FBIRN AHM March 13-14, 2006 David B. Keator University of California, Irvine FBIRN NeuroInformatics Working Group Update

October 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 Vision DICOM, NIFTI

FBIRN Federated Data UNM HID UMN HID UI HID Duke HID UCSD HID UCI HID BWH HID MGH HID Yale HID UCLA HID Stanford HID p1 p2 = Data Integration Environment = PostgreSQL test site = Phase 1 / Phase 2 data p1 p2 Duke: 48 BWH: 18 MGH: 11 UCLA: 37 UCSD: 5 UCI: 58 UNM: 44 UI: 63 UMN: 52 Yale: 56 Duke: 48 BWH: 18 MGH: 11 UCLA: 37 UCSD: 5 UCI: 58 UNM: 44 UI: 63 UMN: 52 Yale: Subject Visits

Architecture Overview OraclePostgreSQL Database CoreHierarchy Schema Clinical / Demographics StudyProtocolsStudyData SubjectManagement Web Application CALM/GAMEAssessmentsMulti-SiteQueryXCEDEServices File System Data Grid Data

Phase I Traveling Subject Dataset

FBIRN Shared Data Files Phase 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 Download 

Architecture Overview OraclePostgreSQL Database CoreHierarchy Schema Clinical / Demographics StudyProtocolsStudyData SubjectManagement Web Application CALM/GAMEAssessmentsMulti-SiteQueryXCEDEServices File System Data Grid Data

HID 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 Overview OraclePostgreSQL Database CoreHierarchy Schema Clinical / Demographics StudyProtocolsStudyData SubjectManagement Web Application CALM/GAMEAssessmentsMulti-SiteQueryXCEDEServices File System Data Grid Data

 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  Pseudo-Mediated Query Interface

Mediator - “View” on HID: Assessments and MR Data

View across fBIRN HID resources

Multi-Site Query Across fBIRN Sites

Architecture Overview OraclePostgreSQL Database CoreHierarchy Schema Clinical / Demographics StudyProtocolsStudyData SubjectManagement Web Application CALM/GAMEAssessmentsMulti-SiteQueryXCEDEServices File System Data Grid Data

CALM Layout Improvements

Architecture Overview OraclePostgreSQL Database CoreHierarchy Schema Clinical / Demographics StudyProtocolsStudyData SubjectManagement Web Application CALM/GAMEAssessmentsMulti-SiteQueryXCEDEServices File System Data Grid Data

E-Prime, Presentation, etc. to XCEDE events Data Acquisition Event extraction into XML XML Stimulus presentation MR scanner Event data 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’]/ons et >= (onset - 9)) XCEDE events to FIPS XPath XCEDE XPath query syntax

XML 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 Browser

Query 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 Slicer  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 2.6

Informatics Working Sessions Monday: 1 – 4:30pm NI Group Working Session (Maybe in UCI BIRN Conference Room if we want to use the SmartBoard or have VTC support) Introduction/Review Previous Milestones from October BIRN AHM (15 min.) Database Maintenance HID Development (see attached) Data QA/QC (30 min.) Tuesday: 8:30 – 10:30 am NI and Stats Group Data Mining Session What is Data Mining, Examples What data mining activities might we want to investigate for October BIRN AHM? (60 min.) How do we need to organize the existing data to support data mining activities? (30 min.) Tuesday: 2:00 – 5:00 pm NI Working Group Session (Maybe in UCI BIRN Conference Room if we want to use the SmartBoard or have VTC support) Derived Data – SRB/HID (60 min.) SRB (30 min.) Mediator (45 min.) XML (30 min.) Milestones/Wrap-Up (15 min.)

Information Technology (IT) vs. 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. …the branch of engineering that deals with the use of computers and telecommunications to retrieve and store and transmit information wordnet.princeton.edu/perl/webwnwordnet.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.“ Information Technology is the general term used to describe general computing. 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.

What Does NI Stand For? NI = No, I will not fix your computer! NI = NeuroInformatics