason, Rebekah Huber, Erin McGlade, Andrew Prescot, Perry F Renshaw, Deborah A Yurgelun-Todd, Nicholas A Allgaier, Julie A Dumas, Masha Ivanova, Alexandra Potter, Paul Florsheim, Christine Larson, Krista Lisdahl, Michael E Charness, Bernard Fuemmeler, John M Hettema, Hermine H Maes, Joel Steinberg, Andrey P Anokhin, Paul Glaser, Andrew C Heath, Pamela A Madden, Arielle Baskin-Sommers, R Todd Constable, Steven J Grant, Gayathri J Dowling, Sandra A Brown, Terry L Jernigan, Anders M Dale, Donald J Hagler Jr, SeanN Hatton, M Daniela Cornejo, Carolina Makowski, Damien A Fair, Anthony Steven Dick, Matthew T Sutherland, B J Casey, Deanna M Barch, Michael P Harms, Richard Watts, James M Bjork, Hugh P Garavan, Laura Hilmer, Christopher J Pung, Chelsea S Sicat, Joshua Kuperman, Hauke Bartsch, Feng Xue, Mary M Heitzeg, Angela R Laird, Thanh T Trinh, Raul Gonzalez, Susan F Tapert, Michael C Riedel, Lindsay M Squeglia, Luke W Hyde, Monica D Rosenberg, Eric A Earl, Katia D Howlett, Fiona C Baker, Mary Soules, Jazmin Diaz, Octavio Ruiz de Leon, Wesley K Thompson, Michael C Neale, Megan Herting, Elizabeth R Sowell, Ruben P Alvarez, Samuel W Hawes, Mariana Sanchez, Jerzy Bodurka, Florence J Breslin, Amanda Sheffield Morris, Martin P Paulus, W Kyle Simmons, Jonathan R Polimeni, Andre van der Kouwe, Andrew S Nencka, Kevin M Gray, Carlo Pierpaoli, John A Matochik, Antonio Noronha, Will M Aklin, Kevin Conway, Meyer Glantz, Elizabeth Hoffman, Roger Little, Marsha Lopez, Vani Pariyadath, Susan Rb Weiss, Dana L Wolff-Hughes, Rebecca DelCarmen-Wiggins, Sarah W Feldstein Ewing, Oscar Miranda-Dominguez, Bonnie J Nagel, Anders J Perrone, Darrick T Sturgeon, Aimee Goldstone, Adolf Pfefferbaum, Kilian M Pohl, Devin Prouty, Kristina Uban, Susan Y Bookheimer, Mirella Dapretto, Adriana Galvan, Kara Bagot, Jay Giedd, M Alejandra Infante, Joanna Jacobus, Kevin Patrick, Paul D Shilling, Rahul Desikan, Yi Li, Leo Sugrue, Marie T Banich, Naomi Friedman, John K Hewitt, Christian Hopfer, Joseph Sakai, Jody Tanabe, Linda B Cottler, Sara Jo Nixon, Linda Chang, Christine Cloak, Thomas Ernst, Gloria Reeves, David N Kennedy, Steve Heeringa, Scott Peltier, John Schulenberg, Chandra Sripada, Robert A Zucker, William G Iacono, Monica Luciana, Finnegan J Calabro, Duncan B Clark, David A Lewis, Beatriz Luna, Claudiu Schirda, Tufikameni Brima, John J Foxe, Edward G Freedman, Daniel W Mruzek, Michael J Mason, Rebekah Huber, Erin McGlade, Andrew Prescot, Perry F Renshaw, Deborah A Yurgelun-Todd, Nicholas A Allgaier, Julie A Dumas, Masha Ivanova, Alexandra Potter, Paul Florsheim, Christine Larson, Krista Lisdahl, Michael E Charness, Bernard Fuemmeler, John M Hettema, Hermine H Maes, Joel Steinberg, Andrey P Anokhin, Paul Glaser, Andrew C Heath, Pamela A Madden, Arielle Baskin-Sommers, R Todd Constable, Steven J Grant, Gayathri J Dowling, Sandra A Brown, Terry L Jernigan, Anders M Dale

Abstract

The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing, nationwide study of the effects of environmental influences on behavioral and brain development in adolescents. The main objective of the study is to recruit and assess over eleven thousand 9-10-year-olds and follow them over the course of 10 years to characterize normative brain and cognitive development, the many factors that influence brain development, and the effects of those factors on mental health and other outcomes. The study employs state-of-the-art multimodal brain imaging, cognitive and clinical assessments, bioassays, and careful assessment of substance use, environment, psychopathological symptoms, and social functioning. The data is a resource of unprecedented scale and depth for studying typical and atypical development. The aim of this manuscript is to describe the baseline neuroimaging processing and subject-level analysis methods used by ABCD. Processing and analyses include modality-specific corrections for distortions and motion, brain segmentation and cortical surface reconstruction derived from structural magnetic resonance imaging (sMRI), analysis of brain microstructure using diffusion MRI (dMRI), task-related analysis of functional MRI (fMRI), and functional connectivity analysis of resting-state fMRI. This manuscript serves as a methodological reference for users of publicly shared neuroimaging data from the ABCD Study.

Keywords: ABCD; Adolescent; Data sharing; Magnetic resonance imaging; Processing pipeline.

Conflict of interest statement

All other authors report no potential conflicts of interest.

Copyright © 2019 Elsevier Inc. All rights reserved.

Figures

Figure 1.. Processing pipeline diagrams.
Figure 1.. Processing pipeline diagrams.
A. Modality-specific processing steps for bias field, distortion, and/or motion correction. B. Processing pipeline input and outputs.
Figure 2.. Bias field correction for sMRI.
Figure 2.. Bias field correction for sMRI.
Sagittal, T1w images for an example ABCD Study participant from a GE scanner, with and without bias field correction. A. Uncorrected image showing bright occipital cortex. B. N3 corrected image with white matter and pial surfaces overlayed in yellow and red, respectively. C. White matter bias corrected (wmbc) image.
Figure 3.. sMRI and dMRI data flow…
Figure 3.. sMRI and dMRI data flow chart.
Initial stages (green) have no filtering. All scanning sessions receive a radiological review; users may optionally exclude participants with incidental findings. Available MRI events pass through mandatory filtering (red) that excludes incomplete or very poor-quality data from the creation of minimally processed data. ROI-based analyses result in the tabulated data (white). The DAIC recommends (blue) that these data should be further filtered to exclude subjects with unacceptable FreeSurfer reconstruction.
Figure 4.. fMRI data flow chart.
Figure 4.. fMRI data flow chart.
Available MRI events (green) pass through mandatory filtering (red) that excludes incomplete or very poor-quality data from the creation of minimally processed data. ROI-based timeseries analyses result in the tabulated data (white). The DAIC recommend (blue) that data should be further filtered to exclude subjects with poor behavioral performance, excessive head motion, or unacceptable FreeSurfer reconstruction.
Figure 5.. Differences between scanners.
Figure 5.. Differences between scanners.
A–C. sMRI-derived measures. A. T1w gray/white contrast averaged across bilateral cortical surface. B. Cortical thickness averaged across bilateral cortical surface. C. Total cortical area. D–F. dMRI-derived measures averaged within AllFibers AtlasTrack ROI. D. DTIIS FA. E. DTIIS MD. F. RSI ND. G–I. EN-back task fMRI differences between scanners. G. Voxel-wise smoothness (mm FWHM) for EN-back task fMRI data. H. tSNR for EN-back task fMRI data. I. GLM-derived t-statistics calculated for middle frontal gyrus Destrieux parcel, 2-back vs fixation contrast. J–L. rs-fMRI derived measures. J. Mean motion: average FD for rs-fMRI scans. K. Number of time points remaining for analysis after motion-censoring for rs-fMRI scans. L. Within-network correlation for default network. Tukey boxplots represent medians, quartiles, and outliers (for additional details, see Statistical Analysis section within Supplementary Information). The numbers of participants included in the analysis for each plot are shown in gray.

Source: PubMed

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