A CASE STUDY IN OPEN SCIENCE Jennifer Stine Elam, Ph.D. Director, Scientific Outreach and Education Human Connectome Project  Effort to chart a comprehensive map of neuronal connections in healthy adults  Whole brain region-to-region connectivity  Large population  1200 young adults (22-35 years old), twins + siblings  Multimodal neuroimaging: MRI at 3T, 7T, and MEG Macro-connectome  T1/T2, dMRI/tractography, rfMRI, tfMRI (7 tasks) (whole-brain, long-distance)  Extensive behavioral (4h), demographic data, and genotyping

WHAT IS THE HUMAN CONNECTOME PROJECT (HCP)? (YOUNG ADULT 2010-2016) 1. Acquired data on brain structure, function, and connectivity in 1000+ healthy adults  Improved scanners, pulse sequences for high quality images  Multimodal imaging (4 hr): structure, function, connectivity  ~1100 subjects scanned at 3T; 183 scanned at 7T (twins); ~100 with MEG (twins)  Extensive behavioral, demographic data on 1200+ subjects; genotyping on 1142+ subjects

2. Analyzed data  Improved HCP preprocessing pipelines – shared on Github  Better alignment, atlases, and visualization (Connectome Workbench)  Advanced analyses (connectivity/behavior; cortical parcellations)

3. Shared data + All methods and tools + Courses to teach use  ConnectomeDB + BALSA databases (>15 PetaBytes shared!)  HCP Paradigm, Educational Course at OHBM, Annual weeklong HCP Course HCP-YA MAJOR SUCCESSES THE HCP-STYLE NEUROIMAGING PARADIGM Seven core tenets (Glasser et al. Nature Neuroscience 2016) that have shaped other projects 1) Collect lots of multimodal imaging data 2) Maximize resolution, data quality (e.g., multiband fMRI, dMRI) 3) Minimize distortion and blurring of each subject’s data 4) Respect geometry of brain structures (‘CIFTI grayordinates’) 5) Align data precisely across individuals and across studies 6) Analyze results using an accurate brain parcellation 7) Freely share the data (including publication-related data)  ConnectomeDB database  Downloads via Aspera server  Per subject and group average  Filter for preset and custom subject groups  Explore Open access and Restricted Behavioral data, download CSVs

 Connectome in a Box  Hard drives loaded with data in organized, per subject directory structure  Shipped to users for cost of hard drives

 Amazon Public Datasets S3 Bucket  Same directory structure as Connectome in a Box

 dbGaP for Genetic Data: Accession: phs001364.v1.p1

MULTIPLE WAYS TO GET DATA Number of TB Downloaded HCP Data Downloaded DataHCP Over Over as “ as Q1 Q3 Connectome 7.2 PB 7.2 PB MEG 500 Data Downloaded Data Downloaded 13.35 Petabytes (1PB = 1000 TB) 11 Petabytes 11 HCP DataHCP Distributed thru 9/2019thru thru 9/2018thru Subjects - in S900 - a - Box” hard drives hardBox” S1200 Data releases

Number of Distinct Users Over Over HCP dataHCP delivered to HCP dataHCP delivered to (March 2013 (March 2013 • • • 11/2019 of As Over 18 Petabytesof *Does not include datainclude AWS not the shared/usedon *Doescloud Announce email listAnnounce 1,896 Users email forum 1,146 DataHCP Terms Use 12,894 20.5 Petabytes users! users! membersthe HCP- of membersthe HCP- of Investigators accepted – – Sept 2018)*Sept Sept 2019)*Sept of of PUBLICATIONS

Cumulative Number of Publications PublicationsHCP citing Q1 S500 S900 USING HCP DATA USING METHODS AND S1200 Data releases

Number of Pubs/Month • • (U54MH091657) HCP grant 900 2019 13, Nov of As independent ~ collaborators + Investigators ~ 750 150 50 reviews research850 articles Publications cite cite Publications by investigatorsby by HCP Consortium Consortium HCP by of HCP consortium HCP of  Leadership: Co-PIs David Van Essen and Kamil Ugurbil + professional Project Management

 Scientific experts for each modality, analysis type + data sharing recruited to HCP from many institutions  Many involved at the grant-writing stage  Extensive Piloting to make early decisions on hardware, collection, and analysis methods  Operational Teams to make ongoing data-driven reevaluations/recorrections when problems arise

HCP TEAM ORGANIZATION  Full time staff dedicated to:  Keeping data collection consistent, making SOPs, training RAs  High quality QC on anatomical scans, segmentations/surfaces  Interacting with other scientists/users, creating documentation and tools that are clear/easy to use  Ongoing development and support of tools

 Culture that all team members viewpoints and roles are valued

IT TAKES A VILLAGE… TO DO GREAT & OPEN SCIENCE  Open source Tools: code on Github  Connectome Workbench (https://github.com/Washington-University/workbench)  HCP Pipelines (https://github.com/Washington-University/HCPpipelines/releases)  Qu|Nex integrated environment for running pipelines  BALSA (Brain Analysis Library of Spatial Maps and Atlases) for sharing analyzed datasets – coming soon to Github  humanconnectome.org: Release Documentation, protocols, software distribution/documentation  wiki.humanconnectome.org for between release documentation + resources  Feedback/Questions  HCP-Users Forum  HCP-Announce email list  Direct contact feedback  JIRA Issues tracker for ConnectomeDB, Workbench and help  HCP Course + open resources (videos to come)  NDA for data sharing: Downloads + Cloud access (in development) HCP SUPPORT AND TOOLS  Young Adult HCP (2010 – 2016) studied 1200 healthy adults (22 – 35)  Many projects are acquiring and sharing HCP-style data via CCF

 Lifespan HCP Aging (2016 – 2020):1200 older adults (ages 36 – 100+)  Lifespan HCP Development (2016 – 2020): 1300 children (ages 5 - 21)  Initial Lifespan data release: May 2019 (via NDA - NIMH Data Archive)  Multimodal MRI and full behavioral data release: Planned for April 2020

 ABCD (Adolescent Brain and Cognitive Development) project: 12,000 children - starting age 9, follow for 10 years  “Baby Connectome Project” (ages 0 – 5)  Developing Human Connectome Project (prenatal – neonatal) (UK)

 14 ”Disease Connectome” projects (2016-2021): ~4,000 subjects total  depression, anxiety, psychosis, dementia, Alzheimer’s, epilepsy, blindness

“HCP-STYLE” CONNECTOME PROJECTS THE “WU-MINN-OX” HCP CONSORTIUM

10 institutions: Saint Louis University Washington University University d’Annunzio University of Minnesota Indiana University, Warwick University Ernst Strungmann Institute (Frankfurt) Oxford University Radboud University (Nijmegen) ~100 on HCP team Duke University