Neuroimage Analysis Center http://nac.spl.harvard.eduAn NCRR National Resource Center

Slicer Workflow Engine: Aim

• Supplement 3D Slicer with Workflow Management System.

• Provide integration and interoperability between 3D Slicer and NA-MIC supported products – XNAT (structured image repository) and Grid Wizard Enterprise (high performance computing system), as well as non-Slicer image processing tools

• Implement it as within currently developed Structural Planning and Implementation in Neurological Exploration (SPINE) System.

Workflow Management System for Image Processing

• Orchestrates automated and human activities required to complete an image processing experiment

• Supports short and long running processes. Tracks all activities.

• Provides standard and scalable solutions for Research and Clinical Trials

Neuroimage Analysis Center http://nac.spl.harvard.eduAn NCRR National Resource Center

Slicer Workflow Engine: Progress to date

Implemented Workflow Scenarios (Since Feb 2010)

Manual Lesion Segmentation with automated MRI

image preprocessing steps and semi-automated

brain anatomy segmentation steps. Practical use:

MS Studies PET/CT Image Processing for Longitudinal

Biomarkers Analysis of Physiological Brain Activity.

Practical use: chemotherapy follow-up, TBI

assessment and follow-up Preprocessing of MRI images for brain atrophy

analysis with EM Segmentation. Practical use:

Aging, HIV, TBI longitudinal studies, MS

longitudinal studies

Integrated Novel Slicer Modules into Workflows BRAINSFit, BRAINSResample for registration N4ITK MRI Biasfield Correction for preprocessing ComputeSUVBodyWiegh for PET scans

biomarkers analysis ROI and Volume Cropping for human activity steps

Neuroimage Analysis Center http://nac.spl.harvard.eduAn NCRR National Resource Center

Slicer Workflow Engine: Progress to date (Continued)

Created Workflow Rich Client GUI Modules Data Organizing and Processing Status Monitoring Computation Pipelines Launching Human Activity Support: Image and Reconstruction Data Exchange with Xnat

Repository User Friendly Modules for Deploying and Upgrading

Workflow Services on Application Server

Two Deployment Scenarios Processing on Local Workstations (larger end user pool,

easier to install and support) Server Side / Computational Cluster Processing (higher

performance)

Workflow Clients Porting into Slicer4 (Prototype) Slicer4 QT Widget Displaying Available Workflows.

Part of Slicer4 Wizards Library Deploying of Workflow GUIs as Slicer4 Thin Client

(or Slicelet) Distribution of Workflow GUIs with Slicer

Neuroimage Analysis Center http://nac.spl.harvard.eduAn NCRR National Resource Center

Slicer Workflow Engine: Progress to date (Continued)

Research Projects Utilizing Slicer WF and SOA Solutions

-EM Segmentation (Slicer3 / Slicer2’s Segmenter Module):-Social Cognition Study for MS Patients. PECS University, Hungary (Completed)

-EM Segmentation (Slicer3): -Brain Atrophy Study for Aging Patient. Jewish Hospital/ BWH (In progress)-Brain Atrophy Study for HIV Patients. National HIV Consortium (In progress)-Traumatic Brain Injury. Dept. of Defense (Under evaluation)-Brain Atrophy for Pediatric MS Patients. MGH/BWH (Currently Testing)

-PET/CT Biomarker Activity Assessment Workflow:-Post-chemotherapy follow-up. BWH (In progress)

-Tractography :-DTI Image processing. Psychiatry Neuroimaging Lab/BWH (Under Evaluation)

Neuroimage Analysis Center http://nac.spl.harvard.eduAn NCRR National Resource Center

Slicer Workflow Engine: Conclusion Plan 2011

• Migrate existing WF Clients into the Slicer4 Wizards Collection as QT Slicelets

• Build and distribute new WF Wizards as QT Modules as part of Slicer4 distribution

• Utilize QT technology advantage by making QT WF Wizards compatible with Slicer3 as Stand-Alone clients

• QT Widgets and Services for Xnat browsing and Project Organizing

• New Workflows to be added• Automated EM Segmentation Workflows:

Brain Anatomy, MS Lesions, WM Hyperintensity

• Universal multi-modal image registration suite for longitudinal studies. User-driven registration planning and preview scenarios

• Upgraded PET/CT biomarker activity pipeline: MRI Images registration and automated segmentation, incorporation of various methods of SUV computations

• Pediatric MS Image Processing