All Hands Meeting 2005 FBIRN Tools: 2005 Subtitle added here.

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Presentation transcript:

All Hands Meeting 2005 FBIRN Tools: 2005 Subtitle added here

2 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

3 Data Collection: Phantom QA methods

4 Time Series Stability

5 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)

6 Current Datasets: Phantom QA Data

7 Data Entry: HID+GUI  Human Imaging Database

8 Data Management: Non-neuroimaging data Screenshot of BIRN HID with breast mammography and clinical data stored and retrieved.

9 Data Management: CALM & GAME  Human Imaging Database

10 Current tools: HID+GUI  Human Imaging Database

11 FBIRN IT - We’re Up and We’re Mediated! UNM HID UMN HID UI HID Duke HID UCSD HID UCI HID BWH HID MGH HID Yale HID UCLA HID Stanford HID p1 p2 = Mediator tested = PostgreSQL test site = ph 1 and/or ph 2 data in DB

12 Data Management: XCEDE schema and tools  XCEDE: XML-based Clinical and Experimental Data Exchange  cede/index.htm cede/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.

13 XCEDE

14 XCEDE 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 eventmetadata stimulus (image, video, sound, text,…) displayed text image name sound name background color response delay code etc. button presswhich button blockblock name QA metricmean intensity center of mass

15 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”

16 Eprime to XML Event GUI Current tools: Eprime to XML Event GUI

17 Current tools: XCEDE schema and tools  Tools to create XCEDE headers fMRI QA tools (spike detection, movement, etc.) Event-averaging tools for analysis  docs/ docs/

18 Coming tools: FIPS FSL Image Processing Scripts  Why? Automated Analysis Assure same analysis Highly flexible Multi-site Calibration Data Sharing Query-Driven Portalized  How? Open-source, built on top of FSL

19

FIPS Vision Scanner Human Upload Hierarchy (Local SRB) Configure First-Level Analysis FLAC Library First-Level Analysis FIPS Database Stimulus Timing Import PixelData ImageWrapper.xml fips-process.xml Stimulus Schedules