na-mic national alliance for medical image computing xnat extenible anatomy archiving toolkit steve...

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.

National Alliance for Medical Image Computing http://na-mic.org

Topics


NIH Data Sharing Policy• http://grants.nih.gov/grants/policy/data%5Fsharing/


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

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Building informatics tools for brain imaging research

Randy Buckner

Dan MarcusMay 10, 2006


Data CaptureDATA INPUTS

NEUROIMAGING

GENETICS

OTHER SOURCES


Data CaptureDATA INPUTS

NEUROIMAGING

GENETICS

OTHER SOURCES

BAD DATA

Integrity: Do I have the data?Quality Control: Are the data any good?


Local UseDATA INPUTS

NEUROIMAGING

GENETICS

OTHER SOURCES

BAD DATA

Application: Can I do things with the data?Automation: Can I do these things automatically?


CollaborationDATA INPUTS

NEUROIMAGING

GENETICS

OTHER SOURCES

BAD DATA

Access: Are colleagues getting the data they need?Security: Are colleagues getting data they shouldn’t?


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?


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


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


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


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


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


XNAT integrates storage, web, and exchange formats

Database

XML Webpages


The XNAT workflow in practice

QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESSCAPTURE

NEUROIMAGING

GENETICS

OTHER SOURCES


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


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



1. Data capture (& quality control



1. Data capture (& quality control)

2. Auto. Image processing (& more QC)





3. Online data analysis & entry (& more QC)






4. Exploration, download






4. Exploration, download

5. Offline analysis & publication


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


XNAT in practice: collaboration

• Freesurfer

• 3D Slicer

• LDDMM

• Teragrid

• SRB

• XNAT

Image acquisition

Segment & visualization

Grid proc. & storage

Shape analysis


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


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


XNAT-based OASIS website


A review of where we’re atQUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESSCAPTURE

NEUROIMAGING

GENETICS

OTHER SOURCES


mBIRN: Data Sharing Applied toMorphometry and Disease

Alzheimer’s IndividualSubcortical SegmentationElderly Control


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


mBIRN Integration

BIRNBIRN

acquisitionprotocols

distortioncorrection

tools

local databases

workflows

analysis tools

populationstatistics

.

.

.

.

.

.

PubMedPubMed

IBVDIBVD

BrainInfoBrainInfo

Visualization&

Interpretation

Visualization&

Interpretation

(.xcat)(.xcat)

(.xar)(.xar)


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)


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


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


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