Transcript XNAT eXtenible aNatomy Archiving Toolkit Steve Pieper, PhD

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
XNAT
eXtenible aNatomy
Archiving Toolkit
Steve Pieper, PhD
Isomics, Inc.
Slides Courtesy
Dan Marcus, Washington U., St Louis
Randy Buckner, Harvard U.
Topics
Data Sharing Goals
XNAT Infrastructure
NA-MIC Use Case and
3D Slicer Integration
National Alliance for Medical Image Computing
http://na-mic.org
NIH Data Sharing Policy
• http://grants.nih.gov/grants/policy/data%5Fsharing/
A data sharing plan must be
included in all applications
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Schedule for releasing data
Format of the dataset
Documentation of the data
What analytic tools will be provided
What restrictions will there be on the use of
the data
• Mode of data sharing
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
National Alliance for Medical Image Computing
http://na-mic.org
NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Building informatics tools for
brain imaging research
Randy Buckner
Dan Marcus
May 10, 2006
Data Capture
DATA INPUTS
NEUROIMAGING
GENETICS
OTHER SOURCES
National Alliance for Medical Image Computing
http://na-mic.org
Data Capture
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Integrity: Do I have the data?
Quality Control: Are the data any good?
National Alliance for Medical Image Computing
http://na-mic.org
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?
National Alliance for Medical Image Computing
http://na-mic.org
Collaboration
DATA INPUTS
NEUROIMAGING
GENETICS
BAD DATA
OTHER SOURCES
Access: Are colleagues getting the data they need?
Security: Are colleagues getting data they shouldn’t?
National Alliance for Medical Image Computing
http://na-mic.org
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?
National Alliance for Medical Image Computing
http://na-mic.org
The XNAT workflow
QUARANTINE
CAPTURE
LOCAL USE
COLLABORATION
NEUROIMAGING
GENETICS
OTHER SOURCES
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Quality control
Data archiving
Data access
Security
National Alliance for Medical Image Computing
http://na-mic.org
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Visualization
Automation
Integration
Data sharing
PUBLIC ACCESS
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
National Alliance for Medical Image Computing
http://na-mic.org
More about XNAT
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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
National Alliance for Medical Image Computing
http://na-mic.org
The XNAT Architecture
Client
applications
Jakarta Turbine
Actions
Screens
Display
XNAT API
XML
Form
Search
handler
engine
XNAT engine
List
Report
generator
generator
XFT
Relational
National Alliance for Medical Image Computing
database
Data store
http://na-mic.org
Data files
Database
generator
Schemas
Welcome to XNAT Database
Data
HTML
JavaDocuments
Classes
Pages
Schema
CRATE TABLE table (
XML Schema
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns:xnat="xnat.xsd"
xmlns:xs="http://www.w3.org/2001/XMLSchem
a" 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">
…
name,
VARCHAR(50),
idMethod,
VARCHAR(50),
DEFAULT
'null‘, Experiment
public class
type,
VARCHAR(50),
extends
ID INTorg.cnl.cnda.om.BaseExperiment
UNSIGNED, NOT NULL
AUTO_INCREMENT,
implements Persistent
PRIMARY KEY (ID)
{
);
… static final long
public
MILLIS_IN_DAY = 86400000;
<!DOCTYPE
html PUBLIC
"-//W3C//DTD
CREATE TABLE
table_column
(
HTML 3.2//EN">
name public staticVARCHAR(50)
long getDays(Calendar
javaName
c1, VARCHAR(50)
Calendar c2)
$page.setTitle("CNDA
-- Integrating the
primaryKey
VARCHAR(50)
{
Neurouniverse")
long time1
=
$page.setLinkColor($ui.alink)
c1.getTime().getTime();
$page.setVlinkColor($ui.vlink)
XNAT
Generator
National Alliance for Medical Image Computing
http://na-mic.org
<?xml version="1.0"
encoding="UTF-8"?>
<html>
<session
id="050202_vc1000">
<body>
<subject map_num="0001"
lab_id="0001">
<table border="0">
<tr> <age>78</age>
<gender>male</gender>
<td bgcolor="#336600">
<handedness>right</handedness>
…
<cohort>ADRC</cohort>
</subject>
<session_info>
<acq_date>5/1/2002</acq_date>
<pi>Randy Buckner</pi>
<operator>Dan
XNAT integrates storage, web,
and exchange formats
Database
XML
National Alliance for Medical Image Computing
http://na-mic.org
Web
pages
The XNAT workflow in practice
QUARANTINE
CAPTURE
NEUROIMAGING
GENETICS
OTHER SOURCES
National Alliance for Medical Image Computing
http://na-mic.org
LOCAL USE
COLLABORATION
PUBLIC ACCESS
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
National Alliance for Medical Image Computing
http://na-mic.org
XNAT in practice: local use
Study
Relationship between white matter lesions and cognition in
nondemented aging and in early-stage Alzheimer’s
Disease
Investigators
Jeff Burns and colleagues at Washington University’s ADRC
XNAT’s role
Data integration, automated image processing, image
visualization, data entry, quality control, data access
National Alliance for Medical Image Computing
http://na-mic.org
XNAT in practice: local use
1. Data capture (& quality
control
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)
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)
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
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
National Alliance for Medical Image Computing
http://na-mic.org
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)
XNAT’s role
Data integration, distribution, image visualization
National Alliance for Medical Image Computing
http://na-mic.org
XNAT in practice: collaboration
Segment &
visualization
Grid proc. &
storage
Image
acquisition
National Alliance for Medical Image Computing
http://na-mic.org
Shape analysis
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Freesurfer
3D Slicer
LDDMM
Teragrid
SRB
XNAT
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 University’s ADRC
XNAT’s role
Data integration, automated image processing, user interface,
image visualization, distribution
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
National Alliance for Medical Image Computing
http://na-mic.org
XNAT-based OASIS website
National Alliance for Medical Image Computing
http://na-mic.org
A review of where we’re at
QUARANTINE
CAPTURE
NEUROIMAGING
GENETICS
OTHER SOURCES
National Alliance for Medical Image Computing
http://na-mic.org
LOCAL USE
COLLABORATION
PUBLIC ACCESS
mBIRN: Data Sharing Applied to
Morphometry and Disease
Subcortical
Segmentation
Elderly Control
National Alliance for Medical Image Computing
http://na-mic.org
Alzheimer’s Individual
mBIRN Goals
• Support Multi-Site MultiVendor 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
National Alliance for Medical Image Computing
http://na-mic.org
BIRN-ADNI Collaboration
mBIRN Integration
acquisition
protocols
distortion
correction
tools
local
databases
PubMed
IBVD
.
.
.
Visualization
&
Interpretation
BrainInfo
(.xcat)
(.xar)
BIRN
workflows
analysis
tools
population
statistics
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)
National Alliance for Medical Image Computing
http://na-mic.org
Query Atlas Module
• BIRN Scientific Interpretation Tool
– Compatible with fMRI and Morphometry Datasets in BIRNStandard Formats
• Provides a Link Between Images and Text Databases
– Uses Anatomic Labeling + Ontologies
– Links to Definitions, Publications, Quantifications
– E.g. Wikipedia, PubMed, IBVD, BrainInfo
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
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
National Alliance for Medical Image Computing
http://na-mic.org