XNAT eXtenible aNatomy Archiving Toolkit
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Transcript of XNAT eXtenible aNatomy Archiving Toolkit
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
XNATeXtenible aNatomy Archiving ToolkitSteve Pieper, PhD
Isomics, Inc.
Slides Courtesy
Dan Marcus, Washington U., St Louis
Randy Buckner, Harvard U.
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National Alliance for Medical Image Computing http://na-mic.org
Topics
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National Alliance for Medical Image Computing http://na-mic.org
NIH Data Sharing Policy• http://grants.nih.gov/grants/policy/data%5Fsharing/
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National Alliance for Medical Image Computing http://na-mic.org
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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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Building informatics tools for brain imaging research
Randy Buckner
Dan MarcusMay 10, 2006
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National Alliance for Medical Image Computing http://na-mic.org
Data CaptureDATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
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National Alliance for Medical Image Computing http://na-mic.org
Data CaptureDATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
BAD DATA
Integrity: Do I have the data?Quality Control: Are the data any good?
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National Alliance for Medical Image Computing http://na-mic.org
Local UseDATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
BAD DATA
Application: Can I do things with the data?Automation: Can I do these things automatically?
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National Alliance for Medical Image Computing http://na-mic.org
CollaborationDATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
BAD DATA
Access: Are colleagues getting the data they need?Security: Are colleagues getting data they shouldn’t?
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National Alliance for Medical Image Computing http://na-mic.org
Public accessDATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
BAD DATA
Privacy: Am I respecting the rights of the study participants?
Convenience: How usable are the data?
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National Alliance for Medical Image Computing http://na-mic.org
QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESSCAPTURE
NEUROIMAGING
GENETICS
OTHER SOURCES
The XNAT workflow
• Quality control• Data archiving• Data access• Security
• Visualization• Automation• Integration• Data sharing
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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
The XNAT Architecture
Clientapplications
XNAT engine
Data storeRelationaldatabase
XFT
Data files
XMLSchemas
XMLSchemas
Jakarta Turbine
Actions Screens Display
XNAT API
Formhandler
Searchengine
Listgenerator
Databasegenerator
Reportgenerator
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National Alliance for Medical Image Computing http://na-mic.org
Data DocumentsWelcome to XNAT
XNATGenerator
<?xml version="1.0" encoding="UTF-8"?><xs:schema xmlns:xnat="xnat.xsd"
xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
attributeFormDefault="unqualified"><xs:element name="Database">
<xs:annotation><xs:appinfo>
<xnat:dbinfo database.name="CNDA" database="MYSQL"/>
</xs:appinfo></xs:annotation>
</xs:element><xs:element name="wm_mod_scheltens">
<xs:complexType><xs:sequence>
<xs:element ref="experiment"/><xs:element name="session_id"
type="xs:string"/><xs:element name="assessment">
…
<?xml version="1.0" encoding="UTF-8"?><xs:schema xmlns:xnat="xnat.xsd"
xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
attributeFormDefault="unqualified"><xs:element name="Database">
<xs:annotation><xs:appinfo>
<xnat:dbinfo database.name="CNDA" database="MYSQL"/>
</xs:appinfo></xs:annotation>
</xs:element><xs:element name="wm_mod_scheltens">
<xs:complexType><xs:sequence>
<xs:element ref="experiment"/><xs:element name="session_id"
type="xs:string"/><xs:element name="assessment">
…
XML SchemaCRATE 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)
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)
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();
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();
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
$page.setTitle("CNDA -- Integrating the Neurouniverse")
$page.setLinkColor($ui.alink)$page.setVlinkColor($ui.vlink)
<html><body>
<table border="0"><tr>
<td bgcolor="#336600"> …
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
$page.setTitle("CNDA -- Integrating the Neurouniverse")
$page.setLinkColor($ui.alink)$page.setVlinkColor($ui.vlink)
<html><body>
<table border="0"><tr>
<td bgcolor="#336600"> …
Database Schema
<?xml version="1.0" encoding="UTF-8"?><session id="050202_vc1000"> <subject map_num="0001"
lab_id="0001"> <age>78</age>
<gender>male</gender> <handedness>right</handedness>
<cohort>ADRC</cohort> </subject>
<session_info> <acq_date>5/1/2002</acq_date>
<pi>Randy Buckner</pi> <operator>Dan
<?xml version="1.0" encoding="UTF-8"?><session id="050202_vc1000"> <subject map_num="0001"
lab_id="0001"> <age>78</age>
<gender>male</gender> <handedness>right</handedness>
<cohort>ADRC</cohort> </subject>
<session_info> <acq_date>5/1/2002</acq_date>
<pi>Randy Buckner</pi> <operator>Dan
Java ClassesHTML Pages
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National Alliance for Medical Image Computing http://na-mic.org
XNAT integrates storage, web, and exchange formats
Database
XML Webpages
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National Alliance for Medical Image Computing http://na-mic.org
The XNAT workflow in practice
QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESSCAPTURE
NEUROIMAGING
GENETICS
OTHER SOURCES
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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
StudyRelationship between white matter lesions and cognition in
nondemented aging and in early-stage Alzheimer’s Disease
InvestigatorsJeff Burns and colleagues at Washington University’s ADRC
XNAT’s roleData integration, automated image processing, image
visualization, data entry, quality control, data access
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality control
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality control)
2. Auto. Image processing (& more QC)
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality control)
2. Auto. Image processing (& more QC)
3. Online data analysis & entry (& more QC)
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality control)
2. Auto. Image processing (& more QC)
3. Online data analysis & entry (& more QC)
4. Exploration, download
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality control)
2. Auto. Image processing (& more QC)
3. Online data analysis & entry (& more QC)
4. Exploration, download
5. Offline analysis & publication
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: collaboration
StudySASHA (Semi-automated shape analysis): quantitative
analysis of shape and size of cortical and subcortical brain regions in non-AD and AD adults.
InvestigatorsBIRN investigators at Washington University (Randy
Buckner), MGH (Bruce Fischl), BWH (Steve Pieper), and Johns Hopkins (Mike Miller)
XNAT’s roleData integration, distribution, image visualization
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: collaboration
• Freesurfer
• 3D Slicer
• LDDMM
• Teragrid
• SRB
• XNAT
Image acquisition
Segment & visualization
Grid proc. & storage
Shape analysis
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National Alliance for Medical Image Computing http://na-mic.org
XNAT in practice: public access
StudyOASIS: 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
InvestigatorsDan Marcus, Randy Buckner, Tracy Wang, Jamie Parker,
Washington University’s ADRC
XNAT’s roleData integration, automated image processing, user interface,
image visualization, distribution
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National Alliance for Medical Image Computing http://na-mic.org
Open Access Structural Imaging Series
• 400 subjects– 100 < 65 years old– 100 > 65 years old– 100 DAT
• 3 or 4 T1-weighted MPRAGE images for each subject
• 20 reliability scans
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National Alliance for Medical Image Computing http://na-mic.org
XNAT-based OASIS website
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National Alliance for Medical Image Computing http://na-mic.org
A review of where we’re atQUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESSCAPTURE
NEUROIMAGING
GENETICS
OTHER SOURCES
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National Alliance for Medical Image Computing http://na-mic.org
mBIRN: Data Sharing Applied toMorphometry and Disease
Alzheimer’s IndividualSubcortical SegmentationElderly Control
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National Alliance for Medical Image Computing http://na-mic.org
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
Interpretation1 Year Volumetric Change
red/yellow 5-20% increase
blue 5-10% decrease
BIRN-ADNI Collaboration
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National Alliance for Medical Image Computing http://na-mic.org
mBIRN Integration
BIRNBIRN
acquisitionprotocols
distortioncorrection
tools
local databases
workflows
analysis tools
populationstatistics
.
.
.
.
.
.
PubMedPubMed
IBVDIBVD
BrainInfoBrainInfo
Visualization&
Interpretation
Visualization&
Interpretation
(.xcat)(.xcat)
(.xar)(.xar)
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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
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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National Alliance for Medical Image Computing http://na-mic.org
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