Andy: Update from Wiki

2006-12-18T13:15:09Z

Update from Wiki

New page

Expected Core 3 Attendees: Andy Saykin(Dartmouth), Martina Panzenboeck (UCI), Jim Fallon (UCI), Jessica Turner (UCI)

Agenda:

* Introduction (Ron)
* Engineering Progress (30 min) (Note: details for this are available in a wiki page [[Engineering:2005_Programming_Week_Results|here]] and a consolidated powerpoint is available [[Media:2005_Programming_Week_Summary.ppt|here]])
** (15 min) Application Projects from Programming Week and more ...(Steve Pieper)
** (15 min) Algorithms and Infrastructure Projects from Programming Week (Bill Lorensen)
* (15 min) Core 3 response to projects content and future direction
* (10 min) Core 3 suggestions for items for discussion in Boston on September 26th

== Minutes ==

=== Background of programmer's week by Bill Lorensen and Ron Kikinis ===

* Core 1 and Core 2 meet and split into small teams
* Setup Sandbox for shared efforts
* Tina Kapur organized reports
* Ron was pleased with interactions between Cores
* Move some emphasis from Core 1 to Core 3 by the Engineering team
** All-hands meeting marks 1/2 time for Core 3, time to start writing papers

=== Overview of Applications project by Steve Pieper ===

* Structural, Functional and Diffussion Imaging were focus
* Main focus has been diffusion
* [http://lmi.bwh.harvard.edu/papers/pdfs/2004/brunMICCAI04.pdf Quantative Fiber Tracking Project]
** Define quantaties, ''i.e.'' fa and ensure consistent implementation
** Unify into ITK, first instance is clustering using Normalized Cuts
** Basic algorithm
*** Generate large numbers of tracks
*** Have the algorithm identify a specified numbers of similar tracks via Normalized Cuts
* DLPFC Semi-automatic Segmentor
** Baysen classifier, and rules to segment the dorsal-lateral prefrontal cortex
** Slicer workflow has been defined
** Rules have been identified for other structures, and new structures should be added soon
* EPI to structural image registration
** Use non-rigid registration ITK tools to address this problem
** Used notion of image orientations to address different acquisition orientations
** Resulted in better ITK support for orientation, useful in clinical settings
** Rigid and Affine registration done, exposed in Slicer
** Soon Demon's and B-Spline based registrations
** Need to compare to existing tools: SPM and FSL
* Some of this work has been published in the Insight Journal

=== Overview of Alogrithms Projects by Bill Lorensen ===

* Spherical harmonics added to ITK
* Database and mechanisms to gather statistics on populations from many different sources
** Much of the infrastructure exists inside Dart
* Bayesian Classifier / edge-preserving affine invariant noise remover algorithm
** Transition from Matlab to ITK
* 3d adaptive tetrahedral meshing
** Generate computational stable solid meshes for deformable registration
** Transition algorithms to ITK
* 2d/3d landmark detection algorithm
** Look for corners in the brain, may be useful for registration tasks
* Flux diffusion algorithm
** Port anisotropic diffusion algorithm for thin structures to ITK
* Intensity correction algorithm
** Port external code to ITK, promote to first class filter

=== Overview of Engineering Tasks by Bill Lorensen ===

* ITKu
** Expose ITK functions at the commandline
** Suitable for batch tasks
* Grid adaption for NAMIC algorithms
** LONI pipeline and Condor job submission
* NrrdIO Image format
** Support for DTI-type structures in files
** Handle measurement frames for tensors, variable length vectors
* DTMRI Nightly Testing
** Nightly regression tests for DTMRI Slicer module
* LONI Pipeline for UNC shape analysis
** Adapt UNC scripts to LONI Pipeline
* Slicer 3.0 Architecture Meeting
** Still in dream/planning stage
** Need significant input from Core 3
** May be completely different from existing Slicer implementation
** What is useful from all available technologies? How do we take best-of-breed
** Need to provide architectural support to preserve algorithm development investments
* ITK Release (2.2)
** Much has been added at the behest of NAMIC

== Core 3 Feedback ==

* Andy: development is really exciting from a Core 3 perspective
** Tools need to migrate into Core 3 day-to-day use
* Some must-haves are already recorded and will be presented in Boston on Sept 26th.
* Bill Lorensen invited Core 3 to participate in future tcons

Engineering:TCON 09 08 2005 - Revision history

Andy: Update from Wiki