cbrain and loni: multi-site brain imaging networks for the ... · cbrain and loni: multi-site brain...

CBRAIN and LONI:Multi-site Brain Imaging Networks for the Study of

Neurodegenerative Disorders

Alan C. Evans, Ph.D.McConnell Brain Imaging CentreMontreal Neurological Institute

McGill University

TOWARDS THE DEVELOPMENT OF EFFECTIVE DRUGS FOR ALZHEIMER’S DISEASE. HOW E‐SCIENCE CAN HELP SOLVE PRESSING SOCIETAL PROBLEMS

Bruxelles, January 26th, 2011

Grand Vision

outGRIDoutGRID

http://www.LONI.ucla.edu

Brain Atlasing

• Atlas Construction– Web-based Vervet monkey brain atlas

• Woods, et al., NeuroImage (2010)

– Chinese Brain Atlas• Tang, et al., NeuroImage (2010)

Biological Shape Modeling and Analysis

• Shape metrics, correspondences & mapping

– Pattern of Hippo shape & volume differences in blind subjects• Lepore, et al. (2009)

• http://dx.doi.org/10.1016/j.neuroimage.2009.01.071

Top view

Bottom

view

LONI Infrastructure

• Databases– Raw Data (e.g., imaging, genetics, phenotypic, meta-data)– Derived Data (e.g., Atlases, models, shapes, masks, labels)

• Grid Computing– Managing efficient back-end hardware computational framework– Job submission, user management and support

• Pipeline Environment (http://pipeline.loni.ucla.edu)– Design, validation, dissemination and execution of heterogeneous

workflows

– Tool discovery (http://iTools.ccb.ucla.edu)

– Tool interoperability

– Distributed computing

– Friendly access to data, hardware and tools• Dinov et al., (2010), PLoS, doi:10.1371/journal.pone.0013070

• Dinov et al. (2009) Frontiers NeuroInfo, doi:10.3389/neuro.11.022.2009

LONI Computational InfrastructureDescriptionDescription ValueValue

GridGrid

Number of Grid NodesNumber of Grid Nodes 380 nodes / 1,256 cores380 nodes / 1,256 cores

RAMRAM 8 8 –– 16 Gigabytes / node16 Gigabytes / node

SpeedSpeed 2.5+ GHZ per core2.5+ GHZ per core

SpecsSpecs Sun V20z and Sun X2200Sun V20z and Sun X2200

Usage StatsUsage Stats ~16,000 average jobs completed/day (past 3 months)~16,000 average jobs completed/day (past 3 months)

Number UsersNumber Users 165 unique users (past 3 months)165 unique users (past 3 months)

NetworkingNetworkingSpecsSpecs Mixed 1GB production and 10GB HPC networksMixed 1GB production and 10GB HPC networks

UsageUsage Average: 20GB/sec. Max: 80GB/secAverage: 20GB/sec. Max: 80GB/sec

BandwidthBandwidth 100Gb+ total throughput to cluster100Gb+ total throughput to cluster

DisksDisksCapacity (online/offline)Capacity (online/offline) 250TB online capacity w/ 4PB+ Offline (tape) virtual storage250TB online capacity w/ 4PB+ Offline (tape) virtual storage

Specs (latency, bandwidth)Specs (latency, bandwidth) Peak max 3 Gigabytes/secPeak max 3 Gigabytes/sec

Number of FilesNumber of Files 10,000,000,00010,000,000,000’’ss

Web ServicesWeb ServicesIDAIDA 1,0001,000’’s users per weeks users per week

iToolsiTools 100100’’s users per weeks users per week

Pipeline Pipeline -- webweb--serverserver 100100’’s users per weeks users per week

PipelinePipeline

QueueQueue pipeline.qpipeline.q

UsageUsage ~12,000 avg jobs completed/day (past 3 months)~12,000 avg jobs completed/day (past 3 months)

Node Allocation Node Allocation Dynamic, approximately 75% of LONIDynamic, approximately 75% of LONI’’s HPC Resourcess HPC Resources

Users/AccountsUsers/Accounts 700+ authenticated users700+ authenticated users

IDAIDA

(database)(database)

number of projectsnumber of projects 5555

number of usersnumber of users >1,200>1,200

number of volumesnumber of volumes DTI: 2,748; fMRI: 1,569: HISTO: 4; MRA: 1,204: MRI: 56,248; PETDTI: 2,748; fMRI: 1,569: HISTO: 4; MRA: 1,204: MRI: 56,248; PET: 2,678 : 2,678

diskdisk--spacespace 1PB1PB

Average Monthly Uploads (2009)Average Monthly Uploads (2009) 1,2001,200

Average Monthly Downloads (2009)Average Monthly Downloads (2009) 25,00025,000

The LONI Pipeline http://pipeline.loni.ucla.edu

DistributedArchitecture

Data Computing

Users

CBRAIN• Canadian Distributed Neuroimaging Platform (5 Canadian Centers)

• Prototype Collaborative 3D Visualization of a High Resolution Brain

CANARIECANADA'S ADVANCED RESEARCH AND INNOVATION NETWORK

DCC

CCC DPCSPC

NIH MRI Study of Normal Brain Development (N=500)

Behavior/MRI for ages 0-18 yrs

Structure-behavior relationships

Disseminate results

BackupSystem

Data AnalysisPipeline

MRI

StudyWorkStation

BVL

DCC

INTERNET

MRI

BVLBVL

MRI

PSC

BehavioralPC (laptop)

MRI Console

MRIScanner

ScientificCommunity

Mass Storage System

Internet &DBMS

Server(s)

Data Marts

DataWarehouse

NIHPD Network Architecture

Acquisition managementProject management toolsDouble data entry/ range checkingAutomated 3D image QCJava-based remote 3D image QC150 behavioral instrumentsMANTIS bug-tracking

Analysis pipelines External pipelines for analysis (MNI, SPM, FSL , LONI, AFNI)Integrated with grid-computing networks (CBRAIN, NeuGrid)

Repository /downloadData types: behavior, clinical, imaging, geneticOn-line remote MRI browserData querying GUI (volumes, surfaces, behavior)e.g. NIH database of normal brain development

50 man-years of developmentWeb-based, secure data transfer of multi-site dataGeneralized open-source MYSQL architecture - flexible, extensibleApplications in development, neurodegeneration (US, Europe, Asia)

LORIS

Cortical atrophy in Alzheimer’s Disease(Lerch J et al., Cerebral Cortex 2005)

CBRAIN Portal& Metadata

DB

CIVET on HPC

CBRAIN data provider

CBRAIN controller

Rotman Database

DB

DRMAA

CBRAIN Scientist

Toronto

MontrealSherbrooke

Real-World Example

RQCHP

CBRAIN Network of Centres of Excellence

Enhanced

public education

network

Novel ethical

framework for

imaging genomics

Cross-disciplinary

HQP Training

National

clinical trial

network

Biomarker

validation

Multivariate

analytic

techniques

Commercialization

Translation to

clinical practice

Advanced

e-communication

CBRAIN

Mechanisms

of disease

Development of

new treatments

Early detection and prevention

Broadband

Network

HPC

Grid

National

imaging

database

International

neuroinformatics

partnerships

Informing

health policyRegenerative

strategies

LORIS in Europe

Innomed / AddNeuroMedAlzheimer’s Disease

NeuGrid – Grid ComputingDistributed processingDistributed databasing

GBRAIN Access to HPCs(November 2009)

Top 500 Rank Name Location # of Cores

13 JUROPA Julich, Germany 26304

22 SciNet UofT, Canada 30240

63 CLUMEQ 2 U. Laval, Canada 7616

230 WESTGRID UBC, Canada 3088

322 SHARCNET UWO, Canada 2688

462 RQCHP U. Sherbrooke, Canada 2464

TBD CLUMEQ 1&2 McGill, Canada ~20000

NA LONI UCLA, USA ~600

NA MNI/BIC McGill, Canada ~400

ComputingInfrastructure

Number of HPCsNumber of Cores AvailableCores per HPCNumber of Nodes Available

9 (8 in Canada, 1 in Germany)33,948From 200 to 20 0004678

Systems Heterogeneous SGI XE320, SUN Blade 6048/6275, HP Blade 2x220c, HP DL145 G2, SUN Fire x4100

Network Heterogeneous Gigabit Ethernet, InfiniBand

Storage Total files storedNumber of Data ProvidersAvailable Space on Main Storage

2,060,00075TB

Tools Number of toolsNumber of jobs submitted

2512,316

Users Total UsersRegistered User ProjectsRegistered Scientific SitesCountries

554720Canada, Scotland, USA, Germany

CBRAIN Infrastructure

24

Platform: Web app, not a desktop app. Available anywhere you have a connection and a browser

General approach:Highly-integrated with single point of entry, i.e. no need for re-authentication

Web-databasing: LORIS supports n-D images, genomics, psych testing

Pipeline processing:Fully-automated. 20 years experience with pipelines

Compute Capacity:Huge processing power and great flexibility in adding new clusters

Collaboration:Built-in. Files, tools, servers, storage, visualization can all be shared as desired

Visualization:Brainbrowser 3D web-viewer. QC mosaic for rapid assessment of pipeline results

CBRAIN Summary

N.B. not restricted to human brain MRI Species: human, primate, rodentOrgans: brain, heart, liver

Modalities: (PET, fMRI, histology, IHC, DNA/RNA)

Ruby on Rails Framework

Rails enforces segregation of presentation layer, database access,business logic in MVC (struts, WebObjects, JavaServer Faces)

Rails is RESTful by design

NIHPD-Obj1up to 3 visits per subject, each visit consisting of 3 (t1, t2, pd) volumes @ 256x256x256 (~5Mb)

866 CIVET runs to generate cortical thickness maps Input: 866 x 3 x 5Mb = 15Gb

Output: 866 x 250 Mb = 211Gb

Cluster Total CPU-hrs

Maximum Performance Typical Performance

# cores Execution time (h)

# cores Execution time (h)

mammouth-ms2

(RQCHP -Sherbrooke)

866 x 4 = 3464 2112 1.6 176 20

CLUMEQ-1

(McGill)

866 x 6 = 5196 90 58 24 216

BIC (Linux) 866 x 8 = 6928 100 69 40 173

Illustrative Performance Comparison

Toga USA

ZillesGermany

Lee S. Korea

GBRAIN

Infrastructure – Grid Computing

• Managing efficient back-end hardware computational framework

• Job submission, user management and support

– SGE

– Permissions

– Ticketing

– Tutorials

– Batch/Pipeline

– SVN/CVS

– Dashboard

www.loni.ucla.edu/Resources/clustervisualization

50K lines of code9 integrated cluster installations (8 Canadian, 1 German) 50,000+ CPUs 21 Virtual Sites (1 USA, 1 Spain, 3 Germany, 1 China, 15 Canada)~50 users (1 Chinese, 5 German, 1 UK, 1 Spanish, 1 American, 44 Canadian)~70 user projects, Approx. 5TB of data12000+ HPC tasks performedTypical sustained compute: 130 compute days/24 hours

CBRAIN Statistics

SPMbatch StatisticsNIAK-fMRIstat-SurfStat StatisticsN-PAIRS StatisticsMINC tools General GRETNA Graph theoretical modellingPLS Network modellingCIVET/CLASP Surface ExtractionN3 Inhomogeneity Correction.AFNI GeneralFSL GeneralNITRC Clearing house

25 tools/converters/pipelines