Difference between revisions of "2008 Engineering review at Utah"

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Will, Ross, and Guido will consult with other people and schedule the event.
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The date is now set at: March 24-26, 2008. 
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Begin: Morning of Monday, March 24.  End: Noon on Wednesday, March 26.
  
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The date is now set at: March 24-26, 2008. 
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'''[[2008_Engineering_review_at_Utah:Summary | **SUMMARY AND ACTION ITEMS**]]'''
  
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Begin: Morning of Monday, March 24.  End: Noon on Wednesday, March 26.
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'''[[2008_Engineering_review_at_Utah:FollowUp | **ACTION UPDATE**]]'''
  
 
Suggested Hotel: [http://www.monaco-saltlakecity.com/ Hotel Monaco].
 
Suggested Hotel: [http://www.monaco-saltlakecity.com/ Hotel Monaco].
  
 
Engineering Attendees: Jim Miller, Xiaodong Tao, Steve Pieper, Will Schroeder, Marco Ruiz
 
Engineering Attendees: Jim Miller, Xiaodong Tao, Steve Pieper, Will Schroeder, Marco Ruiz
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(Full list of attendees in the end of page)
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'''Place: SCI Institute, 72 South Campus Drive, Warnock Engineering Building WEB ([http://www.sci.utah.edu/map.html Directions]), 3rd floor Jones conference room 3840 (elevator to 3rd floor, room is to the left). '''
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'''Proposed discussion items:'''
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'''Discussion of engineering issues related to the 3 major Utah projects DTI Analysis, Shape Analysis, Segmentation including Pathology. Main aim: Discuss and coordinate Slicer-3 integration efforts of the Utah R&D efforts, in particular w.r.t. ''pipelines'' or ''sequences of processing steps'' that are necessary in most medical image analysis procedures.'''
  
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Proposed discussion items:
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'''Schedule'''
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* Monday 24
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*** 9am: Goals, aims and organization of the meeting (Ross / Guido / Will / Jim / Steve)
 +
*** Introductions to kick off discussions:
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*** Slicer3 Plugins Presentation [[Media:Slicer3Plugins.ppt|[ppt]]]
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*** Segmentation (Marcel) [[Media:NA-MIC-Core1%2B3_UtahPrastawa_Segmentation_Mar24_2008.ppt| [ppt] ]]
  
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* DTI processing modules/pipeline
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** 12pm to 1.30pm: Lunch / Possibility to attend SCI distinguished lecture by Andy van Dam titled ''When is the Pen Mightier Than the Keyboard?'' [http://www.sci.utah.edu/cgi-bin/ALLseminars.pl?display=2008032400]
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** 2pm: DTI analysis pipeline (Casey / Tom / Guido) [[Media:Namic-DTI-core2-slc-review.pdf| [pdf] ]]
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*** Shape analysis (Josh / Tom / Ross )
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*** Summary of open issues to be further discussed
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** Dinner (tbd)
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* Tuesday 25
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** 9am Continue discussion of engineering issues
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** Noon to 1.30pm: SCI seminar: "The NAMIC Kit", Presenters: Jim Miller, GE Research, Steve Pieper, Isomics, Will Schroeder, Kitware
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** 1.30pm Continue discussion of engineering issues
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** 3 - 4pm: Breakout to work on a few major issues identified in previous discussions.
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*** Summary of open issues to be further discussed
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** 7pm Dinner at Gerig's (525 L Street, Salt Lake City) http://maps.google.com/maps?f=q&hl=en&geocode=&q=525+L+Street,+Salt+Lake+City&sll=40.751431,-73.976041&sspn=0.006665,0.013561&ie=UTF8&ll=40.78873,-111.858501&spn=0.053287,0.10849&z=13&iwloc=addr
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* Wednesday 26
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** 9am Discussion of action items:
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*** Strategic plan for software integration (who decides on what, coherence, interoperability)
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*** Which modules will be integrated by whom (paired Core-1 / Core-2 effort)
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*** Detailed plan with deliverables and timeline
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*** Noon: adjourn
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'''[[2008_Engineering_review_at_Utah:Summary | **SUMMARY AND ACTION ITEMS**]]'''
 +
 
 +
'''Project-specific details to be discussed'''
 +
* ''DTI processing modules/pipeline''
 
** Infrastructure for DWI/DTI data types
 
** Infrastructure for DWI/DTI data types
 
*** How to handle coordinate frames
 
*** How to handle coordinate frames
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*** Hypothesis testing
 
*** Hypothesis testing
  
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* Shape analysis pipeline (Should Martin S. be here?)
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* ''Shape analysis pipeline''
 
** How to organize data
 
** How to organize data
 
** How to break pipeline in to steps
 
** How to break pipeline in to steps
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** How to accommodate new modules/techniques
 
** How to accommodate new modules/techniques
  
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* [[DBP2:UNC:Cortical_Thickness_Roadmap Cortical Thickness Measurement (UNC DBP)]]
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* ''Segmentation pipeline''
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** Typical sequence of processing steps / procedures
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** Prototyping optimal sequence/parameters via GUI
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** Batch job for large number of image data
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** Segmentation of healthy/pathology
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** What do different procedures have in common (using shared modules)
 +
 
 +
* [[DBP2:UNC:Cortical_Thickness_Roadmap]]
  
 
* The general problem of registration and atlases
 
* The general problem of registration and atlases
 
** Status of spline-based methods
 
** Status of spline-based methods
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** Intertability
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** More general concept of providing a set of procedures
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** Properties: linear/nonlinear, low vs. highdimensional, invertability, diffeomorphic
 
** How to incorporate registration/atlases/atlas building in to slicer3
 
** How to incorporate registration/atlases/atlas building in to slicer3
  
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** Command-line vs built in modules
 
** Command-line vs built in modules
 
*** Policies for supporting one versus the other
 
*** Policies for supporting one versus the other
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* GSlicer3. Slicer3 with embedded grid computing capabilities (Powered by GWE)
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** GWE Core: [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/ Project Site]
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** GSlicer3: [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Project Site]
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'''[[2008_Engineering_review_at_Utah:Summary | ***SUMMARY AND ACTION ITEMS***]]'''
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* '''Attendees'''
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** Ross Whitaker
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** Tom Fletcher
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** Ran Tao
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** Josh Cates
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** Guido Gerig
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** Marcel Prastawa
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** Sylvain Gouttard
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** Casey Goodlett
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** C-F Westin
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** Will Schroeder
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** Steve Pieper
 +
** Jim Miller
 +
** Xiaodong Tao
 +
** Marco Ruiz

Latest revision as of 18:27, 3 April 2008

Home < 2008 Engineering review at Utah

The date is now set at: March 24-26, 2008. Begin: Morning of Monday, March 24. End: Noon on Wednesday, March 26.

**SUMMARY AND ACTION ITEMS**

**ACTION UPDATE**

Suggested Hotel: Hotel Monaco.

Engineering Attendees: Jim Miller, Xiaodong Tao, Steve Pieper, Will Schroeder, Marco Ruiz (Full list of attendees in the end of page)

Place: SCI Institute, 72 South Campus Drive, Warnock Engineering Building WEB (Directions), 3rd floor Jones conference room 3840 (elevator to 3rd floor, room is to the left).

Proposed discussion items:

Discussion of engineering issues related to the 3 major Utah projects DTI Analysis, Shape Analysis, Segmentation including Pathology. Main aim: Discuss and coordinate Slicer-3 integration efforts of the Utah R&D efforts, in particular w.r.t. pipelines or sequences of processing steps that are necessary in most medical image analysis procedures.

Schedule

  • Monday 24
      • 9am: Goals, aims and organization of the meeting (Ross / Guido / Will / Jim / Steve)
      • Introductions to kick off discussions:
      • Slicer3 Plugins Presentation [ppt]
      • Segmentation (Marcel) [ppt]
    • 12pm to 1.30pm: Lunch / Possibility to attend SCI distinguished lecture by Andy van Dam titled When is the Pen Mightier Than the Keyboard? [1]
    • 2pm: DTI analysis pipeline (Casey / Tom / Guido) [pdf]
      • Shape analysis (Josh / Tom / Ross )
      • Summary of open issues to be further discussed
    • Dinner (tbd)
  • Wednesday 26
    • 9am Discussion of action items:
      • Strategic plan for software integration (who decides on what, coherence, interoperability)
      • Which modules will be integrated by whom (paired Core-1 / Core-2 effort)
      • Detailed plan with deliverables and timeline
      • Noon: adjourn

**SUMMARY AND ACTION ITEMS**

Project-specific details to be discussed

  • DTI processing modules/pipeline
    • Infrastructure for DWI/DTI data types
      • How to handle coordinate frames
    • Preprocessing pipeline for DWI->DTI->analysis
      • Filtering
      • Registration
      • Estimation
      • White mater mask
      • User interfaces/interaction
    • Analysis of DTI data
      • Tractography
      • Atlases
      • Derived quantities
      • Hypothesis testing
  • Shape analysis pipeline
    • How to organize data
    • How to break pipeline in to steps
      • Segmentation, preprocessing, parameterization, visualization
    • How to accommodate new modules/techniques
  • Segmentation pipeline
    • Typical sequence of processing steps / procedures
    • Prototyping optimal sequence/parameters via GUI
    • Batch job for large number of image data
    • Segmentation of healthy/pathology
    • What do different procedures have in common (using shared modules)
  • The general problem of registration and atlases
    • Status of spline-based methods
    • More general concept of providing a set of procedures
    • Properties: linear/nonlinear, low vs. highdimensional, invertability, diffeomorphic
    • How to incorporate registration/atlases/atlas building in to slicer3
  • General architecture issues
    • How to provide coherent user interfaces for specific tasks
      • Pipelines for specific data or analyses
      • E.g. see Siemens workstation software with modules/pages
    • Command-line vs built in modules
      • Policies for supporting one versus the other

***SUMMARY AND ACTION ITEMS***

  • Attendees
    • Ross Whitaker
    • Tom Fletcher
    • Ran Tao
    • Josh Cates
    • Guido Gerig
    • Marcel Prastawa
    • Sylvain Gouttard
    • Casey Goodlett
    • C-F Westin
    • Will Schroeder
    • Steve Pieper
    • Jim Miller
    • Xiaodong Tao
    • Marco Ruiz
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