fbirn use case: data storage and retrieval. user query results with standard descriptions in hidb...
TRANSCRIPT
![Page 1: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/1.jpg)
FBIRN Use Case: Data Storage and Retrieval
![Page 2: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/2.jpg)
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
![Page 3: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/3.jpg)
FMRI ImagesAutomated Image Upload to SRB/HID for sharing
FBIRN Neuroinformatics: ImagesFBIRN Neuroinformatics: Images
HIDB
SRB/Local
fMRI Scanner URL links
![Page 4: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/4.jpg)
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.
![Page 5: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/5.jpg)
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?
![Page 6: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/6.jpg)
FMRI Images
HIDB
SRBfMRI Scanner
Generic Image Upload ScriptsGeneric Image Upload Scripts
Local
File System
Run Upload Script
Which Project?Which Subject?Which Visit?
S
RB
SM
= L
oc
al S
M
SR
B S
IRP
= L
oca
l S
IRP
S
RB
BH
= L
oca
l B
H
S
RB
AO
= L
oc
al A
O
UR
L L
ink
![Page 7: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/7.jpg)
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
![Page 8: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/8.jpg)
Research Project
Institution
Subject
Series
k-Space…....Native
XML
Visit
Study
![Page 9: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/9.jpg)
FBIRN Neuroinformatics: Clinical DataFBIRN Neuroinformatics: Clinical Data
HIDB
SRB/Local
•Clinical Data•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface
URL links
![Page 10: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/10.jpg)
Clinical data in the HID:Clinical data in the HID:Clinical Assessment Layout Manager (CALM)Clinical Assessment Layout Manager (CALM)
![Page 11: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/11.jpg)
CALM Layout DesignerCALM Layout Designer
![Page 12: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/12.jpg)
User Query
FBIRN Neuroinformatics: Data RetrievalFBIRN Neuroinformatics: Data Retrieval
HIDB
SRB/Local
URL links
Public query to the mediated database system
![Page 13: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/13.jpg)
Distributed Data Retrieval: Distributed Data Retrieval: Query InterfaceQuery Interface
![Page 14: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/14.jpg)
• Mediated Query across distributed databases
Distributed Data: Query InterfaceDistributed Data: Query Interface
Same traveling subject
At different sites
![Page 15: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/15.jpg)
Automated Weekly Data ManagementAutomated Weekly Data Management
![Page 16: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/16.jpg)
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
![Page 17: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/17.jpg)
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
![Page 18: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/18.jpg)
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”
![Page 19: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/19.jpg)
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
![Page 20: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/20.jpg)
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.
![Page 21: 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](https://reader035.vdocuments.us/reader035/viewer/2022062805/5697bff31a28abf838cbc8b5/html5/thumbnails/21.jpg)
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