Difference between revisions of "2008 Engineering review at Utah"

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.

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)

Tuesday 25
- 9am Continue discussion of engineering issues
- Noon to 1.30pm: SCI seminar: "The NAMIC Kit", Presenters: Jim Miller, GE Research, Steve Pieper, Isomics, Will Schroeder, Kitware
- 1.30pm Continue discussion of engineering issues
- 3 - 4pm: Breakout to work on a few major issues identified in previous discussions.
  - Summary of open issues to be further discussed
- 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

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)

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

***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

@@ Line 1: / Line 1: @@
 The date is now set at: March 24-26, 2008.
 Begin: Morning of Monday, March 24.  End: Noon on Wednesday, March 26.
+'''[[2008_Engineering_review_at_Utah:Summary | **SUMMARY AND ACTION ITEMS**]]'''
+'''[[2008_Engineering_review_at_Utah:FollowUp | **ACTION UPDATE**]]'''
 Suggested Hotel: [http://www.monaco-saltlakecity.com/ Hotel Monaco].
@@ Line 13: / Line 17: @@
 '''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'''
+'''Schedule'''
 * Monday 24
 *** 9am: Goals, aims and organization of the meeting (Ross / Guido / Will / Jim / Steve)
 *** Introductions to kick off discussions:
 *** Slicer3 Plugins Presentation [[Media:Slicer3Plugins.ppt|[ppt]]]
-*** DTI analysis pipeline (Casey / Tom / Guido)
+*** Segmentation (Marcel) [[Media:NA-MIC-Core1%2B3_UtahPrastawa_Segmentation_Mar24_2008.ppt| [ppt] ]]
-*** 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?'' [http://www.sci.utah.edu/cgi-bin/ALLseminars.pl?display=2008032400]
-** 2pm: Continue discussions
+** 2pm: DTI analysis pipeline (Casey / Tom / Guido) [[Media:Namic-DTI-core2-slc-review.pdf| [pdf] ]]
+*** Shape analysis (Josh / Tom / Ross )
+*** Summary of open issues to be further discussed
 ** Dinner (tbd)
 * Tuesday 25
 ** 9am Continue discussion of engineering issues
-** Noon to 1.30pm: Lunch / ev. SCI presentation by Will Schroeder (tbd)
+** Noon to 1.30pm: SCI seminar: "The NAMIC Kit", Presenters: Jim Miller, GE Research, Steve Pieper, Isomics, Will Schroeder, Kitware
 ** 1.30pm Continue discussion of engineering issues
-** Dinner (tbd)
+** 3 - 4pm: Breakout to work on a few major issues identified in previous discussions.
+*** Summary of open issues to be further discussed
+** 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
 * Wednesday 26
-** Discussion action items:
+** 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
+'''[[2008_Engineering_review_at_Utah:Summary | **SUMMARY AND ACTION ITEMS**]]'''
 '''Project-specific details to be discussed'''
@@ Line 82: / Line 90: @@
 ** 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: [[Media:GWE-Core.ppt|Overview Presentation]] / [[Media:GWECore-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/ Project Site]
+** GSlicer3: [[Media:GWE-GSlicer3.ppt|Overview Presentation]] / [[Media:GSlicer3-Demo.mov|Video Demo]] / [http://gridwizardenterprise.org/integration/slicer.html Project Site]
+'''[[2008_Engineering_review_at_Utah:Summary | ***SUMMARY AND ACTION ITEMS***]]'''
 * '''Attendees'''

Difference between revisions of "2008 Engineering review at Utah"

Latest revision as of 18:27, 3 April 2008

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