All Hands Meeting 2005

FBIRN Tools: 2005

Subtitle added here

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Tools being made available November 2005

Data collection• MRI QA protocol and phantoms• E-prime programs used in data collection

Data management:• Human Imaging Database schema/Graphical User Interface Code• Clinical Assessment Layout Manager/General Assessment Manager

Engine• XCEDE XML schema

Tools for reading and writing XCEDE XML image wrappers

• Standardized, general purpose directory hierarchy

Datasets• Phase I, 10-site traveling subjects dataset• MRI QA datasets

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Data Collection: Phantom QA methods

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Data Collection: Phantom QA methods

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Time Series Stability

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Data Collection: Phantom QA methods

BIRN website: The QA methods Includes:

• The protocol• The agar recipe• The .m script• MCW-GCRC AFNI version of the same (a result of the

GCRC interaction)

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Current Datasets: Phantom QA Data

https://portal.nbirn.net/BIRN/cgi-bin/DataGrid/MRIs/publicMRIStability.cgi

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Data Entry: HID+GUI

Human Imaging Database

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Data Management: Non-neuroimaging data

Screenshot of BIRN HID with breast mammography and clinical data stored and retrieved.

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Data Management: CALM & GAME

Human Imaging Database

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Current tools: HID+GUI

Human Imaging Database

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FBIRN IT - We’re Up and We’re FBIRN IT - We’re Up and We’re MediatedMediated!!

UNMHID

UMNHID

UIHID

DukeHID

UCSDHID

UCIHID

BWHHID

MGHHID

YaleHID

UCLAHID

Stanford

HID

p1

p1

p1

p1

p1

p1

p1

p2

p2

p2

p2

p2

= Mediator tested= Mediator tested

= PostgreSQL test site= PostgreSQL test site

= ph 1 and/or ph 2 data in DB= ph 1 and/or ph 2 data in DB

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Data Management: XCEDE schema and tools

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.

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XCEDE

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XCEDE updates: EventsXCEDE 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

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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”

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Current tools: XCEDE schema and tools

Tools to• create XCEDE headers• fMRI QA tools (spike detection, movement, etc.)• Event-averaging tools for analysis

http://www.biac.duke.edu/home/gadde/xmlheader-docs/

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Coming tools: FIPS

FSL Image Processing Scripts Why?

• Automated Analysis• Assure same analysis• Highly flexible• Multi-site Calibration• Data Sharing• Query-Driven• Portalized

How? http://www.nmr.mgh.harvard.edu/~greve/fbirn/fips/• Open-source, built on top of FSL

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FIPS Vision

Scanner

Human Upload

Hierarchy(Local SRB)

ConfigureFirst-LevelAnalysis

FLAC Library

First-LevelAnalysis

FIPSDatabase

StimulusTiming

Import

PixelDataImageWrapper.xmlfips-process.xmlStimulus Schedules