Projects:ARRA:SlicerWF

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Aim

Supplement 3D Slicer and Extensible Neuroimaging Archive Toolkit (XNAT) with workflow management system. Provide integration and interoperability between 3D Slicer, XNAT Services and 3-rd party image processing applications and high performance computing systems. Implement it as within currently developed Structural Planning and Implementation in Neurological Exploration (SPINE) System.

SPINE Project Documentation

SPINE Docs

Research Plan

• Create a stand-alone SPINE desktop agent with fully functional data exchange and communication mechanisms towards 3D Slicer and XNAT.
• Develop Service Oriented Architecture (SOA) SPINE System that will include 3D Slicer image processing modules deployed as web services as well as a workflow management system to orchestrate interaction between 3D Slicer, XNAT, and 3-rd party tools.
• Implement two-way control and communications between 3D Slicer and SPINE modules.
• Adapt SPINE System for cluster and grid computing scenarios.
• Provide with workflow and 3D Slicer web service wrappers editing tools.
• Use Case scenarios

Key Personnel

• Charles Gutmann, MD., 4%, 9-17-2009 through 9-16-2011
• Alexander Zaitsev, Ph.D., 75%, 9-17-2009 through 9-16-2011

Progress

• February 26, 2010
  
• Use Cases.

- Social Cognition Study. Slicer EM Segmenter module:
A) parameters tuning for EM Segmenter itself (work with EM Segmenter developer), template scenes creation
B) update preprocessing pipeline - deep gray matter atlases included
C) test and debug preprocesing pipeline
D) identified missing modules: atlas autocalibration for EM Segmentation scene, Island removal for ICC mask

• Infrastructure

- Review currently deployed modules.

• February 19, 2010
  
• Use Cases.

- Social Cognition Study. Slicer EM Segmenter module: reviewed firts seven subjects' outputs, added volume orientation module into pipeline (prevents ICBM atlas linear registration failures)
- Fused ICC(brainmask) extraction module with EM Segmenter preprocessing. Three scenarious implemented: start with pre-extracted ICC mask (longitudinal studies case), run with ICC ectration, run with ICC extraction AND ICC correction before ICBM atlas preporcessing.
- Completion of Human activities GUI (QC, ICC Correction) planned for coming week

• Infrastructure

- The following Slicer3.5 Modules deployed as web services: Volume Orientation.

• February 12, 2010
  
  • Use Cases.

- Social Cognition Study. Slicer EM Segmenter module: automated preprocessing pipeline for Slicer2 EM Segmenter test version deployed. Seven cases pre-processed. - PET Quantitative measurements: Preliminary design specs discussion.

• • Infrastructure

- The following Slicer3.5 Modules deployed as web services: BSplineRegistration (for non-linear registration), ResampleVolume2 (for atlases resampling based on image atlase templates registration). Local and Network runs are implemented, Cluster/GridWizard implementation pending.

• February 5, 2010
  
  • Use Cases.

- Slicer EM Segmenter module: preprocessing design for Slicer2 EM Segmenter

• • Infrastructure

- Adapting for Slicer2 EM Segmenter (mostly from pipelines and services for previous projects)

 -- Integration with FreeSurfer modules for bisafield correction, brainmask extraction, and linear registration of ICBM atlases
 -- Preprocessing updates for non-linear registration of ICBM atlases with Slicer2 (image re-orientation service designed)

• January 29, 2010
  
  • Use Cases.

- EM Segmentaton pipeline: preprocessing results are being transferred to XNat (anonymized data, Central XNat)
- Slicer EM Segmenter module: discussed agenda and scheduled a work meeting for Social Cognition Study image segmentation.

• • Infrastructure

- Work on Web Services for structured data exchange between XNat and Workflow Instances (Testing stage, 95% completion)
- SPL XNat server: verified data exchange via RESTfull web services.

• January 22, 2010
  
  • Use Cases.

- Follow up with White Matter Lesion Segmenter and Scull Stripping Modules developers: Work in Progress

• • Infrastructure

- Work on Web Services for structured data exchange between XNat and Workflow Instances (Work in Progress, 60%+ completion)
- Discussed SPINE image repository migration to XNat

• January 15, 2010
  
  • Use Cases.

- Social Cognition Study: Work-in-progress on intermediate (reconstruction) and results (resources) data storage at XNat.
Reviewing and preparation more cases for EM Segmentor (Slicer 3.5) tuning.

• NA-MIC Project Week

Selecting candidate Slicer modules for other than Lesion EM Segmentation topics of Social Cognition study: Withe Matter Lesion Segmenter (UNC), Scull Stripping utility from UIOWA. Reviewing issues of currently used Scull Stripping Slicer Extension and Slicer 3.5 EM Segmenter.
XNat Data organizing training

• January 1, 2010
  
  • Use Cases. Preparation of Demo for NA-MIC work week:

- COPD Study. Added Remote pipepline start interface (represents real world scenario where Xnat repository, Processing modules and User are at different sites)
- EM Segmentation. Added human activities steps to the workflow: ICC (brainmask) correction and EM Segmantation scena load per se.

• December 25, 2009
  
  • Use Cases. Pilot workflow pipeline for EM Segmentation (all steps except user-activity step: ICC correction assignment and tracking)

• December 18, 2009
  
  • Use Cases. Build and tested web services for EM Segmentation image preprocessing: DICOM-to-NRRD conversion, registration, skull stripping, image masking.

Started building workflow pipeline (subject to finish first version next week)

• • Infrastructure.

Started Collecting Library of Slicer Build number vs. functional modules and extensions. Plan for NAMIC project week: scheduled meetings for XNat data customization, Skull-stripping modules tuning, identified Social Cognition study cases that fail EM Segmentation processing.

• December 11, 2009
  
  • Use Cases. Updating and verification of EM Segmentation Scenario

http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF:UseCaseScenarios#Usecase_MS_lesion_Assessment

• • Infrastructure.

Familiarizing with Slicer3.4/5 Modules required for implementation of EM Segmentation Scenario. Participation in debugging and/or usage tuning of Dicom Conversion, Registration, Skull Stripping, Masking, and Image Casting modules.

• December 4, 2009
  
  • Use Cases. Slicer3.4's EM Segmentation and Visual QC as part of image processing pipeline for Social Cognition Study for MS Patients.

Project emerged. EM Segmentation template creation debugged.

• • Infrastructure

Emphysema Measurements (COPD Study) - workflow stability and scalability test.

• November 27, 2009
  
  • Use Cases. Emphysema Measurements (COPD Study).

Added compensation for long running calculations and time-outs to the main computing pipeline. Visual QC (work in progress)

• • Infrastructure

XNat data structure customization, metadata storage, results consolidation: new feature request list creation (work in progress)

• November 13, 2009
  
  • Use Cases
    • Pilot system for whole processing cycle for Emphysema Measurements (COPD Study) including the following:

Web query for CT session file list download Pilot user interface for submitting the file list and starting processing pipeline Notification about processing steps and failures Upload results to XNat repository (at this stage results are uploaded into same folder where original scans are(*))

• • • Immediate Plans

Complete Visual QC module Design and implement meta-data transfer to XNat (including processing details and MRML files for loading images into the 3D Slicer)

(*)Customization of results storage

• November 6, 2009
  
  • Use Cases
    • Tuned and debugged multiple subjects processing for: Fetch Data From XNat - Process Emphysema Measurements - Upload Results to XNat.
    • Started working on quality control embedding into the above scenario. Plan to complete and video-record demo next week.
  • Infrastructure
    • Published general Product Integration scenario flow chart to collaborators' community. Discussion is open and in progress

• October 30, 2009
  
  • Use Cases
    • Piloted and tested the sequence: Fetch Data From XNat - Process Emphysema Measurements - Upload Results to XNat(1).
    • Performance test of overall cycle: data transfer from remote serve is a bottleneck as expected
      
  • Infrastructure
    • XNat customization and data browsing features reviewed.

(1) Not automated yet

• October 23, 2009
  
  • Use Cases
    • Defined COPD processing scenario with interoperability between Xnat, 3D Slicer Command Modules, Workflow, and Gridwizard Enterprise.
    • Pilot version of Emphysema Measurements workflow pipeline deployed.
      
  • Infrastructure
    • XNat customization and data transfer features reviewed. Use account at XNat Central during learning curve.
    • Feasibility test of 3D Slicer fiducials module for ROI highlights during QC and manual image processing activities.
• October 16, 2009
  • Lung CT Scans Processing. Pilot project emerged. GenerateEmphysemaMeasurements module deployed as a webservice that submits jobs to computational cluster.
  • EM Segmentation. Familiarized with GUI steps. Started working on automation steps outlining
  • 3D Slicer and XNat interaction. Got an overview from Wendy Plesniak.
• October 1 - 7, 2009
  • Selected two first priority Projects: EM Segmentation of brain MRI images; Lung CT Scans Processing (COPD Study)
  • Got initial outline of user requirements and design specs