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.

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.

Draft 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]
    • DTI analysis pipeline (Casey / Tom / Guido) [pdf]
    • Shape analysis (Josh / Tom / Ross )
    • Segmentation (Marcel) [[Media:NA-MIC-Core1%2B3_UtahPrastawa_Segmentation_Mar24_2008.ppt]| [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: Continue discussions
  • Dinner (tbd)

• Tuesday 25
  • 9am Continue discussion of engineering issues
  • Noon to 1.30pm: Lunch / ev. SCI presentation by Will Schroeder (tbd)
  • 1.30pm Continue discussion of engineering issues
  • 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

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)

• DBP2:UNC:Cortical_Thickness_Roadmap

• 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

• GSlicer3. Slicer3 with embedded grid computing capabilities (Powered by GWE)
  • GWE Core: Overview Presentation / Video Demo / Project Site
  • GSlicer3: Overview Presentation / Video Demo / Project Site

• 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