NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Slicer Update

Jim Miller, Ph.D.

Steve Pieper, Ph.D.

National Alliance for Medical Image Computing http://na-mic.org

Topics

• 2007 Year in Review

• Highlights of Slicer3 Features and Application Projects

• Plans for This Week and Beyond

National Alliance for Medical Image Computing http://na-mic.org

Progress in 2007

• Numbers– Subversion Commits: 3,407– Lines of Code*: 371,428– Bugs & Features:

• 154 Submitted• 63 Closed

– Active Developers†: 33

*: find . -iname \*.h -o -iname \*.cxx -o -iname \*.tcl -o -iname \*.java -o -name \*.py | grep -v svn | xargs wc†: svn log | grep "^r" | cut -d " " -f 3 | sort | uniq | wc

National Alliance for Medical Image Computing http://na-mic.org

Current State

• Major Functional Blocks are Implemented– MRML, IO, Module Support, GUI, Volume

Rendering

• Several Modules Becoming Usable– EMSegmenter, Diffusion Image Analysis,

Registration, Informatics, QueryAtlas, IGT, Editor, Meshing, Editor, Python

• Bugs and Performance are Still Major Issues

National Alliance for Medical Image Computing http://na-mic.org

Base Features

• Linux (32/64), Mac (ppc/x86), Win32

• All-in-one build and test script

• Nightly builds and tests

• Doxygen/Wiki Developer Docs

• Basic Developer and User Tutorials

National Alliance for Medical Image Computing http://na-mic.org

Volume Rendering

• VTK Hardware and Software Based– Selectable Volume mixed

with Opaque Geometry– Flexible Threshold,

Lookup Table, Cropping, and Interactive Performance Options

• Andy Freudling (BWH) with Lisa Avila and Sebastien Barre (Kitware)

• See Andy for a Demo!

National Alliance for Medical Image Computing http://na-mic.org

EM Segmenter

• Complete Reimplementation of slicer2 based code in slicer3

• Now contains complete registration and segmentation framework

• Kilian Pohl (MIT/BWH) and Brad Davis (Kitware)

• Attend the breakout session at 4!

National Alliance for Medical Image Computing http://na-mic.org

Diffusion Tools

• Core Infrastructure (Yarmarkovich, Isomics; O’Donnell & San Jose Estepar, BWH)

– DWI, DTI, FiberBundles in Scene– Fully load/save including all vis

parameters– DICOM to NRRD (Tao, GE)– Tensor Estimation– Scalar Invariant Volumes– ROI Tractography

• Rician Filtering (Gouttard, Utah)• Stochastic Tractography (Ngo,

MIT)• All Day Breakout Wednesday!

National Alliance for Medical Image Computing http://na-mic.org

Registration

• ITK-based Registration Command Line Modules (Lorensen, Blezek, GE)– Rigid, Affine, B-Spline

• Optimized Multi-Threaded (Aylward, Ibanez, Kitware)

• Tensor ITK Resampling (Bouix, Budin BWH)

• Attend the Breakout Session Tuesday at 3!

National Alliance for Medical Image Computing http://na-mic.org

mBIRN Informatics

• XNAT Web Database of Neuroimages (Marcus, WashU)

• Query, Design, Estimate, Contrast of Population Statistics (Greve, MGH)

• Web Queries to Identify Population

• Population GLM Statistics Run on Grid

• Analysis Results Open in Slicer3 or Interactive Visualization and Plotting (Aucoin, BWH)

• Welcome Dan and the Wash U team to NA-MIC!

National Alliance for Medical Image Computing http://na-mic.org

Query Atlas Features

• Integrated Ontology / Anatomy / Statistics System Volumes and Models Labeled with Controlled Vocabulary

– Co-Registered Individual or Population Statistics

• High Performance Interactive Picking and Labeling

• Launch Web Queries Using Anatomy, Demographic, Diagnostic & Behavioral Terms

• Integrated with BIRN Informatics (Plesniak, BWH; Pieper, Isomics)

• See Wendy or Steve for a Demo!

National Alliance for Medical Image Computing http://na-mic.org

IGT

• Several Groups have NIH Funding to do Slicer3-based Image Guided Therapy

– NCIGT Neurosurgery, Prostate, (Hata, Lui, Tokuda, BWH)

– IGSTK Liver RF Ablation (Cleary, Yanic, Cheng, Georgetown; Ibanez, Kitware)

– NA-MIC Protstate Robot (Fichtinger, Gobbi, Queens; Kazanzides, Csoba, JHU)

– Neuroendoscopy ( Barre, Kitware)

• Real-Time Tracking and Images Needed

• This is very cool!

National Alliance for Medical Image Computing http://na-mic.org

Editor

• General Purpose Label Map Editor– Paint and Draw Tools with Integrated

Thresholding (Pieper, Isomics)

– Level Tracing Auto Segmentation (Miller, GE)

– Clean GUI Based on User Centered Design Process (Plesniak, BWH)

– Module Tool Implementation to Plug in Additional Effects

• There’s still a lot of work to do!

National Alliance for Medical Image Computing http://na-mic.org

Meshing• Workflow to go from CT to FE

Mesh - IA-FEMESH– MIMX Infrastructure

(Grosland, Magnotta, UIowa)– VTK Unstructured Grid

Infrastructure (Kitware)– Voxel Meshing (Magnotta)

and Hexahedral Mapping (Magnotta, Shivanna)

– Slicer Implementation (Lisle, Isomics)

• Additional Benefits– Mesh Infrastructure in MRML– VTK 3D Widgets in Slicer3

• See Curt for a Demo!

National Alliance for Medical Image Computing http://na-mic.org

Python

• Leverage the Scientific Python Community

– Numpy Provides Powerful Interactive Numerical Processing

– MATPLOTLIB Provides MATLAB-Like Publication Quality Plotting

– Variety of Utilities in Scientific Python (scipy)

• Python/Tcl/VTK Bridge– Direct Pointer Access to Slicer

Volumes (Blezek, Mayo/GE/Isomics)

• Python Based Modules– VMTK - Vascular Modeling Toolkit

(Antiga, Mario Negri Institute)

• See Dan and Luca for a Demo!

National Alliance for Medical Image Computing http://na-mic.org

Major Projects for 2008

• Increased Focus on Applications and Community Involvement– Slicer3 is Open for Business!

• Modularity Project– Make the Slicer Base “Lean and Mean”– Expand ModuleFactory for GUI Modules– NITRC (gforge-based) Developer Site

• Event Broker– Replace AddObserver Calls with

National Alliance for Medical Image Computing http://na-mic.org

Modularity Project

• Goals– Address Scalability for New Modules– Only Load what YOU Need– Improved Testability and Efficiency

• Firefox Analogy– Slicer3 Base as has well defined set of supported

functions (volumes, models, transforms… are like text, forms, images, tables)

– Modules/plugins can be downloaded from independent servers

• Project is Underway (Terry Lorber, Alex Yarmarkovich) with Support from NITRC

National Alliance for Medical Image Computing http://na-mic.org

Modularity Targets

• Benefits– Slicer3 Base becomes streamlined and

efficient with clear scope– Modules have distinct identity (web site, wiki,

svn…)

• Features– Integrated with build, test, and package

systems (nightly builds of Base plus compatible Modules available for download)

– Easy for Users to Browse/Install Module Packages