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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
CoreCoreHierarchyHierarchy
SchemaSchema
Clinical /Clinical /DemographicsDemographics
Clinical /Clinical /DemographicsDemographics
StudyStudyProtocolsProtocols
StudyStudyProtocolsProtocols
StudyStudyDataData
StudyStudyDataData
SubjectSubjectManagementManagement
SubjectSubjectManagementManagement
Web ApplicationWeb Application
CALM/GAMECALM/GAMEAssessmentsAssessments
CALM/GAMECALM/GAMEAssessmentsAssessments
Multi-SiteMulti-SiteQueryQuery
Multi-SiteMulti-SiteQueryQuery
XCEDEXCEDEServicesServices
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/
Architecture OverviewArchitecture Overview
OracleOracleOracleOracle PostgreSQLPostgreSQLPostgreSQLPostgreSQL
DatabaseDatabase
CoreCoreHierarchyHierarchy
CoreCoreHierarchyHierarchy
SchemaSchema
Clinical /Clinical /DemographicsDemographics
Clinical /Clinical /DemographicsDemographics
StudyStudyProtocolsProtocols
StudyStudyProtocolsProtocols
StudyStudyDataData
StudyStudyDataData
SubjectSubjectManagementManagement
SubjectSubjectManagementManagement
Web ApplicationWeb Application
CALM/GAMECALM/GAMEAssessmentsAssessments
CALM/GAMECALM/GAMEAssessmentsAssessments
Multi-SiteMulti-SiteQueryQuery
Multi-SiteMulti-SiteQueryQuery
XCEDEXCEDEServicesServices
XCEDEXCEDEServicesServices
File SystemFile SystemFile SystemFile System Data GridData GridData GridData Grid
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
Architecture OverviewArchitecture Overview
OracleOracleOracleOracle PostgreSQLPostgreSQLPostgreSQLPostgreSQL
DatabaseDatabase
CoreCoreHierarchyHierarchy
CoreCoreHierarchyHierarchy
SchemaSchema
Clinical /Clinical /DemographicsDemographics
Clinical /Clinical /DemographicsDemographics
StudyStudyProtocolsProtocols
StudyStudyProtocolsProtocols
StudyStudyDataData
StudyStudyDataData
SubjectSubjectManagementManagement
SubjectSubjectManagementManagement
Web ApplicationWeb Application
CALM/GAMECALM/GAMEAssessmentsAssessments
CALM/GAMECALM/GAMEAssessmentsAssessments
Multi-SiteMulti-SiteQueryQuery
Multi-SiteMulti-SiteQueryQuery
XCEDEXCEDEServicesServices
XCEDEXCEDEServicesServices
File SystemFile SystemFile SystemFile System Data GridData GridData GridData Grid
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
Architecture OverviewArchitecture Overview
OracleOracleOracleOracle PostgreSQLPostgreSQLPostgreSQLPostgreSQL
DatabaseDatabase
CoreCoreHierarchyHierarchy
CoreCoreHierarchyHierarchy
SchemaSchema
Clinical /Clinical /DemographicsDemographics
Clinical /Clinical /DemographicsDemographics
StudyStudyProtocolsProtocols
StudyStudyProtocolsProtocols
StudyStudyDataData
StudyStudyDataData
SubjectSubjectManagementManagement
SubjectSubjectManagementManagement
Web ApplicationWeb Application
CALM/GAMECALM/GAMEAssessmentsAssessments
CALM/GAMECALM/GAMEAssessmentsAssessments
Multi-SiteMulti-SiteQueryQuery
Multi-SiteMulti-SiteQueryQuery
XCEDEXCEDEServicesServices
XCEDEXCEDEServicesServices
File SystemFile SystemFile SystemFile System Data GridData GridData GridData Grid
DataData
CALM Layout ImprovementsCALM Layout Improvements
Architecture OverviewArchitecture Overview
OracleOracleOracleOracle PostgreSQLPostgreSQLPostgreSQLPostgreSQL
DatabaseDatabase
CoreCoreHierarchyHierarchy
CoreCoreHierarchyHierarchy
SchemaSchema
Clinical /Clinical /DemographicsDemographics
Clinical /Clinical /DemographicsDemographics
StudyStudyProtocolsProtocols
StudyStudyProtocolsProtocols
StudyStudyDataData
StudyStudyDataData
SubjectSubjectManagementManagement
SubjectSubjectManagementManagement
Web ApplicationWeb Application
CALM/GAMECALM/GAMEAssessmentsAssessments
CALM/GAMECALM/GAMEAssessmentsAssessments
Multi-SiteMulti-SiteQueryQuery
Multi-SiteMulti-SiteQueryQuery
XCEDEXCEDEServicesServices
XCEDEXCEDEServicesServices
File SystemFile SystemFile SystemFile System Data GridData GridData GridData Grid
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