All Hands Meeting 2004
Clinician’s Requirements for HIDQuery and Statistics Interface
Christine Fennema-Notestine, Ph.D.
David Kennedy, Ph.D.
The Human Imaging Database (HID)
Secure database and query tools for exploring datawithin and across sites
•Site-specific HID schema using Oracle label security
•Data maintenance and assessment management
On-line clinical assessments for data entry (CALM)
•Query interface to navigate and combine clinical andanatomical derived data
Resultant text data can be exported
•Mediation for multi-site HID queries
•Univariate and bi-variate statistical interface
Helps to get a flavor of the data available to inform new queries
•Access to imaging data in Storage Resource Broker (SRB)for viewing, browsing, and downloading
Multi-site Alzheimer’s Testbed
GOAL:
To demonstrate how BIRN infrastructure can be used formining multi-site clinical MRI studies with a BIRN-enabledpreliminary study of Alzheimer’s disease (AD).
Together, data from more than one site may provide a larger,improved sample of individuals to better understand elderlyindividuals at risk for AD and those at various stages of AD.
Type of data available in AD project
•MR data: Legacy T1 data from UCSD (PI: T. Jernigan)and BWH/MGH (PI: M. Albert)
NATIVE de-identified/defaced volumes
ANALYZED data volumes (FreeSurfer subcortical segmentations)
•Demographic information required across sites
Age, Education, Gender, Handedness
•Clinical assessments varied across sites (UCSD ADRCPI: L. Thal; BWH/MGH), with some overlap
Minimum requirement MMSE
Review your questionnaire to make notes as we gothrough the following example query
Welcome and Portal Login
demo
demo
Begin Query Assessment
Regular user interface
Save Query forlater use orediting
Single orMulti-site(mediated)Query
Query Results
Single subject data: view, browse, download
Statistical options through Portal
Univariate Statistics
Box Plot Outlier Datasets
Bi-variate Statistics
Box Plot of Left Hippocampal Volumeby Diagnostic Group
If you like your query results….
Export CSV text data for local analysis
Working Plans
Extension and improvement for the StatisticalPrototype (currently based in R)
•Improve readability of text
•Improve graphical capabilities
Ability to perform more complex graphical plots
•E.g., hippocampal volume by diagnosis by site plots
Quick generation of readable plots and graphs
Dynamic graphics with live datapoints
•Extend analysis capabilities
Multivariate and covariate analyses
Continue development of on-line data entry (CALM)
Add different types of data, e.g., genotypic, DTI
Enhancements to Statistical Interface
•Enable ‘By’ Functionality
•Hierarchical ANOVA / MANOVA
Total Brain
•Cerebrum, Cerebellum, Brainstem, Ventricular System
Cerebral Cortex, White Matter, Thalamus, Caudate, Accumbens,Putamen, Pallidum, Hippocampus, Amygdala
Frontal, Occipital, Parietal, Temporal Lobes
Gyral Regions within Lobe
•Enable laterality functions (L+R, L-R, average, symmetryindex, etc.)
User Feedback Hints
•Site needs may differ
•Navigation suggestions
•Mediation for multi-site HID queries and Ontology needs
Each site will have different assessments available
Each site may have different variable names for assessments
Preference to visualize available databases at Welcome page andto know in advance what each site may have available – requiresontology base
•Single subject information
What’s missing?
Different text format?
Different data format for image volumes?
•Access to imaging data in the Storage Resource Broker(SRB) for viewing, browsing, downloading
Links to other types of software/tools to view data?
Other download formats?
•Meta data related to data provenance incorporated intoHID for querying
Public Demo site will be available for testing
Public Demo to orient users with on-line tutorial forHID Query Interface
Without tutorial
Statistics and data browsing can also be done atthese sites if you have a BIRN Portal account foraccess privileges, until a guest account is created.
Additional current options:
From outliers in UnivariateStatistics, launch 3DSlicer toview anatomical data and useQuery Atlas tool
