An introduction to selected WU resources (…mostly human MR and PET)

Tamara Hershey, PhD NIL Lab Chief

5/21/21 Goals of this talk

1. To orient new (and old) WU neuroimagers to commonly used resources for human MR/PET 2. To clarify relationships between entities 3. To provide contacts for more information 4. To provide answers to your questions from the experts

Caveats – This talk is not meant to be a comprehensive review of • …groups that focus on human neuroimaging (e.g. CIL, ORL, HCP, Dev Psych). • …WU resources that relate to neuroimaging at different scales and species, to other imaging techniques (DOT, EEG) or to human research more generally (RadCore, ICTS) • …the history of neuroimaging at WU Acronym Quiz

• NIL • RIIS • Neuroimaging Lab • Research Imaging Information System • CIL • SDS • Computational Imaging Lab • Shared Data Storage • MIR • NP • Mallinckrodt Institute of Radiology • neuro PET protocol? • CNDA • WUNIC • Central Neuroimaging Data Archive • Wash U Neuroimaging Community • CHPC • Center for High Performance Computing • CSG • Computer Support Group • CCIR • Center for Clinical Imaging Research Organization of talk

• Birdseye view of resources/entities • NIL https://sites.wustl.edu/nillabs/ • WUNIC https://wunic.wustl.edu/display/WUN/WUNIC • Facilities https://www.mir.wustl.edu/research/research-support-facilities • East Blg (Josh Shimony) • CCIR (Hongyu An, Pam Woodard) • NICU PET (Joel Perlmutter) • CNDA (Jenny Gurney, Dan Marcus) • SDS (Steve Wiese, Dan Marcus) • CHPC (Malcolm Tobias) • CSG https://sites.wustl.edu/nillabs/computer-support-group/ • Steve Wiese, Joel Perlmutter • NIL Computational Core https://sites.wustl.edu/nillabs/nil-core-services/ Human neuroimaging resources in context

MIR Chair Rich Wahl

Research Facilities Division Director Rad Sci Division Director Pam Woodard Rob Gropler McDonnell Center EB Imaging NIL Josh Shimony Tamara Hershey for Systems NS

CCIR NIL Comp Core Pam Woodard Snyder / Seitzman NNICU PET CSG Joel Perlmutter Joel Perlmutter CNDA WUNIC Dan Marcus Hershey / Marcus

SDS Dan Marcus

CHPC Malcolm Tobias NIL in context

Radiological Sciences Labs

PRTL2 Biomedical Radiology lab Computational Imaging Lab Optical Imaging Lab Neuroimaging Lab Will Tu Joe Ackerman Dan Marcus Sam Achilifu Tamara Hershey

17 faculty 16 faculty 6 faculty 8 faculty 32 faculty

3 departments The NIL

• is an interdepartmental group of faculty who live and work together

East Building, 2nd floor 4525 Scott Avenue NIL’s mission

• To pursue the best neuroimaging science built on interdisciplinary collaboration • To provide a shared physical environment and collegial atmosphere • To be an incubator for trainees interested in neuroimaging • To be a hub for the neuroimaging community at WU NIL Collaboration 2018 size of circle = # papers

Courtesy of Tyler Blazey, circa 2018 NIL Collaboration 2021, current faculty size of circle = h index WUNIC collaboration, circa 2010 2018 WUNIC 2021 WUNIC n = 244, Depts = 24 n = 456

Radiology

Neurology

P & BS

Psychiatry What neuroimaging techniques do you use?

200 180 160 # 140 120 100 80 60 40 20 0 PET MRI Task resting DOT EEG Other fMRI state fMRI WUNIC Initiatives

• Enhance interactions • WUNIC emails, talks, website • WUNIC retreat? • Improve documentation, dissemination and training of software/analysis approaches • 4dfp documentation • NIL Computational Core • Provide access to large datasets • ABCD • Petersen Lab dataset (coming) • Petersen processed HCP dataset (coming)

Department of Psychiatry Department of Neurology Department of Psychological & Brain Sciences WUNIC

• https://wunic.wustl.edu/display/WUN/WUNIC • Sign up for emails Interested• Get notified of talks, in newhelping resources, events to improve WUNIC? • Share info to WUNIC, use Blog • Talks (JanineEmail: Bjisterbosch [email protected]) • Explore resources • NIL Comp Core • 4DFP documentation Imaging Facilities

• East Blg (1st floor) • CCIR (10th floor Barnes West) • NICU PET (10th floor) • Owned/run by MIR • Owned/run by MIR • Run by Joel Perlmutter • Directed by Josh Shimony • Directed by Pam Woodard, Hongyu An • Affordable fee structure • Linda Hood, MR Tech • Lots of techs, nurses, support staff • Technician • Jon Koller, CSG • Help with protocols • 1 PET scanner • 3 3T Prisma Siemens • 1 3T Prisma • Mock Scanner • 1 3T Vida Siemens • Connectome offices • 1 PET/MR (3T Verio) • Cyclotron • Exam rooms • 2 PET/CTs (Vision and Biograph 40) • East Building • Parking spots • Exam rooms • TR-19 Cylotron • RDS Eclipse Cyclotron • GMP facility • Barnard • CS-15 • JSW168 16 Central Neuroimaging Data Archive (CNDA) Jenny Gurney Dan Marcus • The CNDA is a resource for storing and distributing neuroimaging and related data. • Accessible via secure web application at https://cnda.wustl.edu • Data automatically received from scanners in CCIR and East Building • Data can also be uploaded via website • Programming interface enables access from command line and other applications • > 600 active users • > 1,500 registered projects • > 40,000 subjects • > 70,000 exams • > 75 TB total storage Shared Data Storage (SDS)

Dan Marcus Steve Wiese • Provides 2 PB of usable storage, 1.8 PB of high speed and 200TB of archive • 700TB expansion expected in May • Accessible by CIFS (Windows/Macs) and NFS (LINUX/UNIX/Macs) • Fully redundant system – no single point of failure • Disks configured using RAID Z2, allows for 2 failed drives per storage segment • Data is replicated every ~30 seconds to off-site location and snapshots of data are taken 5 days a week • Thirty snapshots stored for recovery of accidental changes/ deletions • Housed in Tier-4 data center (99.995% uptime per year) • Archive storage: single copy, has to be brought online to use • Annual cost for high-speed redundant storage $160 per TB, archive storage $53 per TB • Contact Steve Wiese @ [email protected] for more information Center for High Performance Computing (CHPC) Malcolm Tobias

• Founded in 2010 • Currently rolling out our 3rd generation cluster (With WUIT's campus-wide HPC now available, the CHPC will focus on supporting Human Imaging going forward) • ~4,000 CPU-cores • ~100 GPGPUs (including NVIDIA V100S GPUs with 32GB of VRAM) • ~1.5PB of high-speed storage • 100Gb Infiniband network fabric • High-memory (3TB) compute nodes • Hundreds of Pre-installed scientific applications • Coming soon? Research Imaging Repository • NIH High-end instrumentation grant • CCF,ADRC,ABCD,CONDR,PACS,UK Biobank,ADNI,TCIA,?

• To find out more: • https://sites.wustl.edu/chpc • email [email protected] Computer Support Group (CSG) services https://sites.wustl.edu/nillabs/computer-support-group/

• End-user hardware/software support • Server hardware/software support • Network security and activation • End-user storage support Joel Perlmutter • Printing service and support Located on the 3rd floor of the East Bldg • Software licensing and contracts Faculty Director: Joel S. Perlmutter • NIL Staff: Steve Wiese Purchasing services Matt Hicks Brian Jenkins • HIPAA oversight Ben Pflanz • Liaison services Karen Klumpp

Courtesy of Joel Perlmutter & Steve Wiese CSG by the numbers

• Support approximately 500 devices on network • Support of ~440 users comprising 136 FTE equivalents @ $3,600 per year (FTEs do not include students) • Service requests (approx. 2,689 this year/52 per week) • Backup approximately 25TB of workstation and server data disk arrays • FY 21 operating budget = $480,000 CSG support costs and problem reporting

• Funded by FTE charges, can be put on NIH grants • $3,600 per FTE (cost based on percent of effort) • 50% FTE = $1,800 • Minimum charge of 5% ($180) • Users do not pay support until beginning of next fiscal year • No proration for users that leave during the current fiscal year • Users requiring accounts to access NIL resources (desktop computer, processing servers, printing services, etc.) must pay for CSG support based on the percent of effort. • Service requests are sent to trouble ticket system ([email protected]) • After-hours support emergency phone (314) 714-5510 • For more information on CSG support, please contact Steve Wiese @ [email protected] CSG support for non-NIL researchers and staff

• Researchers at WUSTL or other research institutions that are collaborating with NIL researchers. • Researchers that require support beyond what WUIT can provide. • Staff in the East Building that only need access to printing services. • NIL researchers that leave WUSTL, but still require access to data and software. Must be approved at department level. • Non-NIL members that pay for storage on Shared Data Storage. Users are provided NIL accounts to access storage, but do not pay CSG support (support provided by SDS personnel). • Support cost based on percentage of time spent using NIL resources (5% minimum) NIL Computational Core (pilot)

• Provides free training and/or advice on post-acquisition neuroimaging analyses • Supported by the NIL, NIAC and the McDonnell Center for Systems Neuroscience. • Collaborates with the IDDRC, which provides additional resources for studies that involve children.

Team • Director: Avi Snyder, MD, PhD • Assistant Director: Ben Seitzman, PhD • IDDRC Neuroimaging Core Director: Josh Shimony, MD, PhD • MRI Analyst: Jerrel Rutlin, B.S. • Programmer: Jon Koller, BME • PET: John Lee, MD, PhD

Avi Snyder Ben Seitzman Josh Shimony Jerrel Rutlin Jon Koller John Lee NIL Computational Core • Areas of expertise for training and/or advice • Acquisition parameters • Existing software for MRI and PET data processing • FreeSurfer and other FSL tools • 4dfp suite of tools • Connectome Workbench • Analysis of processed MRI and PET data • Resting State • Diffusion Imaging • SUV measurements for all PET tracers • Binding potential estimates for PET tracers with receptor-specific affinities • Quantitative tracer kinetics estimates for PET obtained with arterial data • Data visualization • MATLAB images • Surface images (Connectome Workbench) • Evaluation of incidental finding on MRI and PET images • Radiology clinical evaluation • Discussion/Recommendation with team and/or subject • To request a consultation from the NIL Core or ask about other unlisted services, email [email protected]. Additional IDDRC-related services

 For neurodevelopmental-relevant studies only  Consultation on  study design/planning  MRI sequence use and development  PET development  Assistance in  MRI data acquisition  PET data acquisition  quality control  data archiving  Assistance in the processing of MRI and PET imaging data

• To request IDDRC services, please contact Josh Shimony ([email protected]) If you want to learn more:

• Review these slides or talk (will be distributed and posted) • Review relevant websites • Sign up for WUNIC emails • Contact me for overall questions, comments, ideas • [email protected] • Contact each individual facility/service director for specific questions Upcoming Talk!

Please join us via Zoom on Wednesday, 5/26/21, at 12:00pm (Central Time) for the following Neuroimaging in Health and Disease Seminar virtual lecture:

Lecturer: Dr. Tammie Benzinger, M.D., Ph.D., Professor of Radiology at Washington University School of

Title: MRI and PET Safety Annual Refresher

Date/Time: Wednesday, 5/26/21 at 12:00pm (Central Time) Questions & Comments? First Human Subjects P #2000 – 1 March 1991 Scanned on PETT III PET VI (1980 – 1993) April 1974

Courtesy of Marc Raichle NIL Early History

Michael Welch joins the Division of Radiation McDonnell Center for Studies First Meeting of the (MIR) of Higher Brain Function Executive Committee (‘Fab 4’) Michel Ter-Pogossian First Quantitative Functional receives his PhD from Studies of Imaging with PET MacArthur NIL Moves to the Washington University Regional Oxygen and Flow Foundation Funds IT East Building Consumption in Introduced Humans

1939 1950 1962 1967 1970 1973 1973-4 1978 1982 1984-90 1991 1992 1994 1995 2001 >

Cyclotron Installed in X-Ray CT PET NP fMRI Dana Foundation the Mallinckrodt Invented Invented Protocol BOLD Funds Training Institute of Radiology (Hounsfield) System Imaging Initiated Begins Main Campus Cyclotron Installed MRI Imaging Introduced NP #1: ACTIVATION STUDY OF ARROW- WORD CONFLICT TASK PI: Terry Early Courtesy of Marc Raichle