FBIRN Use Case: Data Storage and Retrieval

User Query Results with standard descriptions in HIDB Results Images in SRB FIPS Result s FMRI Images Automated Image Upload to SRB/HID for sharing FIPS: FSL Image Processing Scripts FBIRN Neuroinformatics HIDB SRB/ Local fMRI Scanner Clinical Data Computer Aided Scale Input (CALM/GAME) Clinical Data Entry Interface URL links

FMRI Images Automated Image Upload to SRB/HID for sharing FBIRN Neuroinformatics: Images HIDB SRB/ Local fMRI Scanner URL links

FBIRN HID/SRB upload scripts Protocol in the HID –Subject groups –Scans and assessments that are part of the protocol are defined Assessment and demographic data for the subject in the HID Images on the SRB –XML metadata files with Images on SRB The upload script consists of over 35,000 lines of code –distributed over 768 files which includes binaries for converting images, –adding/editing/changing XML, inserting and querying the database, instructions/manuals..... Etc.

FMRI Images HIDB SRB fMRI Scanner Generic Image Upload Scripts Local File System Run Upload Script XML Wrapped FMRI Images Which Project? Which Subject? Which Visit?

FMRI Images HIDB SRB fMRI Scanner Generic Image Upload Scripts Local File System Run Upload Script Which Project? Which Subject? Which Visit? SRB SM = Local SM SRB SIRP = Local SIRP SRB BH = Local BH SRB AO = Local AO URL Link

Images on the SRB Directory hierarchy –Generalized for all experiments/subjects –Designed to be software friendly –Set to include derived data as well Meta-data in the XCEDE wrapper

Research Project Institution Subject Series k-Space ….... Native XML Visit Study

FBIRN Neuroinformatics: Clinical Data HIDB SRB/ Local Clinical Data Computer Aided Scale Input (CALM/GAME) Clinical Data Entry Interface URL links

Clinical data in the HID: Clinical Assessment Layout Manager (CALM)

CALM Layout Designer

User Query FBIRN Neuroinformatics: Data Retrieval HIDB SRB/ Local URL links Public query to the mediated database system

Distributed Data Retrieval: Query Interface

Mediated Query across distributed databases Distributed Data: Query Interface Same traveling subject At different sites

Automated Weekly Data Management

User Query FIPS Result s FMRI Images Automated Image Upload to SRB/HID for sharing FIPS: FSL Image Processing Scripts FBIRN Neuroinformatics Vision HIDB SRB/ Local fMRI Scanner Clinical Data Computer Aided Scale Input (CALM/GAME) Clinical Data Entry Interface URL links

XCEDE: 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

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”

FIPS: Analysis Levels Preprocessing – MC, STC, B0, Smoothing, Brain Extraction, Registration First Level – Estimate amplitude of HDR, Significance Higher Levels Visit, Subject, Group, Cross-Group, … Fixed, Random, Mixed Effects Stimulus Schedule – EPrime FIPS Database and Web page QA – All Levels (nothing in FIPS yet) Mostly FSL-based

FIPS: Local or SRB Data Hierarchy 1.$LOCAL_SRB_HOME_BIR N/ 2.ProjectName_ProjectId 3.SubjectID/ 4.Visit__SiteId_VisitNo/ 5.Study__StudyId/ 6.ExperimentSeries/ 7.Native/ 8.Original__0001/ 9.Analyze_7.5/ /space/BIRN/ fBIRNPhaseII__000010/ / Visit__009_0001/ Study__0001/ sm3/ Native/ Original__0001/ Analyze_7.5/ In Analyze_7.5/: Pixel Data: f0001.img, f0002.img, … (analyze format +.mat) ImageWrapper.xml – geometry, voxel size, slice order fips-process.xml – paradigm, run, site, BIRN Id, etc (redundant) XML files contain data-specific information.

User Query Results with standard descriptions in HIDB Results Images in SRB FIPS Result s FMRI Images Automated Image Upload to SRB/HID for sharing FIPS: FSL Image Processing Scripts FBIRN Neuroinformatics: Complete Circuit HIDB SRB/ Local fMRI Scanner Clinical Data Computer Aided Scale Input (CALM/GAME) Clinical Data Entry Interface URL links