FBIRN AHM March 13-14, 2006 David B. Keator University of California, Irvine FBIRN NeuroInformatics Working Group Update

FBIRN AHMMarch 13-14, 2006

David B. Keator

University of California, Irvine

FBIRN NeuroInformatics Working Group Update

October MilestonesOctober Milestones

Phase I data uploaded and downloadable for public analysis

Phase II image upload Tools available for Society for Neuroscience roll-out Phase II clinical data uploads Prepare for derived data uploads

Multi-Site User Query

Results with standard descriptions in HIDB (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FMRI Images•Automated image upload to Data Grid/HID for sharing

FIPS: FSL Image Processing Scripts

HIDB(s)(Local)

Data Grid(Local)

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN IT VisionFBIRN IT Vision

DICOM, NIFTIDICOM, NIFTI

FBIRN Federated DataFBIRN Federated Data

UNMHID

UMNHID

UIHID

DukeHID

UCSDHID

UCIHID

BWHHID

MGHHID

YaleHID

UCLAHID

Stanford

HID

p1

p1

p1

p1

p1

p1

p1

p2

p2

p2

p2p2

= Data Integration Environment= Data Integration Environment

= PostgreSQL test site= PostgreSQL test site

= Phase 1 / Phase 2 data= Phase 1 / Phase 2 data

p1

p1

p2

p2

p2

p2

Duke: 48BWH: 18MGH: 11UCLA: 37UCSD: 5UCI: 58UNM: 44UI: 63UMN: 52Yale: 56

Duke: 48BWH: 18MGH: 11UCLA: 37UCSD: 5UCI: 58UNM: 44UI: 63UMN: 52Yale: 56

392 Subject 392 Subject VisitsVisits

392 Subject 392 Subject VisitsVisits

Architecture OverviewArchitecture Overview

OracleOracleOracleOracle PostgreSQLPostgreSQLPostgreSQLPostgreSQL

DatabaseDatabase

CoreCoreHierarchyHierarchy


SchemaSchema

Clinical /Clinical /DemographicsDemographics


StudyStudyProtocolsProtocols


StudyStudyDataData

StudyStudyDataData

SubjectSubjectManagementManagement


Web ApplicationWeb Application

CALM/GAMECALM/GAMEAssessmentsAssessments


Multi-SiteMulti-SiteQueryQuery


XCEDEXCEDEServicesServices


File SystemFile SystemFile SystemFile System Data GridData GridData GridData Grid

DataData

Phase I Traveling Subject DatasetPhase I Traveling Subject Dataset

https://portal.nbirn.net/BIRN/cgi-bin/Downloads/fBIRN_PhaseI.cgi

July 05 Aug 05 Sept 05 Oct 05 Nov 05 Dec 05 Jan 06

Num

ber

of F

iles

(Mill

ions

)

9.0

8.5

8.0

7.5

7.0

6.5

6.0

5.5

5.0

FBIRN Shared Data Files

Phase II Study: Image Data VolumePhase II Study: Image Data Volume

21,038 raw image files per subject

2.4 GB of raw image data per subject

25 GB to 40 GB of processed image data per subject (depending on hypotheses tested)

10 million slices of functional imaging data in Phase II

7 Terabytes of image data for all of the Phase II analyses (conservative estimate of 25 GB/subject)

BIRN Tools DownloadBIRN Tools Download

http://www.nbirn.net/Resources/Downloads/



DatabaseDatabase



SchemaSchema





StudyStudyDataData

StudyStudyDataData











DataData

HID ImprovementsHID Improvements

Created the following scripts to streamline HID creation process:• Create HID database schema• Add initial data set to HID so that HID web application can

function• Create database users for mediator to access HID

Created the following programs for HID data management:• Migrate assessment data when an assessment is modified• Export subject assessment data to a file in csv format• Add experimental visits, studies and segments to HID• Export HID clinical data in XCEDE formatted XML



DatabaseDatabase



SchemaSchema





StudyStudyDataData

StudyStudyDataData











DataData

Can query all sites with HID installation Pseudo-mediated

• SQL query sent to each “registered” site “Registered” means your HID has been told about the other sites

Can query Oracle and PostgreSQL installations• Currently can only drill down to more detailed results from

a returned query if logged into the same database platform

Export CSV formatted clinical data returned from a multi-site query

http://head.bic.uci.edu:8080/clinical/index.jsp

Pseudo-Mediated Query InterfacePseudo-Mediated Query Interface

Pseudo-Mediated Query InterfacePseudo-Mediated Query Interface

HID Subjects by Site

0

5

10

15

20

25

30

35

40

45

50

Site

Nu

m.

Su

bje

cts

in H

ID

Number of Phase II Assessments in HID by Site

0

50

100

150

200

250

300

350

400

450

500

Site

Nu

m.

Ph

ase

II A

sses

smen

ts

Mediator - “View” on HID: Mediator - “View” on HID: Assessments and MR DataAssessments and MR Data

View across fBIRN HID resources View across fBIRN HID resources

Multi-Site Query Across fBIRN SitesMulti-Site Query Across fBIRN Sites



DatabaseDatabase



SchemaSchema





StudyStudyDataData

StudyStudyDataData











DataData

CALM Layout ImprovementsCALM Layout Improvements



DatabaseDatabase



SchemaSchema





StudyStudyDataData

StudyStudyDataData











DataData

E-Prime, Presentation, etc. to XCEDE E-Prime, Presentation, etc. to XCEDE eventsevents

Data Acquisition

Event extraction into XML

XML

Stimulus presentation

MR scanner

Event data

XML events(stimulus/response)

Red

sq

uare

Blu

e sq

uare

Red

sq

uare

Red

sq

uare

Low

to

neLo

w

tone

Low

to

neH

igh

tone

Low

to

neLo

w

tone

Button 1

Button 2

0 secs

10 secs

2

Event data from various stimulus presentation programs is converted from tabular text into a standard XML representation.

This process is driven by a “parsing” file, mapping rows and columns to events and event characteristics.

“Queries” of the XCEDE events files extract timing for selected events into format required for analysis package

Queries can be simple:• description=‘stimuli\1000.wav’• type==‘encode’ & description==‘listone’

Queries can be complex:• description=‘stimuli\1200.wav’ and

not(preceding sibling::*[description=‘stimuli\1200.wav’]/onset >= (onset - 9))

XCEDE events to FIPSXCEDE events to FIPS

XPath

XCEDE

XPath

query syntax

XML tools releasedXML tools released

BXH/XCEDE Tools released to the public through the BIRN website.• binaries for Linux• includes tools for:

creating wrappers for image data QA programs event-based analysis tools XCEDE events files

Query Atlas Anatomy BrowserQuery Atlas Anatomy Browser

Query AtlasQuery Atlas

Plans for Coming Year: Develop readers and an intuitive interface for loading BIRN

data into Slicer, and tools for saving modified Slicer scenes to BIRN database.

Improve information visualization in Slicer’s 3D viewer (improved text rendering, label and marker arrangement and dynamic behavior, and interactive selection of scene elements).

Develop queriable comment-markers that can be anchored in the 3D scenes to convey relevant information (visibility toggles on/off, clicking opens wiki page where text/images narrate an observation or comment associated with the marker);

Improve ways to visualize fMRI activation maps along with anatomical data and FreeSurfer parcellation labels.

Ibrowser and fMRIEngine tools in Ibrowser and fMRIEngine tools in SlicerSlicer

Multi-volume processing and fMRI analysis have been included with the Slicer 2.6 release.

Ibrowser permits timeseries data reorienting, smoothing, preview, and timecourse plotting.

FMRIEngine permits first level GLM-based fMRI analysis, supports anatomy- and activation-based ROI analysis, permits interactive visualization of the activation map and voxel timecourse plotting.

Currently adding the ability to incorporate Ising Priors into the computation of parametric maps.

Detailed use-case tutorial for the fMRIEngine has been developed.

Test the tutorial on local user-groups and refine it; then we will make the tutorial and tutorial dataset available to the wider community.

fMRIEngine – Slicer 2.6fMRIEngine – Slicer 2.6

Informatics Working SessionsInformatics Working SessionsMonday: 1 – 4:30pm NI Group Working Session Monday: 1 – 4:30pm NI Group Working Session (Maybe in UCI BIRN (Maybe in UCI BIRN

Conference Room if we want to use the SmartBoard or have VTC support)Conference Room if we want to use the SmartBoard or have VTC support)

Introduction/Review Previous Milestones from October BIRN Introduction/Review Previous Milestones from October BIRN AHM (15 min.)AHM (15 min.)Database MaintenanceDatabase MaintenanceHID Development (see attached)HID Development (see attached)Data QA/QC (30 min.)Data QA/QC (30 min.)

Tuesday: 8:30 – 10:30 am NI and Stats Group Data Mining Tuesday: 8:30 – 10:30 am NI and Stats Group Data Mining SessionSessionWhat is Data Mining, ExamplesWhat is Data Mining, ExamplesWhat data mining activities might we want to investigate for What data mining activities might we want to investigate for October BIRN AHM? (60 min.)October BIRN AHM? (60 min.)How do we need to organize the existing data to support data How do we need to organize the existing data to support data mining activities? (30 min.)mining activities? (30 min.)

Tuesday: 2:00 – 5:00 pm NI Working Group Session Tuesday: 2:00 – 5:00 pm NI Working Group Session (Maybe in UCI (Maybe in UCI BIRN Conference Room if we want to use the SmartBoard or have VTC support)BIRN Conference Room if we want to use the SmartBoard or have VTC support)

Derived Data – SRB/HID (60 min.)Derived Data – SRB/HID (60 min.)SRB (30 min.)SRB (30 min.)Mediator (45 min.)Mediator (45 min.)XML (30 min.)XML (30 min.)Milestones/Wrap-Up (15 min.)Milestones/Wrap-Up (15 min.)

Information Technology (IT) vs. Information Technology (IT) vs. Neuroinformatics (NI)Neuroinformatics (NI)

Processing information by computer. IT is the latest moniker for the industry. There have been several before it, namely "electronic data processing" (EDP), "management information systems" (MIS) and "information systems" (IS). The term became popular in the 1990s and may embrace or exclude the telecom industry, depending on whom you talk to. http://www.pcmag.com/

…the branch of engineering that deals with the use of computers and telecommunications to retrieve and store and transmit information wordnet.princeton.edu/perl/webwn

IT is a term that encompasses all forms of technology used to create, store, exchange, and use information in its various forms (business data, voice conversations, still images, motion pictures, multimedia presentations, and other forms, including those not yet conceived). It's a convenient term for including both telephony and computer technology in the same word. It is the technology that is driving what has often been called "the information revolution.“ www.planetech.co.uk/glossary.htm

Information Technology is the general term used to describe general computing.www.z2z.com/site01/itglos02.html

Neuroinformatics is an emerging discipline which attempts to integrate neuroscientific information from the level of the genome to the level of human behavior. A major goal of this new discipline is to produce digital capabilities for a web-based information management system in the form of interoperable databases and associated data management tools. Such tools include software for querying and data mining, data manipulation and analysis, scientific visualization, biological modeling and simulation, and electronic communication and collaboration between geographically distinct sites. The databases and software tools are designed to be used by neuroscientists, behavioral scientists, clinicians, and educators in an effort to better understand brain structure, function, and development. http://neurovia.umn.edu/IGERT/

What Does NI Stand For?What Does NI Stand For?

NI = NI = NNo, o, II will not fix your computer! will not fix your computer!

NI = NI = NNeuroeuroIInformaticsnformatics

Documents

FBIRN AHM March 13-14, 2006 David B. Keator University of California, Irvine FBIRN NeuroInformatics Working Group Update