XCEDE Use Cases:

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XCEDE Use Cases
QueryAtlas other scenarios 2008 fBIRN AHM
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Overview

• User Centered Design for fBIRN tools
• Example Users of Slicer with informatics
  infrastructure
• fBIRN researchers (QueryAtlas population
  statistics)
• Neuroscience labs (image analysis workflow)
• Retrospective data sharing (mark-up)
• CVRG (statistics multi-scale information
  integration)
• Image-guided therapy (real-time image access)
• Scenarios
• Requirements

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User-centered design approach
Drive tool development with user needs, use cases
ensure that XCEDE web services address use
cases of interest.
1. Assess user developer needs, priorities
develop model
2, 3, 4 Design, Implement, Test, Iterate
Users evaluate and shape the design (features
interaction) that works for them. Developers
ensure the designs technical merit, assess
community interest compatibility with
priorities.
5 Disseminate support
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Use case fBIRN Neuroscientists

• Using a webGUI or a Slicer query mechanism
  Search for all SZ subjects that have FreeSurfer
  FIPS analyses for a particular experiment.
• Or find SZ population statistical analyses and
  FreeSurfer average morphology data
• View downloaded results in QueryAtlass ontology-
  and atlas-based context choose search terms and
  query for relevant multi-scale information.
• View integrated search results save all data of
  interest for continued study.
• Export descriptions/data compatible with other
  atlases
• Query must be simple powerful. Tools must
  manage display returned results for clarity.

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Use case Neuroscience labs

• Example Schizophrenia Research
• Structural Imaging, DTI, fMRI
• Demographics, Protocols, Clinical Assessments
• Label Maps, Activation Maps
• Labs often use Ad Hoc methods for data transfer,
  description tracking provenance
• Shared Network Drive, Access Database,
  Spreadsheets
• Reluctant to Change if Database Administrator is
  Required
• Would Greatly Benefit from Informatics
  Infrastructure if Reliable Easy To Use

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Use case Sharing Retrospective Data

• Over 1000 Slicer-Guided Open MR Craniotomies
• Large Subset (200) Cases Collated with Pre- and
  Intra-Operative Images
• Various acq., 1.5T and 0.5T
• GE or NRRD format (not DICOM)
• National Center for Image Guided Therapy (Jolesz,
  BWH) Goal to Share the Data
• Talos, Archip, and Haker Working with Marcus et
  al. for Upload to XNAT Central
• Mark-up of image data and derived data
• Prostate Brachytherapy Data Also Available for
  Upload

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Use case CVRG

• Cardiovascular Research Grid (Winslow, JHU)
• Broad Range of Potential inputs CT, MR, EKG,
  Pet, DWI
• Initial Three Cases of CT Torso Cases Uploaded to
  XNAT Central
• Data from Drs. Triedman and Jolley, Boston
  Childrens Pediatric Cardiology
• Includes Detailed Heart Segmentation
• JHU Canine Heart DTI

(Want to use QueryAtlas-style ontology- and
atlas-based query for related multi-scale data.)
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Use case Image Guided Therapy

• Collect Pre-Therapy Imaging
• Run Diverse Analysis Routines
• Evolving Research Code
• Multiple Investigators
• Bring Patient Maps into Real Time Navigation /
  Robotic System
• Feed Procedure Images and Data Back to Database

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Scenario 1 Manual Per-Subject

• Target Clinical Study Scenario
• Search XNAT or HID for Target Data (via web GUI
  or Slicer queries)
• - Search for project name or subject name of
  interest
•   - Search for particular data assigned to you
  for that project
• Select datasets of interest for download.
• Download .xcat file containing URIs for selected
  datasets
• Slicer3 Retrieves Data and Metadata
• Analysis, Visualization, Annotation
• Select particular datasets for upload and tag
  them
• New Data and Provenance is Uploaded and Linked to
  Original Data

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Scenario 1 Manual Per-Subject
XCEDE Working Group discussion find_subjects
request returns a list of subjects and their
IDs.  get_subjects could be used to retrieve
details in XCEDE format. This
find_subjects(projectPNL-PROJECT") Returns
this ltListgt       ltItem id"1234"
type"subject"/gt       ltItem id"3456"
type"subject"/gt       ltItem id"5678"
type"subject"/gt lt/Listgt      
Some return fields could also be
included   This find_subjects(project"OASIS",
fields"CDR,Age,Dx") Returns this ltListgt      
ltItem id"1234" type"subject"gt            
ltField name"CDR"gt0lt/Fieldgt             ltField
name"Age"gt87lt/Fieldgt              ltField
name"Dx"gtNormallt/Fieldgt       lt/Itemgt      
ltItem id"3456" type"subject"gt            
ltField name"CDR"gt0.5lt/Fieldgt             ltField
name"Age"gt84lt/Fieldgt              ltField
name"Dx"gtADlt/Fieldgt       lt/Itemgt       ltItem
id"5678" type"subject"gt             ltField
name"CDR"gt0lt/Fieldgt             ltField
name"Age"gt65lt/Fieldgt              ltField
name"Dx"gtNormallt/Fieldgt       lt/Itemgt lt/Listgt    
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Scenario 1 Manual Per-Subject
Slicer MRML representation for holding results in
scene state vtkMRMLSlicerTableNode
vtkMRMLSlicerTableStorageNode (M. Halle) Parse
and store data in table form  

• Also allows useful CSV input format for
  collections of URIs
• Any URI table data handed off to appropriate
  vtkMRMLURIHandler
•  

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Scenario 2 Population Analysis

• Target Population Study Scenario
• Search XNAT or HID Target Population (How will
  people want to specify search?)
• Receive .xcat File of Result URIs
• Search or Load Parameter Files for Tools
  intuitive UI or script
• Specify Group Statistics Parameters intuitive
  UI or script
• Dispatch Analysis for Remote Processing
  intuitive UI or script
• Results are Uploaded to Database from Remote
  Analysis Machines
• ? Identify fBIRN tool users who can help us flesh
  out this scenario understand user needs?

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Scenario 3 Visualization of Statistics

• Target Visualization Scenario
• Search XNAT or HID Processed Studies for
  diagnosis (SZ), protocol (SIRP), that have both
  FreeSurfer and FIPS analyses.
• Select among returned results for studies of
  interest.
• Receive .xcat File of Result URIs
• Parse load into Slicer / QueryAtlas (tags
  distinguish data types/formats for intelligent
  loading)
• Query for explanatory information
• Add notes, save query record and relevant
  information as part of MRML scene
• Upload MRML scene to database

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Requirements

• Easy To Install XCEDE Compliant Server
• XNAT Desktop?
• Web Services API and Web services client tools
• The Simpler the Better
• Several Examples are Available
• DigitalBucket, GeneNetwork
• Capability to represent data provenance, and mark
  up data with custom tags (Assigned To, Completed
  By)
• Good user feedback (is transfer running? Was it
  successful?)
• Server-to-Server Data Migration
• Automatic Synchronization?
• cvs/svn-like checkouts and commits?