FBIRN Use Case: Data Storage and Retrieval

User Query

•Results with standard descriptions in HIDB

•Results Images in SRB

FIPS Results

FMRI ImagesAutomated Image Upload to SRB/HID for sharing •FIPS: FSL Image

•Processing Scripts

FBIRN NeuroinformaticsFBIRN Neuroinformatics

HIDB

SRB/Local

fMRI Scanner

•Clinical Data•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface

URL links

FMRI ImagesAutomated Image Upload to SRB/HID for sharing

FBIRN Neuroinformatics: ImagesFBIRN Neuroinformatics: Images

HIDB

SRB/Local

fMRI Scanner URL links

FBIRN HID/SRB upload scriptsFBIRN 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

SRBfMRI Scanner

Generic Image Upload ScriptsGeneric Image Upload Scripts

Local

File System

Run Upload Script

XML W

rapped FMRI Im

ages

Which Project?Which Subject?Which Visit?

FMRI Images

HIDB

SRBfMRI Scanner

Generic Image Upload ScriptsGeneric Image Upload Scripts

Local

File System

Run Upload Script

Which Project?Which Subject?Which Visit?

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Images on the SRBImages 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 DataFBIRN 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 data in the HID:Clinical Assessment Layout Manager (CALM)Clinical Assessment Layout Manager (CALM)

CALM Layout DesignerCALM Layout Designer

User Query

FBIRN Neuroinformatics: Data RetrievalFBIRN Neuroinformatics: Data Retrieval

HIDB

SRB/Local

URL links

Public query to the mediated database system

Distributed Data Retrieval: Distributed Data Retrieval: Query InterfaceQuery Interface

• Mediated Query across distributed databases

Distributed Data: Query InterfaceDistributed Data: Query Interface

Same traveling subject

At different sites

Automated Weekly Data ManagementAutomated Weekly Data Management

User Query

FIPS Results

FMRI ImagesAutomated Image Upload to SRB/HID for sharing •FIPS: FSL Image

•Processing Scripts

FBIRN Neuroinformatics VisionFBIRN Neuroinformatics Vision

HIDB

SRB/Local

fMRI Scanner

•Clinical Data•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface

URL links

XCEDE: EventsXCEDE: 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

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”

FIPS: Analysis LevelsFIPS: 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 HierarchyFIPS: Local or SRB Data Hierarchy

1. $LOCAL_SRB_HOME_BIRN/

2. ProjectName_ProjectId3. SubjectID/4. Visit__SiteId_VisitNo/5. Study__StudyId/6. ExperimentSeries/7. Native/8. Original__0001/9. Analyze_7.5/

/space/BIRN/fBIRNPhaseII__000010/00900000103/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 Results

FMRI ImagesAutomated Image Upload to SRB/HID for sharing •FIPS: FSL Image

•Processing Scripts

FBIRN Neuroinformatics: Complete CircuitFBIRN Neuroinformatics: Complete Circuit

HIDB

SRB/Local

fMRI Scanner

•Clinical Data•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface

URL links