2004 All Hands Meeting

FBIRN 2005 – Database and Informatics Working Group

David Keator

FBIRN Informatics MilestonesFBIRN Informatics Milestones

Database Schema• Insert functions for PostgreSQL instance• Official documentation (user manual, testing, etc)• Official release (HID 1.0)• CVS reorganization/integration of mBIRN/fBIRN

Graphical User Interface• Double entry assessment forms, conflict forms• Phase II assessment forms• Interface options for intentionally blank data items• Mediator integration

XML Schema• Packaged fMRI visit (images+assessments+behavioral data)• Packaging of SRB metadata

Upload Scripts• Raw data human upload script• Upload script + XML metadata integration• BIRNDUP integration into workflow with upload script

Web GUI AdditionsWeb GUI Additions

Web GUI AdditionsWeb GUI Additions

Web GUI AdditionsWeb GUI Additions

Generic Online Assessment Generic Online Assessment Generation and ManagementGeneration and Management

Clinical Assessment Layout Clinical Assessment Layout Manager (CALM)Manager (CALM)

CALM HelpCALM Help

CALM Help – Full-text searchCALM Help – Full-text search

CALM multiple answer questions/ CALM multiple answer questions/ unanswered questions supportunanswered questions support

Clinical Assessment Layout Clinical Assessment Layout Manager (CALM/GAME)Manager (CALM/GAME)

What's new

• More refined form layout management with enhanced layout container editing

• Static and SQL backed dropdown support

• Multiple answer/ unanswered question support

• Enhanced help facility including full text search (Help -> Help Contents)

• More fault tolerant operation including type/structure validation via XML schema, consistency checking/correction of XML layout files.

• Available online assessments (XML layout files for the large ones are generated automatically by Karen Pease's tool )

SAPS SANS Calgary Depression Scale Simpson Angus Scale Barnes Akathisia Rating Scale Fagerstrom Test for Nicotine Dependence Premorbid Adjustment Scale Abnormal Involuntary Movement Scale Beck Depression Scale Quick Mood Scale

• Acknowledgement:: Special thanks for Karen Pease for automatic tool and extensive input on CALM.

FBIRN Informatics MilestonesFBIRN Informatics Milestones

Database Schema• Insert functions for PostgreSQL instance• Official documentation (user manual, testing, etc)• Official release (HID 1.0)• CVS reorganization/integration of mBIRN/fBIRN

Graphical User Interface• Double entry assessment forms, conflict forms• Phase II assessment forms• Interface options for intentionally blank data items• Mediator integration

XML Schema• Packaged fMRI visit (images+assessments+behavioral data)• Packaging of SRB metadata

Upload Scripts• Raw data human upload script• Upload script + XML metadata integration• BIRNDUP integration into workflow with upload script

XML updates: Name changeXML updates: Name change

XCEDE: XML-based Clinical and Experimental Data Exchange

http://www.nbirn.net/Resources/Users/Applications/xcede/index.htm

Submitted Manuscript:• Keator, D; Gadde, S; Grethe, J ; Taylor, D; FIRST BIRN;

Potkin, S. A General XML Schema and Associated SPM Toolbox for Storage and Retrieval of Neuro-Imaging Results and Anatomical Labels. Submitted to Neuroinformatics, 2005.

XML updates: InteractionsXML updates: Interactions

Worked with mBIRN colleagues to help integrate XCEDE schema into XNAT (Extensible Neuroimaging Archive Toolkit)

Worked with UTHSCA BrainMap folks to map their local structures into our XML schema

Interactions with NIfTI Data Format Working group continues• 3 versions of reference data set has been posted to NIfTI

group, combines NIfTI 1.0 data format and XML extension data

XML updates: EventsXML updates: Events

We have defined an XML structure to store events, which are time intervals [onset,

onset + dur) that are associated with arbitrary user-defined metadata. Types of events might include stimuli, responses, blocks, QA metrics, etc.

kind of event metadata

stimulus (image, video, sound, text,…)

displayed text

image name

sound name

background color

response delay

code

etc.

button press which button

block block name

QA metric mean intensity

center of mass

Eprime to XML Event GUIEprime to XML Event GUI

XML updates: Events (cont’d)XML updates: Events (cont’d)

Generic XML-based event descriptors support:

• swappable analysis pipeline modules

• word-based event queries “tonetype==deviant” “shape==square & color==red &

quadrant==upperleft”

• automated creation of design matrices and other configuration info for FSL, SPM, AFNI, etc.

XML updates: Events (cont’d)XML updates: Events (cont’d)

Work is in progress on modules that maintain event lists throughout an analysis pipeline

Proof-of-concept pipeline in use at Duke:• inputs: functional image data, E-Prime

event data• output: 4-D image showing averaged

hemodynamic response over selected events, correlations to hemodynamic response templates

XML updates: Events (cont’d)XML updates: Events (cont’d)

MR scanner

stimulus presentation

software

scanner- or software-specific

file formats

XML-based events file

XML-based image header

image pre-processing

event analysis

fBIRN pipeline“big picture”

XML updates: Events (cont’d)XML updates: Events (cont’d)

FBIRN Informatics MilestonesFBIRN Informatics Milestones

Database Schema• Insert functions for PostgreSQL instance• Official documentation (user manual, testing, etc)• Official release (HID 1.0)• CVS reorganization/integration of mBIRN/fBIRN

Graphical User Interface• Double entry assessment forms, conflict forms• Phase II assessment forms• Interface options for intentionally blank data items• Mediator integration

XML Schema• Packaged fMRI visit (images+assessments+behavioral data)• Packaging of SRB metadata

Upload Scripts• Raw data human upload script• Upload script + XML metadata integration• BIRNDUP integration into workflow with upload script

Which Project?Which Subject

Which Visit

SR

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l D

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SR

B D

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al D

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SR

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Clinical Data

fMRI Images

HIDB

SRBfMRI Scanner

Generic Image Upload ScriptsGeneric Image Upload Scripts

Local

File System

fMR

I Images

Run Upload Script

SR

B D

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= L

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UR

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ink

HIDB

SRBfMRI Scanner

•Results with standard descriptions in HIDB

•Results Images in SRB

FIPS Results

•Automated Image Upload to Automated Image Upload to SRB/HIDB for sharingSRB/HIDB for sharing•QC/QA Automatic AnalysisQC/QA Automatic Analysis•XML Wrapped ImagesXML Wrapped Images•Scan Metadata/descriptionsScan Metadata/descriptions

•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface•Query Interface

•FSL AutomatedFSL AutomatedAnalysis Pipeline Analysis Pipeline (FIPS)(FIPS)

Query

FBIRN IT VisionFBIRN IT Vision

FBIRN ’05 AHM IT CalendarFBIRN ’05 AHM IT Calendar

Mon. 1:00 – 1:30pm            Free Discussion

Mon. 1:30 – 5:00pm            Day 1 - Introduction to Database and Data Grid Infrastructure

1:30 – 2:30pm   Database Schema Training and Overview (Jeff Grethe)

2:30 – 3:00pm   Database GUI Installation/Usage (Burak Ozyurt)

3:00 – 3:30pm   XML Schema Overview (Syam Gadde)

3:30 – 4:00pm   Image Upload Scripts (David Keator, Dingying Wei)

4:00 – 4:30pm   SRB Data Grid Standard Storage Hierarchies (Jeff Grethe)

4:30 – 5:00pm   FIPS Analysis Pipeline Interactions (Doug Greve, David Keator)           

6:00pm              Croquet and Beer!

Tues 9am – 10am          Clinical group meets with the IT for HID GUI Training

Tues 10am – 11am        FIPS and fMRI QA toolbox training

Tues 2pm – 5pm            Day 2 – Milestones and Future Work

                   2:00 – 2:30pm   Phase I and Phase II Data Discussions (Dingying Wei)

2:30 – 3:30pm   Database Schema and GUI Development (Jeff Grethe)

3:30 – 4:30pm   XML Schema (Syam Gadde)

4:30 – 4:45pm   QC Measures (David Keator)

                   4:45 – 5:00pm   Milestones Wrap-Up (David Keator)

Thanks to all the hard Thanks to all the hard work from the IT Group!work from the IT Group!

KEEP IT UP!KEEP IT UP!