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

Presentations

  • Segmentation Workflow. PECS University Social Cognition Study.

File:SlicerWF NAC PECS Workflow.pdf

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
  • PETCTWorkflow

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

Quarterly Progress

  • 3d Qtr, 2010
    • Concentrated on building downloadable workflow applications that could run both in desktop (new) and server environment, and that require minimum IT administrative resources. The desktop deployment is in compliance with Slicer3 general deployment concept.
      • The following use case scenario had been chosen: PET/CT image processing for longitudinal studies, EM Segmentation for longitudinal Aging Study.
    • Released workflow application for PET/CT image processing for longitudinal studies. Provided end users with training and documentation.
      • The PET/CT processing workflow was designed to be a general application used whenever both structural patterns and metabolic activities are within the research scope.
      • The desktop version is tuned to use minimal computer resources, so the automates processing instances do not interfere with human activities. Automated activities may include, for example, registration and PET scan's standard uptake values computing, and manual human activities may include image cropping, quality control, and labeling voxels of interest.
    • Core services and EM Segmentation preprocessing workflow was build for retrospective Aging Study. Tuned the Slicer3 webservices for processing low grade images acquired in mid 90s. Entire workflow is implemented with Slicer3 only modules and can be deployed locally and on the servers. Usage of Service Oriented Architecture (SOA) as a core technological approach allowed reusing most of the web services that had been build for PET/CT project.
    • Continued embedding Slicer3 application and modules into previously released processing pipelines: replaced MIPAV with Slicer3 GUI for lesion assessment step in the multi-center Pediatric MS Cohort image processing


  • 2d Qtr, 2010
    • Completed Social Cognition Workflow Implementation. This includes EM Segmetnation pre- and post-processing pipelines, data tracking, and integration with 3d party image processing utilities, as well as processing results acquired manually with Slicer GUI.
    • Multi-modality image registration and ROI selection/alignment workflow for longitudinal studies.
      • Use case: PET/CT image processing for longitudinal studies.
      • Build portable library of Slicer modules as web services and workflow that are deployed and run on a end-users' worksatations without utilization of SPL and other servers. The web services include novel Slicer3 modules, such as BRAINSFit and BRAINSResamle
      • Started working with Slicer3 developers on Slicer 3.8 GUI wizard to communicate with workflow instances.
    • Participated at NA-MIC Summer 2010 Project Week: Summer_project_week_2010_Workflows_SOA

Progress

  • October 22, 2010

AGING STUDY - Retrospective Segmentation

  • All back-end functionality are implemented
  • EM Segmentation scene usability is confirmed by end-user
  • Plans for next week: add Label Statistics computation for CSF/Brain/ICC


  • October 15, 2010

AGING STUDY - Retrospective Segmentation

  • The latest (October) builds of Slicer 3.6.2 produced acceptable results. This was verified by the target users. The EM Segmentation will be performed on Slicer 3.6.2 or later
  • The new Web services had been created and added to the pipeline as optional processing steps: Biasfield correction (implement novel N2ITKBiasFieldCorrection module) and Volume's scalar datatype casting (as workaround for Biasfield correction module not preserving image scalar datatype - the bug is filed)
  • Discussed the Front-End GUI design with target users. The design pattern is taken from the PETCT project


  • October 8, 2010

PET/CT ROI/Longitudinal Study

  • Post-deployment support. Tuned CT registration as of user's feedback.
  • Adapting to the Single Slicer build: Slicer 3.6.2. Found label duplicates in the label lookup table - will ask user if it's tolerable. Waiting for the Slicer 3.6.2 build that contains all required modules. Rolling back label tag appending code for SUVs - the latest Slicer build appends the tags.


AGING STUDY - Retrospective Segmentation

  • Resumed development. The priorities are set for usage of Slicer 3.6.2 - subject for EM Segmentation scene tuning. Continued coding for Scene creation for Slicer 2.8 - as a backup option for ongoing research project.


  • October 1, 2010

PET/CT ROI/Longitudinal Study

  • Finalized V1.0 release based on end-user feedback: updates relate mostly to error proofing and SUV values representation
  • Post-deployment support. Users pre-processed first set of patients


  • September 24, 2010

PET/CT ROI/Longitudinal Study

  • System deployed and tested at End Users' site.
    Users are trained to perform all tasks required by the workflow.
  • Got positive feedback with suggestions on Slicer Scenes' layouts improvement and PET scans' SUV (standard uptake values) results display
  • Two distribution packages are assembled: Lunix and MAC OS versions. The difference in two packages is in specific Slicer3.6/3.7 builds - subject to Slicer Linux builds debugging.
    As a workaround for Linux deployment - multiple Slicer builds are used to perform various tasks (registration, opening editing scenes in Slicer, SUV computing)
  • Plans for coming week - finalize V1.0 release based on end-user feedback


  • September 17, 2010

PET/CT ROI/Longitudinal Study

  • Embedded SUV computations into the workflow (as system calls - will be translated into web service later)
  • Pre-release demo for end users.


  • September 10, 2010

AGING STUDY - Retrospective Segmentation

  • Create and debug EM Segmenter scenes template for Slicer 3.6 and 2.8


  • September 3, 2010

AGING STUDY - Retrospective Segmentation

  • Preprocessing webservices for EM Segmentation - workflow pipeline and deployment verified
  • Tested EM Segmentation scenes within Slicer 2.8
  • Started migration of EM Segmentation to Slicer 3.6. Discovered issues had been reported to EM Segmenter module designers


  • August 29 2010

AGING STUDY - Retrospective Segmentation

  • Preprocessing webservices for EM Segmentation completed. Preprocessing Pipleine completed 80% (subject for input registration parameters tuning)
  • Most webservices (for registration and resampling steps) had been taken and re-used from PET/CT ROI/Longitudinal Study - showing the advantage of service-oriented software design and deployment.
  • Continued on distribution and deployment of the service/workflow applications: on PET/CT and AGING STUDY projects.

PEDIATRIC Multiple Sclerosis Cohort. Support of multi-center distributed processing project

  • Introduced Slicer 3.6 for the MS Lesion Assessment step performed at Mayo Clinic. Images are being transferred from image repository at BWH and automatically opened and arranged within Slicer GUI for reading. This was replacement of Client GUI using MIPAV that stopped working on new computers at Mayo Clinic.

The images are being loaded via generated MRML Scenes same way as in PET/CT and AGING STUDY projects

  • August 22 2010

PET/CT ROI/Longitudinal Study
- Preprocessing pipeline merge with SUV computations
- QA for SUVs computation was performed by Wendy Plesniak for images with known uptake values.
- Discovered that image cropping step (not related to automated registration pipeline and SUVs computing) smoothes the images by doing interpolation when used with default settings. Got suggestions from Steve Piper using Nearest-Neighbor interpolation ("no interpolation") for a time being

AGING STUDY - Retrospective Segmentation
- This is the new project candidate. Requested for the images with failed manual segmentation and/or segmentation with FreeSurfer. The EM Segmentation run showed most acceptable results on one of the problem images back in February
- The workflow will be developed and deployed similar to PET/CT ROI Longitudinal study approach - all preprocessing steps will be done with Slicer modules, all runs will be performed on local end-user machines.


  • August 15 2010

PET/CT ROI/Longitudinal Study
- First 5 cases with 3-4 time points preprocessed for SUVs computation

  • August 8 2010

PET/CT ROI/Longitudinal Study
- Testing of installation and operation at users' site (Performed by Wendy Plesniak)

  • July 2010

PET/CT ROI/Longitudinal Study
- Delivered beta version of registration pipeline
- Prepared installation and user manuals


  • June 11, 2010

PET/CT ROI/Longitudinal Study
- Registration modules completed
- Irregular cases registration problem solved (when whole body and brain only scans are mixed for a timepoint)
- Live demo of case setup and registration workflow for end users. Real case with 4 timepoints used

Coming week plans
- Adjust workflow based on end users' feedback
- Integration with SUVs computing for PET scans
- GUI for workflows dispatching and data organizing
- (TBD) Integration with 4D time series analysis Slicer module

  • May 28, 2010

PET/CT ROI/Longitudinal Study Registration :
- Migration to the latest Slicer 3.6 release candidate
- Added webservice for new registration module: BRAINSFit
- Test runs for new patients with 4 timepoints' scans

Plans for next week:
- integrate workflow with SUVs values computing for PET/CT fusion in Slicer GUI
- processing workflow demo for end user

  • May 21, 2010

PET/CT ROI/Longitudinal Study Registration :
Pilot version of portable web services and automated workflow tested:
Linux: workflow and visual review passed
Stress test for 25 timepoints passed
MAC OS: workflow passed, visual review failing when PET/CT images are loaded into GUI simultaneously (bug report submitted)
Windows: need to adapt command line modules and workflow management system to sygwin environment
Plans for next week: integrate workflow with SUVs values computing for PET/CT fusion in Slicer GUI

  • May 7, 2010
  • Use Cases:

PET/CT ROI/Longitudinal Study Registration :
Selected registration and resampling modules with more precise and stable outputs.
Started building portable web services and automated workflow

  • April 30, 2010
  • Use Cases:

PET/CT ROI/Longitudinal Study Registration :
- manual walk through the processing steps: ROI cropping, registration/resampling, PET pharmaceutical DICOM data retention.
- testing workflow and web services packages distribution to end-users' machines

  • April 23, 2010
  • Use Cases:

PET/CT ROI/Longitudinal Study Registration : testing various registration and re-sampling algorithms (work in progress)
EM Segmentation: as of collaborators' request, run existing EM Segmentation workflow for older low resolution pseudo-T1 images. The EM Segmentation works for those images with manual sampling.

  • April 16, 2010
  • Use Cases: 
 Social Cognition Study: started Cortical Thickness Measurement module build (bases on NA-MIC ARCTIC pipeline) 

 PET/CT ROI/Longitudinal Study Registration : Design specs, PET-to-CT images registration tests on training data.
  • April 9, 2010
  • Use Cases.

Social Cognition Study. GUI update based on end-user experience.
User request: automated label maps' volumes calculation (Currently possible from Slicer3 GUI)
PET/CT ROI Project. Initial design specs discussion with end-users and co-developers

  • Infrastructure

Verification of segmentation workflow GUI: from registering new case to reviewing results
Cross study test of segmentation workflow: MGH/MS Center data - success, HIV Project data - some EM Segmentation scene tuning is needed

  • April 2, 2010
  • Use Cases.

Social Cognition Study. Segmentation workflow completed

  • Coming Week plans:

- Document Segmentation Workflow. Follow up with end users
- Start with Cortical Thickness and ROI-in-longitudinal studies workflows

  • March 26, 2010
  • Use Cases.

Social Cognition Study.
- All essential processing and workflow interaction clients are ready.
- Completed segmentation for 10 out of 50 patients. The remaining cases will be finalized upon manual lesion segmentation and QC verification of WM/GM/CSF and Deep GM segmentation's.
- TODO next week: refine QC GUI and data tracking / progress monitoring schema.

  • Infrastructure

- New Slicer3 web services added: re-slicing with reference image volume, casting image scalar type

  • Use Cases.
  • March 19, 2010
  • Use Cases.

Social Cognition Study.
- Segmentation maps Merging Services for GM/WM/CSF (Slicer EM Segemnter), Lesion (Slicer, Manual), and Deep GM (FreeSurfer)
- Deep GM segmentation pipeline adopted as optional service for Social Cognition Study (22 out of 50 cases processed)
- (In progress) GUI client for Launching Segmentation results merging with optional Deep GM segmentation with FreeSurfer

TODO next week:
- Complete GUI Client for Segmentation result merging
- Progress Monitoring services for entire Study processing: EM Segmenter Preprocessing, EM Segmentation, Lesion Segmentation (including human activities assignments), Deep GM segmentation, and results consolidation.


  • March 12, 2010
  • Use Cases.

Social Cognition Study.
- All 50 cases went through "basic" One-channel EM segmentation (GM/WM/CSF)
- Basic pipeline start-up command line client created: user has two options - request brainmask extraction or provide with previously extracted brainmask for a given subject
- Comparison of GM/WN/CSF performed for Slicer EM Segmenter and FreeSurfer recon-all (used with default settings).
-- EM Segmenter provides more accurate output
-- EM Segmentation pipeline runs faster (40 minutes vs 12 hrs when no brainmask extraction requested)

TODO:
- merging modules for automatic 1-channel EM segmentation and manual lesion segmentation
- Emerge Cortical Thickness pipeline project: use NAC ARCTIC processing steps and modules

  • March 5, 2010
  • Use Cases.

Social Cognition Study.
- Selected stable EM Segmentation scenario: White Matter, Gray Matter, and Cerebrospinal Fluid
- First 16 cases are segmented for selected scenario. Nine more cases are preprocessed for EM Segmentation.
- Comparison to segmentation with FreeSurfer showed better accuracy for Slicer2 EMSegmenter

  • Infrastructure

- Three prerpcocessed cases failed during volume ICC masking with in-house build utility. Evaluated switching to Slicer3 Mask and island removing modules.
- Initial design specs discussion for cortical thickness measurement pipeline. ARCTIC pipeline selected. ARCTIC preprocessing steps signifficantly overlap with EM Segmentation preprocessing workflow.

  • 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
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