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)
- Shape analysis (Josh / Tom / Ross )
- Segmentation (Marcel)
- 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
- 9am Discussion of 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
- Infrastructure for DWI/DTI data types
- 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
- How to provide coherent user interfaces for specific tasks
- 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