Projects:ARRA:SlicerQA

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Motivation

A core design feature of the Slicer 3 medical image data analysis and visualization platform, cross platform compatibility, enables the widest possible user community to benefit from this valuable research tool. To support this key functionality, all software code in the core and modules (built-in, loadable, scripted, and command line) must be fully tested on each of the supported platforms (Windows, Solaris, Linux 64 and 32-bit, Mac OSX Intel and PowerPC). All documentation and training materials (tutorials, demonstrations, practice data sets. etc) must also be developed and tested on each supported platform.

With the recent release of Slicer 3 (Stable Release version 3.4) the number of available modules that need testing and training materials has substantially increased. This is compounded by the fact that an increasing number of users are contributing new modules to the consortium. Unlike NA-MIC engineers, most members of the user community develop their algorithms and/or workflows on a single software platform, thus never encounter any bugs or other cross platform incompatibilities that must be resolved.

Funding of this supplement will enable the NA-MIC project team to more effectively and rapidly disseminate Slicer modules and capabilities to the user community and to minimize sources of errors in the use of the software.

Research Plan

The new Q/A engineer will work with the team of Core 2 Engineers overseeing Slicer 3 development to devise an efficient protocol for testing each type of module (built-in, loadable, scripted, and command line) on each supported platform. This testing forms a baseline so we can confirm that new versions of the code can be used to accomplish the same tasks. This workflow will be implemented for all existing Slicer 3.4 modules and applied to new modules as they become part of the standard distribution. The testing protocol will leverage the engineering methodologies adopted by the NA-MIC effort, which emphasize automated testing to the extent technically possible, augmented by human spot checking of functionality that cannot be efficiently automated. Specifically, the Slicer 3 effort relies heavily on core NA-MIC Kit components such as VTK and ITK that include extensive automated testing frameworks to ensure that fundamental operations are successfully completed on all supported platforms. These automatically testable operations include: compiling the code, reading and writing files, performing a defined set of image processing operations, etc. For each of these operations the testing system can confirm that a correct result is obtained. For some aspects of the software, no fully automated testing solutions exist; for example, the addition of a new button on a dialog box may make one or more other buttons impossible to access. For this type of functionality, we must rely on human spot checking of core functions as the code is developed. Our approach in these situations is to capture the essential functionality through the tutorials that describe the module. By assuring that the tutorial can be accomplished successfully on all platforms we develop confidence in proper functionality.

The Q/A engineer will then work with the Training Core team (R. Gollub and S. Pujol) to develop new tutorials or extend existing ones to all supported software platforms for each module as soon as it has reached a level of stability and maturity such that the interface and input/output values are not being rapidly revised.

Key Personnel

• Stuart Wallace
• Kathryn Hayes

Progress

Week ending 04/08/11

• Met with Randy and Sonia at HMS to discuss future training core activities
• Revised RSNA draft proposal
• Revised tutorial slides to bring up to date with 3.6.3
• Talking with DBPs to make sure tutorials are done by Project Week

Week ending 04/01/11

• Tested final versions of 3.6.3 for JHU workshop on all platfotms
• Handled registrations for upcoming workshop at JHU
• Met with Randy and Sonia at HMS to discuss future training core activities

Week ending 03/25/11

• Set up Windows machine at 149
• New video card installed in panamint

Week ending 03/18/11

• Tested existing tutorials with the Slicer 3.6.3 release
• Handled registrations for upcoming workshop at JHU
• Moved NA-MIC Windows workstation to Building 149
• Learned about histology imaging rig

Week ending 03/11/11

• Tested existing tutorials with the Slicer 3.6.3 release
• Assisted at Harvard Catalyst Slicer tutorial
• Handled registrations for upcoming workshop at JHU
• Met with Randy and Sonia at HMS to discuss future training core activities
• Learned about longitudinal study workflows

Week ending 03/04/11

• Tested existing tutorials with Slicer 3.6.3 Release Candidate 2
• Arranged to install new Slicer binaries/datasets on their laptops with Countway Library
• Completed CITI training to be added to IRBs

Week ending 02/25/11

• Meeting with Randy and Sonia at HMS to discuss training core tasks
• Coordinated with HMS/Countway to get new software and data installed on the Countway laptops before the next training session
• Worked on DTI validation project code rewrite
• Tested Slicer 3.6.3 binaries in NMR environment, filed bug reports
• Became maintainer of Slicer binaries in the NMR environment
• Went through Freesurfer tutorials
• Started exploring longitudinal Freesurfer workflow

Week ending 02/18/11

• Meeting with Randy at CNY149 about prioritizing tutorial changes
• Meeting with Allison, Nick, and Martin about Freesurfer related tasks
• Assist with Slicer Tutorial in Countway Library on Friday

Week ending 02/11/11

• Meeting with Sonia at BWH
  • DTI validation project code rewrite
• Meeting with Randy and Sonia to discuss progress
  • Upcoming Catalyst biomarker events with Valerie
  • Tutorials at Utah and JHU
  • Reworking existing tutorial slides
  • Converting older tutorials to Slicer 3.6

Week ending 02/04/11

• Reworking existing PPT presentations
  • Increasing readability
  • New screenshots
  • More consistent look and feel

Week ending 01/28/11

• Meeting with Sonia at BWH to discuss action items
  • Need to clean up tutorial presentations
  • Streamlined workflow for DTI validation project
  • Upcoming training events at Utah and JHU
  • Upcoming proposals for RSNA, MICCAI
• Moved from 1st floor to 2nd floor of CNY149
• Attended Fischl group lab meeting
  • Brainstorming workflow changes to speed up processing of FHS scans
  • Submitted request to be added to Fischl group IRBs in order to access data

Week ending 01/21/11

• Monday holiday
• On-site orientation at MGH main campus (2 days)
• Got badge/credentials
• Occupational health appointment
• Set up NMR account, email, mailing lists
• Looked in to cleaning up existing BIRN data and relocating it onto other servers

Week ending 01/14/11

• Attended NA-MIC All Hands Meeting in Salt Lake City, UT
• Worked with DBP leads to brainstorm ideas for the June Programming Week tutorials
• Discussed format of a possible DTI validation tutorial or contest

Week ending 10/24/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Uploading of most recent Slicer3.6 slide versions for consistency and improved display, and updated logos across wiki pages
  • update logos
  • improve display
  • specific version Slicer3.6 used ( Slicer.3.6.1-2010-08-23 (Windows & Linux64) and Slicer.3.6.1-2010-08-20 (Mac and Linux32))
• Continued work on modules from Slicer 3.4 101 Training Page
  • EM Fibre Clustering
  • VMTK Centrelines
  • Confocal Microscopy
• Continued slide revisions to reflect 3.6.1 UI
• Preparation for UCSF Training Workshop
  • Data Loading, Interactive Editor, and Manual Registration tutorials
• Updating of Slicer 3.6 Slicer Test Table
• HST DTI course preparation
  • Revisions of MIT slides for DTI for Slicer3.6.1
• Update of Dicom to Nrrd tutorial for Slicer3.6 with DicomToNrrd module using Dartmouth dataset--> add the type of scanner supported and specify which scanner was used to acquire the DTI Data and send slides to Sonia.
• Update Liver Segmentation to Slicer3.6.1 in preparation for RSNA

Week ending 10/17/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Updating of Journal of Slicer Workshop Tests
• Uploading of most recent Slicer3.6 slide versions for consistency and improved display, and updated logos across wiki pages
  • update logos
  • improve display
  • specific version Slicer3.6 used ( Slicer.3.6.1-2010-08-23 (Windows & Linux64) and Slicer.3.6.1-2010-08-20 (Mac and Linux32))
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest
  • Fiducials
  • RSS
  • Longitudinal Lesion Comparison
  • Prostate Biopsy
  • Stochastic Tractography
  • Perk Station
• Continued slide revisions to reflect 3.6.1 UI
• Preparation for UCSF Training Workshop
  • Data Loading, Interactive Editor, and Manual Registration tutorials
• Updating of Slicer 3.6 Slicer Test Table
• HST DTI course preparation
  • Revisions of MIT slides for DTI for Slicer3.6.1
• Update of Dicom to Nrrd tutorial for Slicer3.6 with DicomToNrrd module using Dartmouth dataset--> add the type of scanner supported and specify which scanner was used to acquire the DTI Data and send slides to Sonia.
• Update Liver Segmentation to Slicer3.6.1 in preparation for RSNA

Week ending 10/10/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Updating of Journal of Slicer Workshop Tests
• Uploading of most recent slide versions for consistency across wiki pages
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest
  • Fiducials
• Troubleshooting for Robust Statistics Segmentation to 3.6.1 stable (Windows memory error)
• Continued slide revisions to reflect 3.6.1 UI
• Updating of Slicer build instructions wiki to reflect linux related build error
  • svn version related error revolving around python/numpy building
• Preparation for UCLA Training Workshop
  • Data Loading, Interactive Editor, and Manual Registration tutorials
• Porting of DICOM to NRRD module to 3.6.1
  • Revision of slides for 3.6.1 UI
• Creation and population of Slicer 3.6 Slicer Test Table

Week ending 10/3/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
  • Uploading of most recent slide versions for consistency across wiki pages
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest
• Porting of Atlas Label Fusion Tutorial to 3.6.1 stable
  • Mac
  • Linux64
  • Linux32
  • Windows
  • Revision of slides to reflect 3.6.1 UI
• Porting of Robust Statistics Segmentation to 3.6.1 stable
  • Mac
  • Linux64
  • Linux32
  • Windows
  • Revision of slides to reflect 3.6.1 UI

Week ending 9/26/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest
• Porting of Atlas Label Fusion Tutorial to 3.6.1 stable
  • Mac
  • Linux64
  • Revision of slides to reflect 3.6.1 UI

Week ending 9/19/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Finalization of tutorials and slides for Chinese PLA General Hospital, Beijing
  • Hello Python
• Finalization of tutorials and slides for Beijing 2010 NA-MIC Workshop
  • Neurosurgery Data
  • Updating of Journal of Slicer Workshop tests
• Assistance in preparation of Slicer tutorial for HST 583
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest

Week ending 9/12/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Updating of Journal of Slicer Tests
• Preparation of tutorials for Chinese PLA General Hospital, Beijing
  • Hello Python
• Preparation of tutorials for Beijing 2010 NA-MIC Workshop
  • Neurosurgery Data
  • Updating of Journal of Slicer Workshop tests
• Assistance in preparation of Slicer tutorial for HST 583
• Continued work on modules from tutorial submissions for Summer 2010 Tutorial Contest

Week ending 9/5/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Further revisions of Freesurfer tutorial slides
• Revisions of Neurosurgical planning tutorial slides for 3.6.1 stable release
• QA/porting of tutorials into 3.6.1 (stable versions, linux 32 bit)
  • Neurosurgical planning
  • Freesurfer
  • Programming in Slicer (python)
  • Diffusion
  • Manual Registration
  • 3D Visualization
  • Interactive Editor
  • Change Tracker
• Updating of Journal of Slicer Tests
• Preparation of tutorials for Chinese PLA General Hospital, Beijing
• Preparation of tutorials for Beijing 2010 NA-MIC Workshop
  • 3D Visualization Data
  • Diffusion Data
  • Neurosurgery Data
  • Updating of Journal of Slicer Workshop tests
  • Assistance in debugging of fiducial seeding module

Week ending 8/29/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Further revisions of Freesurfer tutorial slides
• QA/porting of tutorials into 3.6.1 (nightly versions, all OS)
• QA/porting of tutorials into 3.6.1 (stable versions, all OS)
  • 3Minute
  • Freesurfer
  • Programming in Slicer (python)
  • Programming in Slicer (cxx)
  • Diffusion
  • Manual Registration
  • 3D Visualization
  • Interactive Editor
  • Change Tracker
• Updating of Journal of Slicer Tests
• Preparation of tutorials for Beijing 2010 NA-MIC Workshop
  • 3D Visualization Data
  • Diffusion Data
  • Neurosurgery Data
  • Updating of Journal of Slicer Workshop tests

Week ending 8/22/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Revision of tutorial slides
  • • Freesurfer tutorial
• QA/porting of tutorials into 3.6.1 (8-16-2010 version)
  • 3Minute
  • Freesurfer
  • Programming in Slicer (python)
  • Programming in Slicer (cxx)
  • Diffusion
  • Manual Registration
  • 3D Visualization
  • Interactive Editor
• Updating of Journal of Slicer Tests

Week ending 8/15/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Final QA of tutorials for UNC/Duke tutorial event in 3.6.1. release
  • Revision of tutorial slides
    • 3D Visualization
    • Interactive Editor
    • Diffusion
    • Manual Registration
• QA/porting of other tutorials into 3.6.1
  • 3Minute
  • Freesurfer
  • Programming in Slicer (python)
  • Programming in Slicer (cxx)
• Updating of Journal of Slicer Tests

Week ending 8/8/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• QA of tutorials for UNC/Duke tutorial event in 3.6.1. release
  • Revision of tutorial slides
    • 3D Visualization
    • Interactive Editor
    • Diffusion
    • Manual Registration
• QA/porting of other tutorials into 3.6.1
  • 3Minute
  • Freesurfer
  • Programming in Slicer
• Updating of Journal of Slicer Tests

Week ending 8/1/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
  • Additional testing of modules in OS's not specified in tutorial slides
    • GAMBIT
    • White Matter Lesion Segmentation
    • Automatic SPHARM

Week ending 7/25/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
  • Additional testing of modules in OS's not specified in tutorial slides
    • GAMBIT
    • White Matter Lesion Segmentation
    • Automatic SPHARM
• Fixed 3.4 tutorials with bad links
• Support for competing renewal (tutorial counts, etc.)
• Begun porting of other 3.4 tutorials into 3.6
  • Freesurfer Tutorial

Week ending 7/18/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
• Updating and curation of Slicer Tutorial Journal
• Updating and curation of Slicer 3.6 Training wiki
• Further testing of Summer 2010 Tutorials
  • Update of tutorial completion dates of previously QA'ed tutorials for 3.6
  • Additional testing of modules in OS's not specified in tutorial slides
    • Stochastic Tractography
    • Prostate Biopsy
    • Perk Station
    • Labelmap Fusion

Week ending 7/11/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
• Updating and curation of Slicer Tutorial Journal
• Further testing of Summer 2010 Tutorials
  • Update of tutorial completion dates of previously QA'ed tutorials for 3.6
  • Additional testing of modules in OS's not specified in tutorial slides

Week ending 7/4/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Further edits of Slicer 3.6 tutorials
  • Neurosurgical Planning
• Finalized QA of tutorials for St. Louis Workshop
  • Neurosurgical Planning
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
• Updating and curation of Slicer Tutorial Journal
  • Addition of Neurosurgical Tutorial QA
  • Addition of Summer 2010 Tutorials QA
  • Update of tutorial completion dates of previously QA'ed tutorials for 3.6

Week ending 6/27/10

• Monitoring of slicer-users and -dev lists
• Monitoring of nightly builds
• Further edits of Slicer 3.6 tutorials
  • Interactive Editor
  • Diffusion
• Finalized QA of tutorials for St. Louis Workshop
• Continued QA of tutorial slides and modules for tutorial submissions for Summer 2010 Tutorial Contest
  • Tutorial Contest judging support
  • Discussion with tutorial authors for further edits in preparation for submission to 3.6 tutorial wiki page

Week ending 6/20/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Refinements of QA for Slicer 3.6
• Updates of Slicer Tutorial Journal
• QA in progress for St. Louis Workshop
• QA in progress for tutorial submissions for Summer 2010 Tutorial Contest
• Met with Randy and Sonia to finalize preparations for Summer Project Week and tutorial contest.

Week ending 6/13/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• QA for Slicer 3.6 completed on
  • Programming in Slicer
  • Manual Registration
  • Change Tracker
  • Interactive Editor
• Tutorial Slide Revisions for 3.6 for:
  • Diffusion Tutorial
  • Programming in Slicer (C++ and Python)
  • Manual Registration
  • Change Tracker
  • Interactive Editor
• Update of Slicer Tutorial Journal

Week ending 6/6/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision of Slicer 3.6 QA
• QA for Slicer 3.6 completed on Windows 64bit
  • Slicer 3 minute
  • Slicer Visualization/Data Loading
  • Diffusion Tutorial
• QA for Slicer 3.6 still in progress for:
  • Programming in Slicer
  • Manual Registration
  • Change Tracker
• Tutorial Slide Revisions for 3.6 for:
  • Slicer 3 Minute
  • Slicer Visualization/Data Loading
  • Diffusion Tutorial (in progress)
  • Programming in Slicer (in progress)
  • Automatic Segmentation (in progress)
  • Manual Registration
  • Change Tracker
  • Editing of Training Portfolio for Summer 2010 Project Week.
• More work on tutorial revisions/QA Slicer Tutorial Journal

Week ending 5/30/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision of Slicer 3.6 QA
• More work on tutorial revisions/QA Slicer Tutorial Journal
  • Work on valgrind scripts with Luis I. for linux and mac installs.
  • Editing of Training Portfolio for Summer 2010 Project Week.

Week ending 5/23/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision of Slicer 3.6 QA
• More work on tutorial revisions/QA Slicer Tutorial Journal
  • Work on valgrind scripts with Luis I. for linux and mac installs.

Week ending 5/16/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision of Slicer 3.6 QA
• More work on tutorial revisions/QA Slicer Tutorial Journal
• Start of Journal of Slicer Workshop Tests in preparation for Summer 2010 Project Week.

Week ending 5/9/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision of Slicer 3.6 QA
• More work on tutorial revisions/QA Slicer Tutorial Journal
• Preparation for 2010 Project Week

Week ending 5/2/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision and completion of Slicer 3.6 QA
  • T-Con with Luis, Andriy, and Steve to discuss, improve and automate QA procedures for all modules

Week ending 4/25/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Revision and completion of Slicer 3.6 QA

Week ending 4/18/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Initiation of Slicer 3.6 QA

Week ending 4/11/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds
• Final testing of HelloNewWorld tutorial for Iowa training.

Week ending 4/4/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds

Week ending 3/26/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds

Week ending 3/19/10

• Continued monitoring of slicer-users list
• Continued monitoring of nightly builds

Week ending 3/12/10

• Continued monitoring of slicer-users list
• Continued work on AHM extension tutorials
  • VMTK Centrelines module on brain CT data
  • VMTK Centrelines module on liver CT data
  • Robust Statistics Segmentation on liver CT data
• Continued adding new tutorials to Slicer 101 page

Week ending 3/5/10

• Continued monitoring of slicer-users list
• Continued work on AHM extension tutorials
  • VMTK Centrelines module on brain CT data
  • VMTK Centrelines module on liver CT data
  • Robust Statistics Segmentation on liver CT data
• Continued adding new tutorials to Slicer 101 page
• Continued monitoring of nightly builds
• Preparations for Slicer3.6 release relating to extensions/plugins.

Week ending 2/26/10

• Continued monitoring of slicer-users list
• Continued work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
  • VMTK Centrelines module on brain CT data
• Started task of adding new tutorials to Slicer 101 page
• Continued monitoring of nightly builds
• Preparations for Slicer3.6 release relating to extensions/plugins.

Week ending 2/19/10

• Continued monitoring of slicer-users list
• Continued work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
  • Robust Statistics Segmentation module
  • VMTK Centrelines module on brain CT data
• Continued work on wiki page for Slicer Training Data
• Continued monitoring of nightly builds

Week ending 2/12/10

• Continued monitoring of slicer-users list
• Continued work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
  • Robust Statistics Segmentation module
• Continued work on wiki page for Slicer Training Data
• Continued monitoring of nightly builds

Week ending 2/5/10

• Continued monitoring of slicer-users list
• Continued work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
  • Robust Statistics Segmentation module
  • VMTK Centerlines used with liver CT data
• Continued work on wiki page for Slicer Training Data
• Continued monitoring of nightly builds

Week ending 1/29/10

• Continued monitoring of slicer-users list
• Continued work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
  • Robust Statistics Segmentation module
  • VMTK Centerlines used with liver CT data
• Created revised wiki page for Slicer Training Data
• Continued monitoring of nightly builds

Week ending 1/22/10

• More work on tutorial revisions/QA Slicer Tutorial Journal
  • Worked on error messages found with DTI Neurosurgery dataset (thank you Alex Y)
• Continued monitoring of slicer-users list
• Met with Randy and Sonia to plan upcoming Slicer training workshops at HMS and UIowa
• Initiated work on revised 'Hello World' tutorial for python
• Continued work on AHM extension tutorials
• Continued monitoring of nightly builds

Week ending 1/15/10

• More work on tutorial revisions/QA Slicer Tutorial Journal
• Followup for tasks given at 2010 AHM
• Continued monitoring of slicer-users list

Week ending 1/8/10

• Creation and initial population of Slicer Tutorial Journal

• 2010 AHM
  • Work on new and revised tutorials for extensions in development
  • Worked with Yi Gao to debug Robust Statistics Segmentation algorithm
  • Tutorial contest polishing
  • QA of DTI Neurosurgery dataset

• Continued monitoring of slicer-users list

• Continued QA of Slicer 101 tutorials

Week ending 1/1/10

• Continued monitoring of slicer-users list.

• Continued monitoring of nightly builds and extensions.

• Preparations for NAMIC AHM (Robust Statistics Segmentation and Tutorial Polishing).

Week ending 12/25/09

• Continued monitoring of slicer-users list.

• Continued monitoring of nightly builds and extensions.

Week ending 12/18/09

• Continued monitoring of slicer-users list.

• Initial work begun for Robust Statistics Segmentation module work/discussion for AHM.

• Met with Ron to refine QA procedures.

• Continued tutorial testing on nightly builds.

Week ending 12/11/09

• Continued monitoring of slicer-users list.

• Post RSNA meeting with Randy and Sonia to discuss points of interest for moving forward with training/tutorial materials and AHM work.
  • Set up meeting with Yi Gao for AHM to further work with and refine the Robust Statistics Segmentation module. Initiated some work on the modeule that could be done pre meeting.

Week ending 12/04/09

• Work with EM Segmenter familiarization

• Drafted email contact list for Slicer extensions for wiki

• Continued familiarization with newer modules, especially those only available in 3.5 currently.

• Continued monitoring of slicer-users email list.

Week ending 11/27/09

• Last revision of liver segmentation tutorial for RSNA/CTSA. Used Python Surface Toolbox for improved smoothing results. Also tried out Robust Statistics Segmentation algorithm, but kept Python Sirface Toolbox results for tutorial.

• Revised liver segmentation tutorial slides to reflect use of updated Slicer version (3.5) and segmentation techniques.

• Finalized handouts for RSNA/CTSA.

• Continued monitoring of slicer-users email list.

Week ending 11/20/09

• Revision of liver segmentation tutorial for RSNA/CTSA. Used Python Surface Toolbox for improved smoothing results.

• Finalized edits to RSNA/CTSA tutorial powerpoints and datasets (RECIST, PET/CT, etc).

• Created and revised handouts for RSNA/CTSA.

• Continued familiarization with newer modules, especially those only available in 3.5 currently.

• Continued monitoring of slicer-users email list.

• Helped Steve debug Partners PC specific bug; could not recreated problem on Partners PC with Slicer 3.4 on Win 32.

Week ending 11/13/09

• Completed most recent round of smoothing for liver segmentation tutorial for RSNA. Worked with Steve and Ron on this; have both short term and long term solutions for the improvement of the smoothing methods.

• Initiated a protocol for QA of nightlies and plug ins with input from Katie. Will be creating new wiki for this task.

• Had first EM Segmenter T-Con with Andriy, Kilian, and Sylvain. Ironed out priorities and responsibilities or each of the group members, and will build on this work.

• Continued to monitor the Silcer Users mailing list.

• Continued familiarization with newer modules, especially those only available in 3.5 currently.

Week ending 11/06/09

• Completed most recent round of 2009 RSNA CTSA tutorial and data QA. This includes updated liver segmentation, PET/CT Fusion, RECIST, and Change Tracker datasets. All tested in Slicer 3.5, Windows 32 bit build.
  • Some of these also tested in Slicer 3.5 for Linux, also with no problems.

• Met with Steve to go over protocol for improved segmentation protocol.

• Met with Ron and Katie to discuss QA protocol for nightlies and plug-ins.

Week ending 10/30/09

• Continued EM Segementer testing; also set up a monthly t-con with Andriy, Killian P., and Sylvain J. to discuss results of module testing.

• Continued 2009 RSNA Conference preparation; Catalyst workshop tutorial dataset and powerpoints tested on Slicer 3.4. Will continue work on segmentation smoothing improvements and their implementation in both 3.4 and 3.5.

• Meeting with Ron and Katie regarding QA and upkeep of extensions.

Week ending 10/23/09

• EM Segmentation testing, including review and revision of tutorials, bug tracking, and introduction to vervet data. Done with Andriy F.

• Followup from SfN 2009 DTI Workshop.

• 2009 RSNA Conference preparation.

Week ending 10/16/09

• Continued work on SFN 2009 DTI Workshop tutorials. Confirmed that the DTI and 3D Visualization datasets worked in Slicer 3.4 stable version across all platforms. Final revisions to tutorial slides completed.

• Continued work on Slicer 3.4+ Stochastic Tractography Module (Slicer Daemon).