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Home < 2007 December Slicer IGT Programming

Introduction

Sponsored by
NA-MIC
NCIGT
IGT program of CIMIT
NAC

This is a working meeting for research groups with funding to work on the IGT extensions of the NA-MIC kit. There will be a follow up meeting during the NA-MIC AHM in SLC.

Summary

Over 20 researchers attended this meeting.

Dates.Location.Hotels

Date: December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. (Directions)

Area hotels: Boston_Hotels

Goal

Continued discussion of Slicer IGT infrastructure, applications, and timelines
Introduce each team's effort in Slicer in the context of IGT
Find unmet needs
Identify high-priority working items
Identify each team's potential contribution to the high-priority tasks

Meeting summery

Twenty three investigators using Slicer for IGT research under NIH funding gathered in Brigham and Women's Hospital from December 12 to 13, 2007.

We discussed current status, unmet needs, future direction, and resource sharing in Slicer engineering. Four live demonstrations using real tracking device and phantoms were performed to facilitate the discussion. In summery, we concluded that the 3D Slicer, which currently centers around medical image processing and visualization, definitely has proven to be also useful for IGT and has potential to become enabling software for new procedures in IGT. However, we also agreed that Slier still has gap in its in feature list to meet requirements of the investigators goals in their own clinical targets. They are 1)

*Plug-in mechanism to develop a high-performance software specifically tailored to a target clinical application
*Controlled and fast Data/communication/event management
*Inter-device communication mechanism to/from Slicer
*Fast Volume rendering for 4D IGT
*Flexible GUI design
As the next step in IGT research using Slicer, we decided to develop the above mentioned mechanism through continuing collaboration and resource sharing.

Agenda

Wednesday, December 12

Theme: Where are we?

12noon: Lunch

12:55pm: Welcome (Ron Kikinis)

1-2pm:Slicer and IGSTK presentation

Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
- History
- Clinical applications
- transition from 2.6 to 3
- resource
- Slicer Core + Loadable Modules
IGSTK
- Architecture Overview (Ibanez)
- Current status, and future plans (Cheng) Refactoring Design Discussion
- IGSTK has time stamping for tracker and event.
- Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
- GUI tools for sample programs are FLTK and Qt

215-330pm: Presentation by Slicer Developers

2:30-3:00pm - NCIGT CIGL Stoll and Demo
- Issues for Slicer

Move toward multi-process model, keep idea of GPU capability in mind for future
online/unsupervised segmentation, online/fast registration (almost like tracking); can trade some accuracy for speed
flexibility in registration techniques - data collection is not perfectly constrained (patient positions vary, image quality varies, fiducials sometimes/not) - tools for anatomy-based registration

3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
3:30pm-3:45pm: Review of today's progress

400pm: Adjourn

4-6pm (optional) MRI Demonstration

Use of Slicer for control and display with MRI (prostate module) presented by Junichi Tokuda. Location: Advanced MRI center, 221 Longwood, Boston
- See slicer-MRI demo

Thursday, December 13

Theme: Where are we?

9-10:00am Demos:

Hata (Tracking at BWH)
Freudling (Pieper) (Volume rendering)

1000-10:30am Demonstrations

- Robot-assisted neurosurgery with Slicer (Kazanzides)
- Robot connected to Slicer via Robot control unit (with Real time OS)
- Slicer CT coords != Stealthstation CT coords
- Needs rasToIjk matrix from xml file
- Inter-computer communication

Slicer 3 IGT update

10:30am: Identifying the unmet needs

(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)

Queens: NA-MIC DBP
JHU: BRP
BWH: NCIGT etc.
Georgetown: Liver RF
Kitware-BWH

Identify the unique needs in IGT
Identify commonality among the projects
which one is to be covered by actively funded project?
Identity and prioritize unmet needs
Find commonality among the needs, consolidate if necessary

Unmet needs #1: Plug-in mechanism

Related wiki page -> Plug-in mechanism / Modules

Currently we use CMake + Slicer3
Compile vs. Run-time -> run-time is current choice for Steve
Slicer Base version 3.0
Binary distributed againg Base version
Firefox extension
How do you balance testing and flexibility.
Version control necessary
effort underway in NA-MIC/NAC
Module/function dependency

Common functions to be implemented in Base

Module/function dependency

Features	Base	Module
Visualization	MRML, Arbitary ViewPoint (Pre-defined)	Liver RF
Filtering	None	Command Line Module
IGT	Tracker I/O (BWH Hata) Tracker On/Off Real-Image I/O (BWH Hata) Video capturing Simple loading image Imager control for each modality MRI (NCIGT Tokuda) Image re-slicing based on tracker (BWH Hata Liu) GUI configuration control (XXX) Human interface control Foot pedal (BWH Liu) Stereo Output to outside display Logging replay and saving IGSTK has fast version MRML scene recorder (Georgetown)	BWH, Georgetown, JHU, Queens applications
Registration	Transform Display, Edit and Save/Resotre	Calculae Transforms, Resample Data
Segmentation	Label Maps, Parcellated Surface	Segmentation Algorighms
Quantification	Label, Image, Volume Statistics; Numpy access to MRML	Applications in Python or MATLAB
Real-time Integration	VTK Rendering, KWWidgets framework, Tracker Support (as Transforms)	Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface
Diffusion Imaging	DWI, DTI, Fiber Bundles	Tractography, Clustering, Atlases
Application	Bundles of Modules in Distribution: Registration Editor, some Filters	Customized Extensions, Domain specific code, optimized Interface

Unmet needs #2 Data/communication/event

Related wiki page Events / Data transfer

Data Workflow I/O
ticking and latency management
Threads to read-in tracker info
Special DICOM and PACS
Priority control of events? -> Event Manager
Realtime needs
Inter-communication mechanism to/from Slicer

Socket mechanism in SlicerDaemon
Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
Scenesnapshot can be used as logging. Replay. Crash recovery
State machines may be useful mechanism in Slicer
- follow up activities in the related wiki page Events / Data transfer
Connection with commercial navigation system
- MR/T BWH
- Brainlab
- Neuromate
- Medtronics

Unmet needs #4: Inter-device communication mechanism to/from Slicer

- Inter-device communication mechanism to/from Slicer
  - Tracker Image
  - Publish subscribe ORB/ACE [Peter]
  - Socket IGSTK [Junichi Patrick]

Unmet needs #5: Volume rendering

- Volume rendering
  - Performance and speed continue to be upgraded
  - GPU, fastere volume rendering
  - 4D IGT
  - Real I/O
  - New MRML? Time-series MRML volume?

- (Regulartory approval) (Legal issue/ form / guideline)

December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration

Unmet needs #3: GUI

GUI
- GUI-Workflow (David)
- David's opening statement from Queens' perspective
- How can we add additional windows?
- KWWidgets has workflow mechanism
- Compacting GUI - necessary
- Single screen? Two screen setup? Two screen setup to be tried by David
- KWWidgets Wizard Workflow Powerpoint presentation.

- Observing events (convenience)
- Status window is nice
- short cut
  - pre-defined view point
  - lower left (two complicated)
- GUI Layout to be stored in MRML (as log)
- Turning off lower left
- Status (window) part
- human interface--
  - configurable GUI using current XML mechanism

5pm: Review day and plan for Friday (Hata)

5:30pm: adjourn

Friday, December 14

9:00am: breakfast, work

9:30-11:00am Review of the meeting

Discuss how we can continue this effort in what way
- Hands on IGT Week
- Outreaching to animal research community
- Training and simulation

Action Items
- NCIGT
- Georgetown
- Kitware
- Queens
- JHU
11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(Hata)
noon: adjourn and head out to group lunch

Confirmed Attendees

Noby Hata, BWH (NCIGT)
Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
Patrick Cheng, Georgetown (NAMIC Collab)
Ziv Yaniv, Georgetown (NAMIC Collab)
Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
Luis Ibanez, Kitware (NAMIC)
Sebastien Barre, Kitware (NCIGT)
Stephen Aylward, Kitware (NCIGT)
Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
Haiying Liu, BWH (NCIGT)
Katie Hayes, BWH (NAC)
Peter Kazanzides (except Friday), JHU (NAMIC Collab)
Csaba Csoma, JHU (NAMIC/NCIGT Collab)
David Gobbi, Queens (NAMIC/NCIGT Collab)
Tina Kapur,BWH (NAMIC/NCIGT)
Ron Kikinis, BWH (NAMIC/NCIGT)
Junichi Tokuda, BWH (NCIGT)
Raul San Jose, BWH (NAC)
Neculai Archip, BWH (Wed only) (NCIGT)
Nicholas Ayache (NCIGT) (Wed only)
Andy Freudling, (NAMIC)
Henrik Keller (NCIGT)
Benjamin Grauer (NCIGT)

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