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XNAT eXtenible aNatomy Archiving Toolkit. Steve Pieper, PhD Isomics, Inc. Slides Courtesy Dan Marcus, Washington U., St Louis Randy Buckner, Harvard U. Topics. NIH Data Sharing Policy. http://grants.nih.gov/grants/policy/data%5Fsharing/. Additional Goals for Data Sharing Tools.

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Xnat extenible anatomy archiving toolkit

XNATeXtenible aNatomy Archiving Toolkit

Steve Pieper, PhD

Isomics, Inc.

Slides Courtesy

Dan Marcus, Washington U., St Louis

Randy Buckner, Harvard U.



Nih data sharing policy
NIH Data Sharing Policy

  • http://grants.nih.gov/grants/policy/data%5Fsharing/


Additional goals for data sharing tools
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


Building informatics tools for brain imaging research

Building informatics tools for brain imaging research

Randy Buckner

Dan Marcus

May 10, 2006


Data capture
Data Capture

DATA INPUTS

NEUROIMAGING

GENETICS

OTHER SOURCES


Data capture1
Data Capture

DATA INPUTS

NEUROIMAGING

GENETICS

BAD DATA

OTHER SOURCES

Integrity: Do I have the data?

Quality Control: Are the data any good?


Local use
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?


Collaboration
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?


Public access
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?


The xnat workflow

CAPTURE

QUARANTINE

LOCAL USE

COLLABORATION

PUBLIC ACCESS

NEUROIMAGING

GENETICS

OTHER SOURCES

The XNAT workflow

  • Quality control

  • Data archiving

  • Data access

  • Security

  • Visualization

  • Automation

  • Integration

  • Data sharing


What is xnat
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
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

Jakarta Turbine

Actions

Screens

Display

The XNAT Architecture

Client

applications

XNAT API

XML

Schemas

Form

handler

Search

engine

List

generator

Report

generator

Database

generator

XNAT engine

XFT

Relational

database

Data files

Data store


Welcome to xnat

XNAT

Generator

Welcome to XNAT

Database Schema

Data Documents

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();

<?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">

<!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">

<?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


Xnat integrates storage web and exchange formats

Database

XNAT integrates storage, web, and exchange formats

XML

Web

pages


The xnat workflow in practice

CAPTURE

QUARANTINE

LOCAL USE

COLLABORATION

PUBLIC ACCESS

NEUROIMAGING

GENETICS

OTHER SOURCES

The XNAT workflow in practice


Mbdr central myxnat
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
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


Xnat in practice local use1
XNAT in practice: local use

  • Data capture (& quality control


Xnat in practice local use2
XNAT in practice: local use

  • Data capture (& quality control)

  • Auto. Image processing (& more QC)


Xnat in practice local use3
XNAT in practice: local use

  • Data capture (& quality control)

  • Auto. Image processing (& more QC)

  • Online data analysis & entry (& more QC)


Xnat in practice local use4
XNAT in practice: local use

  • Data capture (& quality control)

  • Auto. Image processing (& more QC)

  • Online data analysis & entry (& more QC)

  • Exploration, download


Xnat in practice local use5
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


Xnat in practice collaboration
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


Xnat in practice collaboration1
XNAT in practice: collaboration

  • Freesurfer

  • 3D Slicer

  • LDDMM

  • Teragrid

  • SRB

  • XNAT

Segment & visualization

Grid proc. & storage

Image acquisition

Shape analysis


Xnat in practice public access
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


Open access structural imaging series
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



A review of where we re at

CAPTURE

QUARANTINE

LOCAL USE

COLLABORATION

PUBLIC ACCESS

NEUROIMAGING

GENETICS

OTHER SOURCES

A review of where we’re at


Mbirn data sharing applied to morphometry and disease

Subcortical Segmentation

Elderly Control

Alzheimer’s Individual

mBIRN: Data Sharing Applied toMorphometry and Disease


Mbirn goals
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


Mbirn integration
mBIRN Integration

distortion

correction

tools

acquisition

protocols

local

databases

PubMed

(.xcat)

BIRN

(.xar)

Visualization

&

Interpretation

IBVD

.

.

.

workflows

analysis tools

population

statistics

BrainInfo


Mbirn informatics
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
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
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


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