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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



  • Segmentation Workflow. PECS University Social Cognition Study.

File:SlicerWF NAC PECS Workflow.pdf

  • EAB10_ARRA Annual Progress Report Slides.

Service Oriented Solutions for 3D Slicer. EAB10_ARRA_WF_2011. PPT
File location: File:EAB10 ARRA WF 2011 Zaitsev.ppt

NAMIC Annual Report 04/2010-03/2011. NAMIC_ARRA_WF_2011_Zaitsev. PPT
File location: File:NAMIC ARRA WF 2011 Zaitsev.ppt

CARMA Workflow. Cardiac Ablation Followup. PPT
File location: File:Slicer WF Slicer4CARMAWorkflow.ppt

All Hands Meeting Pages

  • MIT 2011 Summer:
Workflows Project MIT_2011_WorkFlow
Segmentation Project (MS Lesions)MIT_2011_LesionsSegmentation

Research Plan

Application Server / Workflow Engine Downloads

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

Annual Progress Statements

The April 2010 – March 2011 period was devoted on developing portable workflow solutions that can be deployed on end-users' workstations or notebooks with minimal or no system administration activities. This is in contrast to the server-side deployment. The following scenarios had been deployed and used for actual projects that require the following types of workflows: PET/CT registration and computation of biomarker driven brain physiological activities, Brain MRI Images segmentation, MRI and MRI Angiography images pre-processing for cardiac ablation outcome estimation. Some workflows (like EM Segmentation) had been utilizing various scenarios, some research projects (like evaluation of chemotherapy outcome) require two types of workflows to assess physiological and structural changes. Starting from the 4th Quarter of 2011, the migration project had been emerged in order to embed Workflow GUIs into newly developed Slicer4 Suite. The existing rich client Java GUI applications are being re-written as C++/QT Sliceletts units, new modules (such as cardiac ablation project support) are had been written from scratch. The latter are being deployed from the Slicer4 GUI and act at a liaison between Slicer4 and Application Server containing workflow and Slicer modules deployed as services. The feedback from the end users indicates that Workflow approach for the complex processing improves productivity, aids to the processing standardization and contributes to the overall experience using 3D Slicer

  • 3d Qtr, 2011
    • PET/CT Longitudinal Study: Follow-up with end-users.
      • End-users started a new study. The multi-study configuration support is confirmed
      • Debugging and workarounds of minor issues addressed
    • Left Atrium Ablation Assessment (CARMA Project)
      • Work on the custom build and packaging of the Slicer4 with CARMA workflow included (90% completion - pending Slicer4/QT compilation framework issues resolution)
      • Presentation and demo outside of NA-MIC community: Moscow Cardiological Center. Slicer4 is under evaluation, checking feasibility of 3T cardioMRIs segmentation
    • Multiple Sclerosis CLIMB Study
      • Reprocessing for lesion segmentation
      • Developed Web-based (Java EE 6) application for submitting cases to the workflows for EM Segmentation of MPRAGE and registration to PD/T2/FLAIR images. Deployed at end-users site, currently used for segmenting the cases that could not be segmented with in-house (Non-Slicer) algorithms.
    • EM Segmentation:
      • Embedded into the Web-based image processing suite (see CLIMB study above)
    • User and developer documentation
      • Documenting steps for integrating 3D Slicer modules with OpenESB workflow engine
  • 2d Qtr, 2011
    • PET/CT Longitudinal Study: Second release deployed.
      • End-users completed the first Project and currently analyzing SUV values and clinical data
      • New features added: Human Brain Hemispheres segmentation, Scull-stripping for total SUV counts calculation, Flexibility of custom designed label look-up table usage (users can define ROI notation according to the Project needs)
    • Left Atrium Ablation Assessment (CARMA Project)
      • Completed workflow pipeline for automated pre-processing and manual intervention
      • Developed front-end GUI for the CARMA Project support in Slicer4.
      • Run the workflow with the end users during NAMIC Project Week
      • Evaluated feasibility of left atrium wall and post-ablation scar segmentation using Robust Statistical Segmentation (RSS). Identified necessary processing controls with RSS module designers
    • Multiple Sclerosis CLIMB Study
      • Reprocessing for lesion segmentation
      • Developed Web-based (Java EE 6) application for submitting cases to the workflows for EM Segmentation of MPRAGE and registration to PD/T2/FLAIR images (60% completion)
    • EM Segmentation:
      • Upgraded EM Segmentation services to Slicer 3.6.4
      • Added brain hemispheres segmentation module to the workflows (used for PET/CT Longitudinal study)
      • Work with EM Segmenter module developers on building pipelines for white matter lesion segmentation (work in progress)
    • Plans for the 3rd quarter
      • Migrate CARMA Project workflow to end-users
      • Packaging of Slicer4 Workflow modules and Slicer4 custom build distribution
      • Completion of Web-base segmentation and registration suite
      • Users and Developers Documentation

  • NAMIC Annual Progress Slides (April 2010 - March 2011):
  • 1st Qtr, 2011
    • PET/CT Longitudinal Study: Second release is under testing by end-users.
      • Added MRI registration to aid ROI drawing on PET scans
      • Improved SUV results reporting and added flexibility to update ROI lookup table
      • Automated EM Segmentation of MRI images for computing SUVs for white matter, CSF, and whole brain (80% completion)
      • Integration with SPECTRE scull stripping module (70% completion)
    • EM Segmentation: Automated WF Pipelines are created
      • Flexible atlas selection (Pediatric, etc) feature added
      • Workflows implemented for EM Segmenter 3.6.2 and 3.6.3 (1st Qtr 2011 release)
    • Cardiac ablation results follow-up: Workflow for registration and ROI selection of cardiac MRI and MR Angiography
    • Wrokflow and Web Services for prospective DTI tractography modules (currently written as Matlab modules at PNL)
    • Web Services for SPECTRE Scull stripping module
      • Accuracy and performance tuning
      • 50% completion
    • Migration Front End GUI to Slicer4/QT:
      • EM Segmentation
      • Cardiac Ablation Study
    • DICOM Uploader and Desktop Browser for XNat Image repository (alpha version - tested for MGH MS Center studies, proposed to use with MI2B2 Clients and Services)

  • 4th Qtr, 2010
    • PET/CT Longitudinal Study and EM Segmentation for Aging Study are deployed at end-user sites and actively used for research.
    • Adopted EM Segmentation preprocessing pipeline for HIV Study: high resolution SPGR images, integration with FreeSurfer brainmask extraction outputs; integration of Slicer SPECTRE module for brainmask extraction is in progress.
    • The following post-release upgrades had been implemented based on end-user feedback: Application Server basic controls are performed from Rich Client GUI as alternative to traditional IT administration activities. The controls are implemented on point-and-click bases and include web services and workflow application deployment and upgrades, application server start and stop as well as warning end user when the server is not accepting request.
    • Added DICOM downloads and results uploads of PET/CT pipelines from and to XNat Repository
    • Created Services and Workflow for Matlab Prototypes modules. Case Study: tractography for DTI images
    • Extended XNAT integration services:
      • Browsing capabilities of XNat data repository from the Workflow Applications
      • Improved DICOM upload and download performance
      • Added Metadata organizing services for uploaded DICOM images: header data extraction, image snapshots creation.
    • Started project for Rich Client GUI migration from Java desktop application to build into SLicer4 QT modules. This affects mostly front-end GUI and has the following approaches: distribution with the Slicer4, end-user will select desired workflow application from Slicer4 menu while QT-written modules provide with the same functionality as Java Rich Clients. Case Study for the Migration process: registration suite for longitudinal studies that include multi-modality images

  • 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


  • September 2, 2011

PETCT Project:

  • New study follow-up
  • Debugging SUV consolidated computation: V2.1 requires all or no MRIs for all cases. Does not work correctly when only a subset of patients has MRIs

  • August 26, 2011

CARMA Project:

  • Packaging on Max OS X 64-bit: troubleshooting QT 4.6 (build tree) QT 4.7 (make package) conflicts

3D Slicer WF. General

  • 3D Slicer and WF Modules presentation at MGH Radiation Oncology

  • August 19, 2011

EM Segmentation

  • Deployed first release (Human Brain EM Segmentation) web request application
  • End-users requested EM Segmentation of MS lesion on PD images (feasibility is being evaluated with EM Segmenter Team)

3D Slicer WF. General

  • Preparation of 3D Slicer and WF Modules presentation for MGH

  • August 12, 2011

CARMA Project

  • Migrating build to updated Slicer4 environment (PythonQT and new added module dependencies issues)

EM Segmentation

  • Tested and reviewed EM Segmentation web app on end-users' data
  • Updated workflow, so EM Segmentation is performed on T1 after registration to T2 or FLAIR. This gives more accurate results comparing to segmentation of high resolution image followed by resampling (have to use nearest neighbor interpolation to retain actual label values) of label map
  • August 5, 2011


  • Follow-up with end users with new Study setup

CARMA Project

  • Documentation (Work in progress)
  • Plans for next week: custom packaging (Mac Snow Leopard 64 bit), building extension, documentation

EM Segmentation

  • Stress-test of online segmentation requests suite for CLIMB Study(for BWH MS Center)
  • Reason for building online suite: the Group is Using mostly MAC OS Tiger machines for legacy reasnos, the most recent Slicer3 builds as well as QT don't work on those machines (QT4.x runtime could not be installed).

  • July 29, 2011

CARMA Project

  • Documentation (Work in progress)

EM Segmentation

  • Work on alpha-release of online submission of segmentation requests (for BWH MS Center)

  • July 22, 2011


  • July 8, 2011

3D Slicer in General and CARMA Project

  • July 1, 2011


  • Migration to new QT building environment (Mac 10 Snow Leopard).
  • Building custom package. Issues: new features (not only WF related) are not shown on the menu of the resulting application
  • Comparing preprocessing workflow results with published in literature data (our module produces better alignment)

  • June 24, 2011

Project Week:

  • Testing RSS module for left atrial wall scar segmentation
  • Testing EM Segmenter for lesion detection on PD (requested by end-users) and FLAIR images

EM Segmentation

  • Web-based segmentation and registration module for MS Center. Goal: facilitate 3D SLicer modules for the cases that could not be processed with in-house build DTS+ algorithm
  • Pipeline: Segment MPGR or T1 (user's choice), Register MPGR to PD/T2, Resample Segmentation Map to PD/T2. Completion: 60-70%.
  • The rest will be done manually or via lesion segmentation with EM Segmenter.

  • June 17, 2011

Preparation for Project Week

  • June 10, 2011


  • Code completed and tested
  • Packaging as extension is pending (Subject for Summer 2011 Project week)


  • Debugging consolidation results issue(SUVs for manual and automated segmentation)

  • June 3, 2011


  • Deployed on end-user's machine
  • TODO next week: fix SUV results consolidation issue (when MRI segmented ROI got SUV computed for some subjects, only those subjects' SUVs are being added into consolidated report. "Raw" SUV values per subject are generated as expected)

  • May 27, 2011


  • Ready for deployment. New Features: hemispheres EM Segmentation, automated ICC/brainmask extraction using EM Segmenter, fixed controls for MRI conversion and registration

  • May 20, 2011

CARMA Project

  • Removing Java web service stubs via creation of RESTFul web service wrappers for workflow instances (SOAP) on application server (work in progress)

EM Segmentation General / PETCT V2.1

SPECTRE Scull Stripping

  • The new version to be tested on coming week (After PETCT MRI processing migrated to Hemispheres scenario )

  • May 13, 2011

CARMA Project

  • Removing Java web service stubs via creation of RESTFul web service wrappers for workflow instances (SOAP) on application server (work in progress)

EM Segmentation General / PETCT V1.1

  • Hemispheres EM Segmentation - technically works with labal values hardcoded in Slicer EM Segmenter - need to add manual label value edition step
  • PETCT WF Cut for Java GUI (Pending Hemispheres label update completion). Next release will be in QT4.

  • May 6, 2011

CARMA Project

  • Code Review/Cleaning
  • Removing Java web service stubs via creation of RESTFul web service wrappers for workflow instances (SOAP) on application server (work in progress)

EM Segmentation General

  • Resume EM Segmentation task creation for Left and Right Hemispheres' WM segmentation (QA of EM Segmenter module, work in progress)

  • April 29, 2011

CARMA Project

  • Code Review/Cleaning
  • Open Discussion for Packaging WF QT Modules as Slicer4 extensions (waiting for SOPs)

EM Segmentation General

Slicer Modules General

  • Standardizing Crop Volumes Output (with A. Fedorov's module). Review for required updates of existing product (PET/CT, CARMA)

  • April 29, 2011

CARMA Project

  • Code Review/Cleaning
  • Open Discussion for Packaging WF QT Modules as Slicer4 extensions (waiting for SOPs)

EM Segmentation General

Slicer Modules General

  • Standardizing Crop Volumes Output (with A. Fedorov's module)

  • April 22, 2011

CARMA Project

  • April 15, 2011

CARMA Project

  • Adding App server auto-config features
  • Finalizing the beta release

  • April 08, 2011

PETCT Project

  • Second release beta build tested on cosutmer side

CARMA Project

  • Review registration quality (with Dr. Meier). Angiography images' Resampling tuned.
  • Work on the beta release

  • April 01, 2011

PETCT Project

  • Finalized the feature set
  • Work on the second release

CARMA Project

  • Finalized the feature set
  • Work on the beta release

  • March 25, 2011

XNat Integration

  • (Java) GUI for Project Browsing and DICOM Series Upload. Post-upload DICOM processing tested and debugged
  • Ready for integration with mi2b2 client.

PETCT / EM Segmenter

  • Migrated to Latest Slicer 3.6.3 stable release: only the Input scene had to be updated, the API remained the same
  • Tested EM Segmenter with CMTK4Slicer extension - processing takes to much time on Linux_64bit machine, rolled back to BRAINSFit registration. When used on Mac OS X build, the Slicer could not start (bug report 1126).

SPECTRE Scull Stripping:

  • Testes for various use cases: the module is extremely sensitive to T1 MRI quality (does not work for most MRIs from PET/CT project
  • TODO next week: check for FLAIR images

  • March 18, 2011


  • Slicer4 QT GUI and Cropping activity in progress.
  • Tried direct MRA to MRA registration option: resampling with LMRI registration transforms works better.

PETCT / EM Segmenter

  • Extra VOI labels revised
  • Debugging of SUV results' renormalization step
  • TODO: ICC extraction / whole brain total uptake computing; EM Segmentation for R_WM, L_WM SUV computing and BPH estimation


  • Installed and tested CLI option on Linux_64bit platform

  • March 11, 2011


  • Workflow interruption before BSPline registraton: BPEL Module completed. Slicer4 QT GUI and Cropping activity in prorgess.

PETCT / EM Segmenter

  • Implemented and Tested with end-users proposed changes: denormalization of SUV results, adding more VOI labels, added FLAIR MRI in addition to T1s for VOI drawing
  • Tested manual ICC extraction using PET scans: works satisfactory with island removal and cropping followed by threshold level labeling

  • March 5, 2011


  • Front-end GUI incorporated into Slicer4
  • Change proposed: interrupt workflow after affine registration and have user crop the VOI. This is to prevent excessive deformations for BSpline registration and resampling

PETCT / EM Segmenter

  • Front-end GUI incorporated into Slicer4. User has option to choose the atlas that fits better for the given subject (NOTE: hardcoding must be rewritten for atlas linking)
  • PETCT test - the problem is that T1s are low resolution and with contrast. Proposed using T1s without contrast
  • PETCT change request: users wants to compute SUV for entire ICC. Had demo how to segment brainmask/ICC using PET scan. The derived brainmask label can be used for SUV computation.

  • February 25, 2011


  • BPEL pipeline coding - cmpleted
  • Sample cases run - excessive deformation after BSpline registration hase
  • Next week plan - pull tuning controls to front-end of pipeline API, start working of QT module for CARMA registration
  • May consider other than BRAINSFit registration modules


  • Design plan for change request: more VOI labels, add FLAIR in addition to T1 for VOI drawing, T1s segmentation
  • Tested segmentation for sample cases - artifacts from poor quality MRIs lead to exclusion of parts of ICC from segmentation

EM Segmentation

  • Completed troubleshooting of EMSegmenter module calling from Java (need TCL libs to be pulled from Slicer environment)
  • Tested EMSegmenter autoruns for HIV and Pediatric MS patiens. Work as expected, subject to improvement of PED MS case segmentation by building better skull/neck/air atalses
  • Suggested usage of two subsets of atalases: with and without neck. The Subject MRIs have to be cropped accordingly or best fit atlas has to be selected
  • Made no-neck cropped atlas collection for default EMSegmenter scenario
  • Tested with PET/CT study MRI cases - see above

  • February 18, 2011


  • BPEL pipeline coding - in progress
  • Next week goal - have back end processing ready

PETCT Longitudinal Study

  • Added MRI registration to the pipeline
  • Troubleshooting of complex XML schema issues on Linux machines (some modules working on MAC do not work on Linux). As a workaround - did not include MRI convert and register part into base BPEL module. Used separate services (transparent for end-user)
  • TODO next week for change request completion: explicit pixel type casting for MRI in BRAINSFit, VOI MRML scene update (currently MRI added on top of schema)

  • February 11, 2011

EM Segmenter

  • Porting existing pipeline for Pediatric MRI. Same scenario as for HIV Project, icbm pediatric atlases (Completed, verified)
  • Collected NIH healthy brain development atlases: various age ranges from 4.5 to 18 yo. Converted to Slicer readable format
  • Work on web services for the new automated EM Segmenter module (release Nov 10 - current). Verified task completion both for adult and pediatric images. Discussed tuning parameters for work load balance on workstations.

PETCT Longitudinal Study:

  • Started working on MRI registration to the reference CT scans.
  • Design specs for optional White Matter segmentation for SUV computing.

  • February 4, 2011

EM Segmenter

  • Porting existing pipelines for Pediatric MRI (in progress)
  • Adapting Pediatric T1 atlases for "Human Brain" build-in EM Segmentation wizard (in progress)

  • January 28, 2011


  • Verifying EM Segmenter module for latest builds and HIV/PED MS Studies (report pending)
  • Work with SPECTRE module developers with pediatric MRI brainmask extraction

  • January 21, 2011


  • Compiling plan for WF FrontEnd GUI migration to Slicer4/QT Widgets
  • Preparing for annual progress report
  • January 14, 2011


  • QT Widget for basic EM Segmentation Workflow GUI: Integrated into the Slicer4 as Slicelet (or thin Client)
  • Participation at AHM-2011, discussing integration of SPECTRE module and updated approach to EM-Segmentation

  • January 7, 2011

AGING STUDY / HIV STUDY - Retrospective Segmentation

  • HIV project workflow delivered. Major additions relate to user convenience:

- Project-specific parameter settings, importing T1s and brainmasks from FreeSurfer outputs with conversion to NIFTI, resampling brainmask to original scans and automatied subject addition.


  • QT Widget for basic EM Segmentation Workflow GUI

PETCT Longitudinal Study:

  • Follow up with end user: need to add MRI scans, if available, addition and registration to CT in order to ease VOI drawings.

  • December 31, 2010

AGING STUDY / HIV STUDY - Retrospective Segmentation

  • Follow-up with user Experience for AGING Study Segmentation (Positive feedback)
  • Target date for HIV project delivery - next week


  • Self-training for QT widget development
  • Outlined Workflow Rich Clients migration strategy from Java to QT/Slicer4:
    • Use Java Stubs (similar to SPECTRE integration) or file binding for envocation of workflow pipelines. (See SOAP remark below)
    • Direct Web Servisec calls must be wrapped into REST protocol. The reason: NON-commerchial QT kit does not include SOAP protocol for web servises.
    • The GUI will be implemented as page widget or QT dialog GUI forms called from within Slicer4.
    • Communications between Slicer4 and WF GUI will be set via child-parent and signal-slot relations
  • Worked on a Prototype for Basic EM Segmentation QT widget (70% complete). Will work on integrtion with SLicer4 during the AHM-2010

XNAT Integration

  • Debugged XNAT RESTFul API usage for uplaoding DICOM series followed by header data extraction and image snapshots creation

  • December 24, 2010

AGING STUDY / HIV STUDY - Retrospective Segmentation

  • Added compensation for failed atlas registration (subject for old poor quality pseudo-T1 images): blank probability maps are created in case of failure.
  • Data preparation module for FreeSurfer data import near completion. Expected time for deployment at end-users workstations - first week of January


  • Discussed strategy for EM Segmentation pipeline solutions collection (K. Pohl, R. Kikinis)

  • December 17, 2010

HIV STUDY - Retrospective Segmentation

  • RE-using the same core workflow as for 1-channel EM Segmentation of AGING STUDY cases
  • Added data input preparation module: ICC label mask preparation and skull-stripping based on FreeSurfer brainmask output volume.
  • Two-channel EM segmentation pipeline (in-progress)


  • Worked on plans for migrating fro rich workflow Java clients to embedded workflow windows inside the Slicer.

The embedded workflow management clients are to be implemented with QT/PyQT toolkits

  • Automated DICOM series upload with triggering DICOM headers parsing at XNat site (in-progress)

  • December 10, 2010

PET/CT Registration and ROI workflow

  • Integration with XNat - work in progress.

- Results upload to XNat (Completed)
- DICOM Downloads from XNat based on user's input (Project + Subject + PET or CT session / scan) (Completed)
- DICOM Downloads from XNat - perfomance boosting solution for downloads found , web services services are created, relinking for the client side in progress
- Xnat querying for subjects and automated subject addition into the workflow (In Progress)

AGING STUDY - Retrospective Segmentation

  • Post-segmentation module added for auto correction of segmentation results. Particularly - relabeling CSF voxels segmented as Air inside the intracranial cavity. This was requested by end-users after processing images with zero-signals in CSF voxels


  • Troubleshooting automated dual-echo DICOM images conversion and split into two NRRD volumes

GENERAL DEVELOPMENT / EM Segmentation pipeline:

  • Troubleshooting memory allocation issues for scull-stripping module SPECTRE

COPD Project:

  • Benchmark test for accelerated DICOM downloads from XNat (remoote XNat Central server): we can handle at least 6 cases (4 CT scans in each) per hour, which is compatible with current workload quotes on SPL cluster processing.

  • December 3, 2010

PET/CT Registration and ROI workflow

  • Integration with XNat - work in progress

AGING STUDY - Retrospective Segmentation

  • Deployed Version 1.


  • Test project chosen as a closest match to registration scenario: Pediatric MS Cases from MGH - requires periodic image preview for different

modalities taken from vaious time points. Label maps for VOIs resampling is also required.

  • November 26, 2010

PET/CT Registration and ROI workflow

  • Work on distribution/installation package and minimization of administrative load for end-user. Version 1 is complete
  • Started working on integration with XNat

AGING STUDY - Retrospective Segmentation

  • Work on input data organizing modules

  • November 19, 2010

PET/CT Registration and ROI workflow

  • Work on distribution/installation package and minimization of administrative load for end-user (70% done)

General Development

  • Universal Registration Workflow for Longitudinal Studies - design specs in progress

  • November 12, 2010

AGING STUDY - Retrospective Segmentation

  • Minor tuning to EM Segmentation template as of users' feedback
  • Users started using the workflow
  • Discussed input data conversion from Genesis to Slicer native or NIFTI format. Our help may be needed in input data organizing.


  • Tuned application according to co-laborators (PNL) needs
  • The webservices and BPEL workflow application are tested ready to accept computation requests from PNL case tracking system

PET/CT Registration and ROI workflow

  • Work on distribution/installation package

General Development

  • Discussed Universal Registration Workflow for Longitudinal Studies
  • Started the thread about possible cooperation with Children hospital's image processing pipelines and integration with Xnat

  • November 5, 2010


  • Webservices and workflow pilot project created and deployed on Psychiatry Neuroimaging Laboratory subnet
  • The V.1.0 deployment is scheduled for coming week

  • October 29, 2010

AGING STUDY - Retrospective Segmentation

  • Most of functionality is completed. Some volume statistics post processing is pending


  • The SPECTRE scull stripping module. Started integration into EMS workflow. Made some test runs from Slicer GUI


  • Identified as a candidate for Workflow Application

  • 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)

- 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

    • 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