XNAT eXtenible aNatomy Archiving Toolkit

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XNATeXtenible aNatomy Archiving Toolkit

• Steve Pieper, PhD
• Isomics, Inc.
• Slides Courtesy
• Dan Marcus, Washington U., St Louis
• Randy Buckner, Harvard U.

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Topics
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NIH Data Sharing Policy

• http//grants.nih.gov/grants/policy/data5Fsharing
  /

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Additional Goals for Data Sharing Tools

• Tools should be painless and even helpful
• Ideally you should want to use the tools
  independent of the Data Sharing requirements
• Tools should be compatible with existing
  methodologies
• DICOM transfers
• easy upload/download of data for processing
• database schema adaptable to application use
  cases
• Tools should not require excessive system or
  database administrator time committment
• Tools must be robust and efficient

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Building informatics tools for brain imaging
research

• Randy Buckner
• Dan Marcus
• May 10, 2006

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Data Capture
DATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
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Data Capture
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Integrity Do I have the data? Quality Control
Are the data any good?
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Local Use
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Application Can I do things with the
data? Automation Can I do these things
automatically?
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Collaboration
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Access Are colleagues getting the data they
need? Security Are colleagues getting data they
shouldnt?
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Public access
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Privacy Am I respecting the rights of the study
participants? Convenience How usable are the
data?
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The XNAT workflow

• Quality control
• Data archiving
• Data access
• Security

• Visualization
• Automation
• Integration
• Data sharing

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What is XNAT?

• The Extensible Neuroimaging (anatomy) Archive
  Toolkit (XNAT) is
• A workflow
• A data archive
• Web-based productivity tools
• New XNAT is now part of the NA-MIC Kit
• WashU is funded by NA-MIC to improve
  ease-of-installation and interoperability with
  other tools

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More about XNAT

• Open Source
• BSD-style license based on Slicer License
• DICOM Server
• Push images directly to XNAT
• Can Attach Arbitrary Files to a Subject or
  Project
• Web Interface, Java API, and Command Line Access
  Utilities
• Leverages standard web database tools
• Java, Apache, Tomcat, Postgres
• Active Developer and User Community
• Core developer group under Dan Marcus at
  Washington University Saint Louis
• Further development and application under Randy
  Buckner at Harvard
• Supported by BIRN, NA-MIC, and other projects

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The XNAT Architecture
Client applications
XNAT API
XML Schemas
Form handler
Search engine
List generator
Database generator
Report generator
XNAT engine
XFT
Relational database
Data files
Data store
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Welcome to XNAT
Data Documents
Database Schema
Java Classes
HTML Pages
CRATE TABLE table ( name, VARCHAR(50),
idMethod, VARCHAR(50), DEFAULT 'null,
type, VARCHAR(50), ID INT UNSIGNED, NOT NULL
AUTO_INCREMENT, PRIMARY KEY (ID) ) CREATE
TABLE table_column ( name VARCHAR(50)
javaName VARCHAR(50) primaryKey VARCHAR(50)
XML Schema
public class Experiment extends
org.cnl.cnda.om.BaseExperiment implements
Persistent public static final long
MILLIS_IN_DAY 86400000 public static long
getDays(Calendar c1, Calendar c2)
long time1 c1.getTime().getTime()
xmlnsxnat"xnat.xsd" xmlnsxs"http//www.w3.org/
2001/XMLSchema" elementFormDefault"qualified"
attributeFormDefault"unqualified" name"Database" tdbinfo database.name"CNDA" database"MYSQL"/ /xsappinfo ement name"wm_mod_scheltens" ssequence ment name"session_id" type"xsstring"/ ent name"assessment"
3.2//EN" page.setTitle("CNDA -- Integrating
the Neurouniverse") page.setLinkColor(ui.alink)
page.setVlinkColor(ui.vlink) ble border"0"

id"050202_vc1000" lab_id"0001" 78
male rightandedness ADRC

5/1/2002 Randy
Buckner Dan
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XNAT integrates storage, web, and exchange formats
XML
Web pages
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The XNAT workflow in practice
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mBDR, Central, MyXNAT

• Morphometry BIRN Data Repository
• Currated, User Support to Coordinate Submissions
• XNAT Central
• Anyone Can Create a Project and Upload
• Your Local Database
• Run your own instance inside your firewall

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XNAT in practice local use

• Study
• Relationship between white matter lesions and
  cognition in nondemented aging and in early-stage
  Alzheimers Disease
• Investigators
• Jeff Burns and colleagues at Washington
  Universitys ADRC
• XNATs role
• Data integration, automated image processing,
  image visualization, data entry, quality control,
  data access

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XNAT in practice local use

• Data capture ( quality control

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XNAT in practice local use

• Data capture ( quality control)
• Auto. Image processing ( more QC)

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XNAT in practice local use

• Data capture ( quality control)
• Auto. Image processing ( more QC)
• Online data analysis entry ( more QC)

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XNAT in practice local use

• Data capture ( quality control)
• Auto. Image processing ( more QC)
• Online data analysis entry ( more QC)
• Exploration, download

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XNAT in practice local use

• Data capture ( quality control)
• Auto. Image processing ( more QC)
• Online data analysis entry ( more QC)
• Exploration, download
• Offline analysis publication

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XNAT in practice collaboration

• Study
• SASHA (Semi-automated shape analysis)
  quantitative analysis of shape and size of
  cortical and subcortical brain regions in non-AD
  and AD adults.
• Investigators
• BIRN investigators at Washington University
  (Randy Buckner), MGH (Bruce Fischl), BWH (Steve
  Pieper), and Johns Hopkins (Mike Miller)
• XNATs role
• Data integration, distribution, image
  visualization

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XNAT in practice collaboration

• Freesurfer
• 3D Slicer
• LDDMM
• Teragrid
• SRB
• XNAT

Segment visualization
Grid proc. storage
Image acquisition
Shape analysis
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XNAT in practice public access

• Study
• OASIS A Cross-sectional sample of MR images and
  related data from 400 individuals across the
  lifespan, including 200 younger, 100 older
  non-demented, and 100 early stage AD
• Investigators
• Dan Marcus, Randy Buckner, Tracy Wang, Jamie
  Parker, Washington Universitys ADRC
• XNATs role
• Data integration, automated image processing,
  user interface, image visualization, distribution

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Open Access Structural Imaging Series

• 400 subjects
• 100
• 100 65 years old
• 100 DAT
• 3 or 4 T1-weighted MPRAGE images for each subject
• 20 reliability scans

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XNAT-based OASIS website
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A review of where were at
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mBIRN Data Sharing Applied toMorphometry and
Disease
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mBIRN Goals

• Support Multi-Site Multi-Vendor Structural
  Neuroimaging Research
• Provide End-to-End Suite of Tools and Techniques
• Sensitive Detection
• Large N for Statistical Power
• Support Scientific Interpretation

1 Year Volumetric Change red/yellow 5-20
increase blue 5-10 decrease BIRN-ADNI
Collaboration
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mBIRN Integration
distortion correction tools
acquisition protocols
local databases
PubMed
(.xcat)
BIRN
(.xar)
Visualization Interpretation
IBVD
. . .
workflows analysis tools population statistics
BrainInfo
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mBIRN Informatics

• BIRN Data Repository (BDR)
• eXtensible Neuroimaging Archive Tool (XNAT)
  http//www.xnat.org
• XML-Based Clinical Experiment Data Exchange
  Schema (XCEDE) http//www.xcede.org
• Stores Images, Demographics, Clinical Data,
  Analysis Results
• 3D Slicer Interoperability (currently read-only,
  read/write prototype exists)

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Query Atlas Module

• BIRN Scientific Interpretation Tool
• Compatible with fMRI and Morphometry Datasets in
  BIRN-Standard Formats
• Provides a Link Between Images and Text Databases
• Uses Anatomic Labeling Ontologies
• Links to Definitions, Publications,
  Quantifications
• E.g. Wikipedia, PubMed, IBVD, BrainInfo

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Query Atlas Features

• Input.xcat or .qdec from .xar
• Hardware Accelerated Interactive 3D Annotation
• Ontology Engine
• FreeSurfer, UMLS, BIRNLex, NeuroNames, IBVD
• Interactive Browser
• Direct Browser Launch to Search Sites using
  Selected Terms

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QDEC

• Query, Design, Estimate, Contrast of Population
  Statistics
• XNAT to Select Subjects
• FreeSurfer QDEC Runs on Server
• .QDEC file in .XAR Web Download
• Slicer3 Interactive Visualization
• Integrated with Query Atlas