Difference between revisions of "Engineering:September 12, 2007"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(31 intermediate revisions by 7 users not shown)
Line 2: Line 2:
  
 
Catch up on latest developments, set priorities, identify issues.  Also brainstorm on competitive renewal.
 
Catch up on latest developments, set priorities, identify issues.  Also brainstorm on competitive renewal.
 
  
 
== Plan ==
 
== Plan ==
  
One day in Clifton Park, 10am to 4pm.
+
One day in Clifton Park, 10am to 4pm. Location is the Comfort Suites Hotel in Clifton Park, NY.
 +
Please go to http://www.kitware.com/profile/Map.pdf for more information.
  
 
Boston people can plan for one (somewhat long) day or stay over.
 
Boston people can plan for one (somewhat long) day or stay over.
  
== Topics ==
+
== Hot Topics ==
  
=== review of the needs of the DBPs===
+
=== Review of the needs of the DBPs===
* UNC
+
* UNC [[DBP2:UNC:Cortical_Thickness_Roadmap]]
 
* JHU/Queens
 
* JHU/Queens
 
* MIND
 
* MIND
 
* Harvard
 
* Harvard
** Structural Pipeline
+
** Structural Pipeline (will be done first)
 
*** bias field correction ''missing'' (independent of EM)
 
*** bias field correction ''missing'' (independent of EM)
 
*** intensity normalization ''missing''
 
*** intensity normalization ''missing''
Line 23: Line 23:
 
*** EMSegmentation (still some issues with slicer3 module vs slicer2 -- being worked on, ball in Sylvain's court)
 
*** EMSegmentation (still some issues with slicer3 module vs slicer2 -- being worked on, ball in Sylvain's court)
 
*** Unbiased atlas creation (several people working on it, no finished tool yet)
 
*** Unbiased atlas creation (several people working on it, no finished tool yet)
** Diffusion Pipeline
+
** Diffusion Pipeline (deferred until Slicer3 DTI infrastructure is in place)
 
*** DICOM to NRRD (general solution would be great if it were possible)
 
*** DICOM to NRRD (general solution would be great if it were possible)
 
*** Eddy Current Correction (also requested by IUPUI; PNL currently using Affine reg in FSL)
 
*** Eddy Current Correction (also requested by IUPUI; PNL currently using Affine reg in FSL)
 
*** Outlier rejection (Marc is working on automated detection tool)
 
*** Outlier rejection (Marc is working on automated detection tool)
 
*** Filtering : Rician noise model (LMI tool from Santi)
 
*** Filtering : Rician noise model (LMI tool from Santi)
 +
* <em> Scope: Ongoing </em>
  
 
===Slicer3 release===
 
===Slicer3 release===
 +
* Technical issues
 +
** Build process
 +
** CPack (see below)
 
* what are roadblocks?
 
* what are roadblocks?
 
** crashes?
 
** crashes?
 
** critical functionality?
 
** critical functionality?
 +
** modules
 +
*** interactive editor
 +
*** EM segmenter
 +
*** DTI functionality
 +
*** data fusion
 +
* Review of release process and schedule
 +
** Code freeze, ...
 +
* <em> Scope: Jan 1 Release (pre-AHM)</em>
 +
 +
== Year 4 Workplan ==
 +
 +
===The "next" EM Segmenter===
 +
* Registration (rigid and non-rigid; modules to create statistical atlases)
 +
* DTI (visualize; advanced queries; rendering performance, Runge-Kutta, etc.)
 +
* Interactive editing
 +
* <em> Scope: July 2008 </em>
  
 
===Documentation===
 
===Documentation===
 
* NAMIC Kit Overview (as requested by NIH)
 
* NAMIC Kit Overview (as requested by NIH)
 
* Practical Software Process
 
* Practical Software Process
 +
* <em> Scope: July 2008 </em>
 +
 +
===BatchMake interface===
 +
* Data sharing
 +
** Access to MIDAS and other database repositories from within Slicer
 +
* Batch(Make) modules
 +
** EMSegmenter
 +
** OtsuThreshold
 +
** Registration(?)
 +
* <em> Scope: Jan 2008 (pre-AHM) </em>
 +
 +
===cpack===
 +
* rpm, deb
 +
* na-mic kit available via standard linux distribution sites?
 +
* visual studio 8 issues
 +
* other topics from project week
 +
* <em> Scope: Dec 2007 (pre-release) </em>
  
 
===Volume rendering in Slicer3===
 
===Volume rendering in Slicer3===
[[Slicer3:Volume_Rendering|View latest work]]
+
* [https://www.slicer.org/wiki/Slicer3:Volume_Rendering View latest work]
 +
* <em> Scope: July 2008 </em>
  
 
===kwwidgets ===
 
===kwwidgets ===
* gui tracing for macros and replay (and for creating tests)?
 
* file browser multithreading
 
* access to events from scripting languages
 
 
* "testing mode"
 
* "testing mode"
 
** avoid the confirmation dialog on exit
 
** avoid the confirmation dialog on exit
 
** avoid being influenced by the user's registry
 
** avoid being influenced by the user's registry
 
** avoid polluting the user's registry
 
** avoid polluting the user's registry
 +
** <small><i>Seb: easy one :) check all KWW examples, they are run both as examples and as nightly tests. vtkKWApplication::PromptBeforeExitOff() will disable the confirmation dialog, vtkKWApplication::SetRegistryLevel(0) will make sure the registry is not affected.</i></small>
 +
* access to events from scripting languages
 +
** <small><i>Seb: do you remember where the corresponding meeting notes are? We discussed that item in the past, and I remember it was all good, awaiting implementation...</i></small>
 +
* gui tracing for macros and replay (and for creating tests)?
 +
* file browser multithreading
 
* other follow ups from [[Special_topic_breakout:_KWWidgets | project week discussions]]
 
* other follow ups from [[Special_topic_breakout:_KWWidgets | project week discussions]]
 +
* <em> Scope: Ongoing, large scope </em>
  
 
===Interactions===
 
===Interactions===
Line 56: Line 97:
 
* Oblique slice plane specifier?
 
* Oblique slice plane specifier?
 
* Disambiguating "picking" with mouse
 
* Disambiguating "picking" with mouse
 
+
* <em> Scope: Ongoing, large scope </em>
===The "next" EM Segmenter===
 
* Registration (rigid and non-rigid; modules to create statistical atlases)
 
* DTI (visualize; advanced queries; rendering performance, Runge-Kutta, etc.)
 
* Interactive editing
 
  
 
===command line modules===
 
===command line modules===
 
* passing mrml scenes back and forth
 
* passing mrml scenes back and forth
 +
* <em> Scope: Jan 2008 (pre-AHM) </em>
  
===BatchMake interface===
+
== Administrative ==
* To MIDAS and other database repositories
 
 
 
===cpack===
 
* rpm, deb
 
* na-mic kit available via standard linux distribution sites?
 
* visual studio 8 issues
 
* other topics from project week
 
  
 
===Competitive Renewal===
 
===Competitive Renewal===
Line 79: Line 110:
 
* what is the state of ''computing'' likely to be?
 
* what is the state of ''computing'' likely to be?
  
===wiki 2 web and download site===
+
=== wiki 2 web and PublicationDB ===
 
* perl script translation
 
* perl script translation
 
* counting downloads
 
* counting downloads
 
* integrated license agreement
 
* integrated license agreement
 +
 +
=== Databases and GRID ===
 +
* Breakout session: 1pm tcon
 +
 +
=== Webpage Rework ===
 +
* TBD
  
 
== Attendees ==
 
== Attendees ==
  
 
Confirmed (please add your name so we can keep count to estimate room size etc):
 
Confirmed (please add your name so we can keep count to estimate room size etc):
* Steve, Ron, Nicole, Katie, Will, Dan, Jim, Alex, Old Bill
+
* Steve, Ron, Nicole, Katie, Will, Dan, Jim, Alex, Old Bill, Sebastien, Zack, Luis, Dave Cole, Stephen, Andy Freudling
 +
 
 +
== Meeting Summary ==
 +
The following summarizes the results of the meeting:
 +
 
 +
The '''agenda''' was as follows:
 +
* DBP Needs Discussion – 10:30-11:30
 +
* Slicer3 Releases – 11:30-12:30
 +
* The “next” EM Segmenter – 12:30-1:00
 +
* Workplan 2007 – afternoon
 +
* Technical discussions – afternoon
 +
** KWWidgets
 +
** 3D Interactions
 +
** Build issues / CMake / CPack
 +
** Command line modules
 +
* Breakouts
 +
** Grid discussion / BatchMake / Database
 +
** PubDB / wiki2web
 +
** Volume rendering
 +
** Licensing discussions
 +
** Slicer Lightbox for pursuing funding opps
 +
 
 +
'''Key Deliverables''' for the coming year
 +
* DBP Related
 +
** Develop end-to-end pipeline(s) inside NAMIC kit (Focus on filling in gaps; getting it in NAMIC-kit)
 +
** In conjunction with Cores 1 and 2, each DBP is putting together wiki description of pipeline needs (this information is actively being gathered)
 +
*** UNC [[DBP2:UNC:Cortical_Thickness_Roadmap]] - Jim Miller Core 2 Lead
 +
*** Harvard [[DBP2:Harvard:Structural_Pipeline_Roadmap]] - Brad Davis Core 2 Lead
 +
*** MIND -
 +
*** JHU/Queens -
 +
 
 +
* Slicer Releases
 +
** Support building a Slicer module from a binary distribution – AHM 2008
 +
** Support for command-line tutorial (Jim)
 +
** BatchMake tutorial AHM 2008 (Stephen)
 +
** Official release v3.0, Code freeze mid-November
 +
** Additional Modules
 +
*** interactive editor (Steve)
 +
*** EM segmenter (Sylvain/Brad)
 +
*** DTI functionality (Alex)
 +
*** Linear data fusion (Luis –registration, oriented images)

Latest revision as of 17:05, 10 July 2017

Home < Engineering:September 12, 2007

Goals

Catch up on latest developments, set priorities, identify issues. Also brainstorm on competitive renewal.

Plan

One day in Clifton Park, 10am to 4pm. Location is the Comfort Suites Hotel in Clifton Park, NY. Please go to http://www.kitware.com/profile/Map.pdf for more information.

Boston people can plan for one (somewhat long) day or stay over.

Hot Topics

Review of the needs of the DBPs

  • UNC DBP2:UNC:Cortical_Thickness_Roadmap
  • JHU/Queens
  • MIND
  • Harvard
    • Structural Pipeline (will be done first)
      • bias field correction missing (independent of EM)
      • intensity normalization missing
      • skull stripping (PNL currently using FSL BET)
      • EMSegmentation (still some issues with slicer3 module vs slicer2 -- being worked on, ball in Sylvain's court)
      • Unbiased atlas creation (several people working on it, no finished tool yet)
    • Diffusion Pipeline (deferred until Slicer3 DTI infrastructure is in place)
      • DICOM to NRRD (general solution would be great if it were possible)
      • Eddy Current Correction (also requested by IUPUI; PNL currently using Affine reg in FSL)
      • Outlier rejection (Marc is working on automated detection tool)
      • Filtering : Rician noise model (LMI tool from Santi)
  • Scope: Ongoing

Slicer3 release

  • Technical issues
    • Build process
    • CPack (see below)
  • what are roadblocks?
    • crashes?
    • critical functionality?
    • modules
      • interactive editor
      • EM segmenter
      • DTI functionality
      • data fusion
  • Review of release process and schedule
    • Code freeze, ...
  • Scope: Jan 1 Release (pre-AHM)

Year 4 Workplan

The "next" EM Segmenter

  • Registration (rigid and non-rigid; modules to create statistical atlases)
  • DTI (visualize; advanced queries; rendering performance, Runge-Kutta, etc.)
  • Interactive editing
  • Scope: July 2008

Documentation

  • NAMIC Kit Overview (as requested by NIH)
  • Practical Software Process
  • Scope: July 2008

BatchMake interface

  • Data sharing
    • Access to MIDAS and other database repositories from within Slicer
  • Batch(Make) modules
    • EMSegmenter
    • OtsuThreshold
    • Registration(?)
  • Scope: Jan 2008 (pre-AHM)

cpack

  • rpm, deb
  • na-mic kit available via standard linux distribution sites?
  • visual studio 8 issues
  • other topics from project week
  • Scope: Dec 2007 (pre-release)

Volume rendering in Slicer3

kwwidgets

  • "testing mode"
    • avoid the confirmation dialog on exit
    • avoid being influenced by the user's registry
    • avoid polluting the user's registry
    • Seb: easy one :) check all KWW examples, they are run both as examples and as nightly tests. vtkKWApplication::PromptBeforeExitOff() will disable the confirmation dialog, vtkKWApplication::SetRegistryLevel(0) will make sure the registry is not affected.
  • access to events from scripting languages
    • Seb: do you remember where the corresponding meeting notes are? We discussed that item in the past, and I remember it was all good, awaiting implementation...
  • gui tracing for macros and replay (and for creating tests)?
  • file browser multithreading
  • other follow ups from project week discussions
  • Scope: Ongoing, large scope

Interactions

  • 3D Widgets
  • Level-of-detail?
  • Oblique slice plane specifier?
  • Disambiguating "picking" with mouse
  • Scope: Ongoing, large scope

command line modules

  • passing mrml scenes back and forth
  • Scope: Jan 2008 (pre-AHM)

Administrative

Competitive Renewal

  • where do we want to be 7 years from now?
  • what is the state of medical image computing likely to be?
  • what is the state of computing likely to be?

wiki 2 web and PublicationDB

  • perl script translation
  • counting downloads
  • integrated license agreement

Databases and GRID

  • Breakout session: 1pm tcon

Webpage Rework

  • TBD

Attendees

Confirmed (please add your name so we can keep count to estimate room size etc):

  • Steve, Ron, Nicole, Katie, Will, Dan, Jim, Alex, Old Bill, Sebastien, Zack, Luis, Dave Cole, Stephen, Andy Freudling

Meeting Summary

The following summarizes the results of the meeting:

The agenda was as follows:

  • DBP Needs Discussion – 10:30-11:30
  • Slicer3 Releases – 11:30-12:30
  • The “next” EM Segmenter – 12:30-1:00
  • Workplan 2007 – afternoon
  • Technical discussions – afternoon
    • KWWidgets
    • 3D Interactions
    • Build issues / CMake / CPack
    • Command line modules
  • Breakouts
    • Grid discussion / BatchMake / Database
    • PubDB / wiki2web
    • Volume rendering
    • Licensing discussions
    • Slicer Lightbox for pursuing funding opps

Key Deliverables for the coming year

  • DBP Related
    • Develop end-to-end pipeline(s) inside NAMIC kit (Focus on filling in gaps; getting it in NAMIC-kit)
    • In conjunction with Cores 1 and 2, each DBP is putting together wiki description of pipeline needs (this information is actively being gathered)
  • Slicer Releases
    • Support building a Slicer module from a binary distribution – AHM 2008
    • Support for command-line tutorial (Jim)
    • BatchMake tutorial AHM 2008 (Stephen)
    • Official release v3.0, Code freeze mid-November
    • Additional Modules
      • interactive editor (Steve)
      • EM segmenter (Sylvain/Brad)
      • DTI functionality (Alex)
      • Linear data fusion (Luis –registration, oriented images)