XCEDE Use Cases:QueryAtlas & other scenarios

2008 fBIRN AHM

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

User-centered design approach

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 design’s technical merit, assess community interest & compatibility with priorities.

5: Disseminate & support

Drive tool development with user needs, use cases – ensure that XCEDE web services address use cases of interest.

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 QueryAtlas’s

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.

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

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

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.)

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

Scenario 1: Manual Per-Subject

Target Clinical Study Scenario:

1. 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

2. Select datasets of interest for download.

3. Download .xcat file containing URIs for selected datasets

4. Slicer3 Retrieves Data and Metadata

5. Analysis, Visualization, Annotation

6. Select particular datasets for upload and tag them

7. New Data and Provenance is Uploaded and Linked to Original Data

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(project=“PNL-PROJECT")

Returns this:

<List>

      <Item id="1234" type="subject"/>

      <Item id="3456" type="subject"/>

      <Item id="5678" type="subject"/>

</List>    

 

Some return fields could also be included: 

This: find_subjects(project="OASIS", fields="CDR,Age,Dx") Returns

this:

<List>

      <Item id="1234" type="subject">

            <Field name="CDR">0</Field>

            <Field name="Age">87</Field> 

            <Field name="Dx">Normal</Field>

      </Item>

      <Item id="3456" type="subject">

            <Field name="CDR">0.5</Field>

            <Field name="Age">84</Field> 

            <Field name="Dx">AD</Field>

      </Item>

      <Item id="5678" type="subject">

            <Field name="CDR">0</Field>

            <Field name="Age">65</Field> 

            <Field name="Dx">Normal</Field>

      </Item>

</List>    

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…

 

Subject ID Age CDR Dx

1234 87 0 Normal

3456 84 0.5 AD

5678 65 0 Normal

• Also allows useful CSV input format for collections of URIs

• Any URI table data handed off to appropriate

vtkMRMLURIHandler 

Scenario 2: Population Analysis

Target Population Study Scenario:

1. Search XNAT or HID Target Population (How will people want to

specify search?)

2. Receive .xcat File of Result URIs

3. Search or Load Parameter Files for Tools – intuitive UI or script

4. Specify Group Statistics Parameters – intuitive UI or script

5. Dispatch Analysis for Remote Processing – intuitive UI or script

6. Results are Uploaded to Database from Remote Analysis Machines

Identify fBIRN tool users who can help us flesh out this scenario &

understand user needs?

Scenario 3: Visualization of Statistics

Target Visualization Scenario:

1. Search XNAT or HID Processed Studies for diagnosis (SZ),

protocol (SIRP), that have both FreeSurfer and FIPS analyses.

2. Select among returned results for studies of interest.

3. Receive .xcat File of Result URIs

4. Parse & load into Slicer / QueryAtlas (tags distinguish data

types/formats for intelligent loading)

5. Query for explanatory information

6. Add notes, save query record and relevant information as part

of MRML scene

7. Upload MRML scene to database

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?