1. 2004 All Hands Meeting FBIRN 2005 – Database and Informatics Working Group David Keator

2. FBIRN 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

3. Web GUI Additions

7. Generic Online Assessment Generation and Management

8. Clinical Assessment Layout Manager (CALM)

9. CALM Help

10. CALM Help – Full-text search

11. CALM multiple answer questions/ unanswered questions support

12. Clinical Assessment Layout 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.

13. FBIRN 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

14. XML updates: Name change  XCEDE: XML-based Clinical and Experimental Data Exchange  http://www.nbirn.net/Resources/Users/Applications/ xcede/index.htm 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.

15. XML 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

16. XML 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

17. Eprime to XML Event GUI

18. 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.

19. 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

20. 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”

21. XML updates: Events (cont’d)

22. FBIRN 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

23. Which Project? Which Subject Which Visit SRB Dir Z = Local Dir Z SRB Dir V = Local Dir V SRB Dir X = Local Dir X Clinical Data fMRI Images HIDB SRB fMRI Scanner Generic Image Upload Scripts Local File System fMRI Images Run Upload Script SRB Dir Y = Local Dir Y URL Link

24. HIDB SRB fMRI Scanner Results with standard descriptions in HIDB Results Images in SRB FIPS Results Automated Image Upload to SRB/HIDB for sharingAutomated Image Upload to SRB/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 Automated Analysis Pipeline (FIPS) Query FBIRN IT Vision

25. FBIRN ’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)

26. Thanks to all the hard work from the IT Group! KEEP IT UP!