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Project Half Week January 10/12, 2007 Held in Conjunction with AHM 2007

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Title: Project Half Week January 10/12, 2007 Held in Conjunction with AHM 2007


1
Project Half Week January 10/12, 2007Held in
Conjunction with AHM 2007
  • AHM Participants 96
  • NA-MIC (56), Collaborators (32), EAB/NIH (8)
  • 56 NA-MIC Algorithms Core (24), Engineering Core
    (13), DBP Core (15), Service Core (1), Training
    Core (1), Dissemination Core (1), Leadership Core
    (1)
  • 32 Collaborators Acoustic Med (1), BWH (12),
    Caltech (1), Duke (1), Harvard IIC (1), Knowledge
    Vis (1), Mario Negri (1), MIT (2), NWU (3),
    Stanford (1), MIND (1), UIowa(6), Virginia Tech
    (1).
  • Projects 38
  • Structural Analysis (9)
  • Diffusion Image Analysis (7)
  • NA-MIC Kit (10)
  • External Collaborations (11)

2
Project Half Week January 10/12, 2007
  • Structural Analysis
  • ITK Spherical Wavelet Transform Filter
  • UNC shape analysis with Spherical Wavelet
    Features
  • EMSegmenter Software Development
  • Data assimilation for NAMIC
  • Parallelization of ITK for deformable
    registration
  • Integrating KWMeshVisu into Slicer
  • Group-wise Registration of Medical Images
  • Genus Zero Slicer3 Module
  • Thickness Slicer3 Module
  • External Collaborations
  • Slicer3 Module for HPC deformable registration
  • Slicer3 IGT, Trackers
  • IGT Workflow for Slicer3 Interventional Imaging
  • Radiology Workstation Module for Slicer3
  • vmtk module for Slicer
  • Diffusion Image Analysis
  • Finsler Tractography
  • Finsler Levelsets
  • Tensor estimation and Monte-Carlo simulation
  • Rician Noise Removal in Diffusion Tensor MRI
  • ITK implementation of POIStat, and Integration
    into Slicer3
  • Image Format issues in application of POIStats to
    Dartmouth data
  • ITK Stochastic Tractography Filter
  • NCBC Collaboration Hexahedral Voxel Meshing
    Slicer3
  • Voxel meshing as an execuation module in Slicer3
  • Mesh Quality Visualization Development
  • Bounding Box Projection Meshing
  • Tetrahedral Mesh Generation Tools in VTK
  • Mapped Meshing Using ITK
  • NCBC Collaboration in Preparation
  • Nonhuman Primate slicer Module (Alcohol Exposure)
  • NA-MIC Kit
  • Slicer3Architecture/Features
  • Slicer3 Data Model / libMRML
  • Slicer3 Interface Design and Usability
  • Slicer3 Modules for DTMRI,Tractography,Editor,
    Colors, Fiducials, FreeSurfer, ModelMaker
  • Build/Test/Deploy System
  • Slicer3 launch and deployment issues
  • Slicer3 LONI Pipeline Integration
  • LONI Pipeline for UNC Shape Analysis
  • Slicer3 Grid Integration
  • Slicer3Performance Analysis
  • Matlab-Slicer3 pipeline enhancement
  • Non-Medical Collaboration
  • Slicer Enhancements for Astronomical Data Cubes

3
Structural Analysis
  • Structural Analysis
  • ITK Spherical Wavelet Transform Filter
  • UNC shape analysis with Spherical Wavelet
    Features
  • EMSegmenter Software Development
  • Data assimilation for NAMIC
  • Parallelization of ITK for deformable
    registration
  • Integrating KWMeshVisu into Slicer
  • Group-wise Registration of Medical Images
  • Genus Zero Slicer3 Module
  • Thickness Slicer3 Module

4
ITK Spherical Wavelet Transform FilterDevelop
algorithm and ITK software module for Spherical
Wavelet computation
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Delphine Nain, GT (algorithms) Yi Gao, GT
(algorithms) Luis Ibanez, Kitware (software) Jim
Miller, GE (software)
Algorithms decomposition of a scalar signal
defined on a spherical mesh into spherical
wavelet coefficients and vice-versa in order to
represent shapes in a multi-scale framework.
  • Software
  • Completed ITK filter class to fulfill the above
    algorithm.
  • To code visualization of spherical wavelet
    functions as colormaps
  • Paper
  • To write ITK Insight journal to be completed by
    the end of the week.

Accomplished by end of the Week
-produce figures to show the spherical wavelet
function on the sphere, at any resolution and
location -completion of the paper for Insight
Journal
.
SWF
Signal to Coeffs Filter
SWF
Coeffs to Signal Filter
5
Scripts to combine UNC Shape Analysis with
Spherical Wavelet Features
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Yi Gao, GT (algorithms) Delphine Nain, GT
(algorithms) Martin Styner, UNC (algorithms)
  • Software tcsh scripts
  • PIPELINE 1 (after UNC preprocessing, before UNC
    statistical scripts)
  • INPUT Read UNC preprocessed META surfaces
  • Re-interpolate the spherical meshes to use a
    recursive icosahedron structure. The output are
    remeshed META surfaces.
  • Run the itkSWavelet filter on re-interpolated
    meshes to obtain spherical wavelet coefficients
  • OUTPUT Write spherical wavelet coefficients
    (SWC) to a text file that will be read by the UNC
    statistics scripts
  • PIPELINE 2 (after UNC stats scripts)
  • INPUT raw and corrected p-values for the SWC
    features
  • Write visualization scripts to visualize the SWC
    p-value map on the mean shape
  • OUTPUT Colormap that can be visualized KWVisu

To be Accomplished by end of Programming Week
-Write and test scripts on the female caudate
structure -Submit code to NA-MIC
repository -Write ITK Insight journal
6
EMSegmenter Software DevelopmentIntegrate
EMSegmenter from Slicer 2 to Slicer 3
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Algorithm Work on user interface of
EMSegmenter in Slicer3 including bug
fixes and new functionality.
Kilian Pohl, BWH-MIT (algorithms) (contact) Brad
Davis, Kitware (software) (contact)Sebastien
Bare, Kitware (software) Yumin Yuan, Kitware
(software) Marc Niethammer , BWH (clinical)
Software Integrate new class overview and graph
window.
Clinical Validate results with Slicer 2 version.
Accomplished by end of Programming Week
Provided tutorial and got feedback Establish
priorities for future directions Began
integrating rules into wizard Added
panel-specific help Intinsity distribution
widget nearly completed Bug fixes http//www.na-m
ic.org/Wiki/index.php/Slicer3EM
7
NA-MIC Data AssimilationCentralize the
archival, analysis, and access of NA-MIC tutorial
data and select project data.
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Data Identify tutorial/demonstration data for
Slicer 3.0 define data assimilation
requirements provide feedback on MIDAS and its
tools and publish available, related, NA-MIC
resources.
Stephen Aylward, Kitware (Data/Software)
(contact) Steve Pieper, Isomics (Data) Julien
Jomier, Kitware (software)
Software Upload data to MIDAS extend BatchMake
for new experimental methods refine MIDAS and
its tools based on feedback refine validation
dashboard look-and-feel, provide template
Batchmake scripts and define script submission
process Related NA-MIC Resources BIRN anonymous
ftp, LONI Pipeline, Imagine2 pipeline.
Accomplished by end of Programming Week
  • Initial data to be hosted has been identified
    and downloaded
  • EM Segment Module Tutorial Data
  • MGH Atlas
  • Killian Pohls MR/MR head registration data
  • Killian Pohls CT/CT abdominal registration data
  • Steve Piepers fMRI/MR registration data
  • Held discussions with BIRN-Grid representative
    Niel Jones and Steve Pieper. Identified means of
    launching Grid tasks from within Slicer for
    parameter space evaluation and batch processing
    (using BatchMake).

8
ITK Registration ParallelizationDevelop
implementations of ITK registration methods to
take advantage of multi-core and multi-processor
systems.
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Stephen Aylward, Kitware (Algorithms/Software)
(contact) Jim Miller, GE (Algorithms) Ross
Whitaker, Utah (Algorithms) Luis Ibanez, Kitware
(Algorithms/Software) Driving problems
Kilian Pohl, BWH-MIT (Inter-subject mapping)
Steve Pieper, Isomics (fMRI to high-res MRI)
Sandy Wells, MIT (EPI/MRI) Sylvain Bouix, BWH
(DTI component registration)
Algorithms Identify ITK registration methods,
specify component tests, collect test data.
Challenge Test speed and maintain accuracy
Software Identify/develop cross-platform timing
system, implement component tests, centralize
data and results, identify bottlenecks,
parallelize and re-test. Challenge
Cross-platform multi-threaded timing
Driving Problem Validation of results.
Expected Date for Insight Journal Publication
August, 2007
Accomplished by end of Programming Week
  • Driving problem will be Killian Pohls head
    MRI/MRI registration task
  • B-Spline registration is the technology
  • Speeding image resample will be initial component
    test
  • Data has been centralized on MIDAS
  • Intel dual-core platform chosen for optimization
    since an open-source, cross-platform, profiling
    tool with multi-core support could not be found
  • Secondary problems for DTI and fMRI also
    identified, and their data has been centralized
  • Optimized code will be delivered using the Slicer
    B-Spline Module

9
Integrating KWMeshVisu into Slicer
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Previously on KWMeshVisu This is a mesh
visualization tool for viewing various attributes
(scalar maps, vector fields, ellipsoid fields,
space curves) on object surfaces. We also used
this as an experiment to use KWWidgets, and have
had very satisfactory results. Insight Journal
Publication We have presented KWMeshVisu in the
MICCAI06 issue.
Ipek Oguz, UNC (algorithms) (contact) Martin
Styner, UNC (algorithms) Sebastien Barre,
Kitware (software) Jim Miller, GE (software)
Software Integration of our tool into Slicer 3.
Accomplished by end of Programming Week
We have successfully integrated KWMeshVisu into
Slicer3 as a command line tool.
10
Group-wise Registration of Medical
ImagesDevelop algorithm for group-wise
non-rigid registration of medical images.
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Apply non-rigid and multi-resolution
registration currently available in ITK to
group-wise registration framework.
Serdar K Balci, MIT (algorithms) Polina Golland,
MIT (algorithms) Mert R Sabuncu, MIT
(algorithms) Lilla Zollei, MIT (collaborator) Sand
y Wells, MIT (algorithms) Luis Ibanez, Kitware
(software)
Software computational speed, parallel
programming.
Clinical Validation of results.
Expected Date for Insight Journal Publication
Accomplished by end of Programming Week
Mean Images before
after
-Incorporated B-Splines into the registration
framework -Implemented multiresolution
registration
11
Genus 0 Slicer3 Module Develop Slicer3 Module
for the topological correction of labelmaps.
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Algorithms finish Slicer3 topology correction
module. Fix orientation issues for model output.
Marc Niethammer, BWH (contact) Sylvain Bouix,
BWH Steve Pieper, Isomics based on work by Steve
Haker, BWH Michael Rabes, BWH
Accomplished by end of Programming Week
Implemented command line module and fixed various
orientation issues.
12
Thickness Measurement Slicer3 ModuleDevelop
simple Slicer3 Module for thickness measurement
of label maps.
2007 Project Half Week
Theme Structural Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Finish a simple module for thickness
measurement based on boundary conditions given
by a labelmap. Improve user interface.
Marc Niethammer, BWH (contact) Sylvain Bouix,
BWH Steve Pieper, Isomics
Accomplished by end of Programming Week
Created command line module for slicer 3.
13
Diffusion Image Analysis
  • Diffusion Image Analysis
  • Finsler Tractography
  • Finsler Levelsets
  • Tensor estimation and Monte-Carlo simulation
  • Rician Noise Removal in Diffusion Tensor MRI
  • ITK implementation of POIStat, and Integration
    into Slicer3
  • Image Format issues in application of POIStats to
    Dartmouth data
  • ITK Stochastic Tractography Filter

14
Finsler TractographyDevelop ITK filter for
Finsler Tractography.
2007 Project Half Week
Theme Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Dynamical programming formulation of
directional open curve segmentation using a
Finsler metric.
John Melonakos, GT (algorithms) (contact)
Software Incorporation into an ITK filter.
Addition of itkImageDirectionalIteratorWithIndex
to ITK.
Luis Ibanez, Kitware (software)
Clinical Validation of neural tract segmentation.
Is this a continuation of a previous programming
week project? If so, please include that slide
as well. - NO -
Marc Niethammer, PNL (clinical) Marek Kubicki,
PNL (clinical)
Expected Date for Insight Journal Publication
April 2007
Accomplished by end of Programming Week
-Created the itkImageDirectionalIteratorWithIndex
-Created the itkFastSweepingImageFilter
-Created the itkFinslerTractographyImageFilter
...
-This project is still under development...
15
Finsler LevelsetsDevelop ITK software module
for levelset-based directional segmentation
framework in arbitrary dimension.
2007 Project Half Week
Theme Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Directional levelset segmentation of
DWI datasets using a surface evolution.
Vandana Mohan, GT (algorithms) (contact) John
Melonakos, GT (algorithms)
Software Incorporation into ITK for arbitrary
dimensions.
Luis Ibanez, Kitware (software)
Clinical Validation of neural tract segmentation.
Is this a continuation of a previous programming
week project? If so, please include that slide
as well. - NO -
Marc Niethammer, PNL (clinical) Marek Kubicki,
PNL (clinical)
Expected Date for Insight Journal Publication
April 2007
Accomplished by end of Programming Week
  • Image functions created for computing shape
    operator and surface derivatives.
  • Formalized implementation approach for the image
    filter.
  • (Development in progress)

16
DTI monte-carlo simulation and tensor
estimationDevelop algorithm and software for
monte-carlo simulation of noise effect on tensor
estimation
2007 Project Half Week
Theme Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Compare existing existing algorithms
for tensor estimation.
Casey Goodlett, UNC (algorithms) (contact) Ran
Tao, Utah (algorithms) Tom Fletcher, Utah
(algorithms) (software) (clinical)
Software MATLAB simulation. ITK filters for
non-linear least squares, weighted least,
maximum likelihood estimation.
Clinical Validation of results in real scans
Accomplished by end of Programming Week
Linear Non-linear Weighted
  • ITK filters for tensor estimation routines
  • Simulated/Experimental comparison of
    estimationmethods

17
Rician Noise Removal in DTIDevelop ITK and
Slicer module for Rician noise removal in DTI.
2007 Project Half Week
Theme Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithm DTI Rician noise removal as described
in Basu, et al MICCAI 2006. Add method to compute
noise sigma from data.
Tom Fletcher, Utah (algorithms) (contact) McKay
Davis, Utah (algorithms)
Software Integration into Slicer.
Jim Miller (software)
Clinical Validation of results.
Accomplished by end of Programming Week
Added method for automatic threshold of air
voxels to find the Rician noise sigma. Created
Slicer plug-in module to run the filter.
Noisy data
Filtered data
18
Poistats, Slicer, and ITK IntegrationFurther
develop algorithm for integration into ITK and
Slicer.
Theme Diffusion Image Analysis
Algorithms Continue c development and adjust
API as needed for integration.
Dennis Jen, MGH (algorithms) (contact) Steve
Pieper, Isomics (software)
ROIs
Path
19
Applying Poistats to Dartmouth DataGeneralize
poistats for applying to Dartmouth data.
2007 Project Half Week
Theme Diffusion Image Analysis
Algorithms Develop current version of poistats
so Darthmouth data can be run successfully.
Dennis Jen, MGH (algorithms) (contact) Steve
Pieper, Isomics (software) Luis Ibanez, Kitware
(software) John West, Dartmouth (clinical) Andy
Saykin, Dartmouth (clinical)
20
Stochastic TractographyDevelop an ITK filter to
generate region connectivity probabilities.
2007 Project Half Week
Theme Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithms Calculate the probability that two
brain regions are connected via a fiber tract
given the measurements in a DWI dataset.
Tri Ngo, MIT (contact) C-F Westin, LMI Polina
Golland, MIT
Software Incorporation into ITK and the creation
of a command line module for Slicer 3.
Clinical Provide measures of confidence about
tractography results and enable detection of
tracts which pass through regions of
low anisotropy.
Based on work by Ola Friman and Raul San Jose
Expected Date for Insight Journal Publication
February 2007
Accomplished by end of Programming Week
  • Finished first Implementation of Filter (results
    shown in left image)
  • Finished Slicer3 Command Line Module with GUI
    interface (right image)

21
NA-MIC Kit
  • NA-MIC Kit
  • Slicer3Architecture/Features
  • Slicer3 Data Model / libMRML
  • Slicer3 Interface Design and Usability
  • Slicer3 Modules for DTMRI,Tractography,Editor,
    Colors, Fiducials, FreeSurfer, ModelMaker
  • Build/Test/Deploy System
  • Slicer3 launch and deployment issues
  • Slicer3 LONI Pipeline Integration
  • LONI Pipeline for UNC Shape Analysis
  • Slicer3 Grid Integration
  • Slicer3Performance Analysis
  • Matlab-Slicer3 pipeline enhancement

22
Slicer 3 ArchitectureAllow components of Slicer
3 project to work well together.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Steve Pieper Bill Lorensen Ron Kikinis Mike
Halle Noby Hata With Slicer 3 Team
  • Plan for 3.0 Release
  • Improving the Stability and Performance
  • Completing Remaining Features
  • Fixing Bugs

Accomplished by end of Programming Week
  • Aim for Base in March timeframe (3.0), and DTI
    enabled release in June (3.1)
  • Much debugging was done as part of programming
    week
  • The program is proving to be pretty stable

23
Data Model / libMRML
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Alex Yarmarkovich Steve Pieper With Slicer 3 Team
  • Collect Feedback from Developers
  • Identify Outstanding Bugs/Issues

Accomplished by end of Programming Week
  • Feedback sessions were very helpful
  • Next focus will be on supporting DTI module with
    its requirements for diffusion volumes and
    tract bundles

24
MRML Hierarchies
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Alex Yarmarkovich (Isomics), Lauren ODonnell
(BWH), Brad Davis (Kitware), Mike Halle (BWH)
Generalize concepts from DTI and EM group nodes
to support atlas hierarchies like in slicer2.
Accomplished by end of Programming Week
  • Discussed requirements for Anatomy Atlas (Mike
    Halle) and DTI (Lauren ODonnell). Here are some
    suggestions
  • Need Hierarchy nodes separate from Models,
    referencing Model and Display nodes.
  • Branch nodes can reference an aggregate Model
    Node.
  • Multiple hierarchies, Models can belong to
    different hierarchies.
  • Model Hierarchy Widget controls visibility and
    open/collapsed state of branch nodes.
  • If Model is a descendent of a collapsed node use
    collapsed node Display Node.
  • Display aggregate model if present instead of
    closed branches.

25
Interface Design and Usability for Slicer3
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Wendy Plesniak, BWH Sebastien Barre,
Kitware Yumin Yuan, Kitware
GUI Present and describe user interface for
Slicer Work toward completing View Control GUI
functionality Refine features according to
feedback
Usability Solicit feedback from application
users, and users of Development infrastructure
for interactive and plug-in modules Organize
and deliver user feedback into the development
effort.
Accomplished by end of Programming Week
  • Disseminated information about interface and
  • GUI development infrastructure.
  • Collected feedback from users.
  • Prototyped View Control GUI elements (shown
    right)
  • and worked on stabilizing code.

26
Tractography in Slicer3Develop Slicer software
module for tractography.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Algorithms Tractography module in future can
provide a base for algorithmic experimentation.
Lauren ODonnell, BWH/LMI/MIT (algorithms/software
) (contact) Steve Pieper, Isomics
(software) Alex Yarmarkovitch, BWH
(software) Wendy Plesniak, BWH (software) Alex
Golby, Marek Kubicki, BWH (clinical)
Software Develop MRML infrastructure for
tractography, loading and saving of files, and
display of tracts with tensor attributes.
Clinical Tractography module will in future
support surgical planning, quantitative analysis,
and interactive tractography editing needs.
Expected Date for Insight Journal Publication
May 2007
Accomplished by end of Programming Week
  • MRML infrastructure for tractography.
  • Load/Save framework for tractography.
  • Initial display capabilities.
  • Increased understanding of slicer3 platform.

27
DTI in Slicer3Develop core functionality to
support DTI processing and display.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Software Currently supported DTI and DWI can
be I/O and MRML nodes can be created. Redesign
Volumes GUI classes to support different
volume types with different display
needs. Develop Geometry Layer infrastructure to
allow the representation of glyphs, and in
general models, in the resliced view.
Raul San Jose, BWH/LMI Steve Pieper, Alex
Yarmarkovik, Isomics Wendy Plesniak,
BWH Sebastien Barre, Kitware
Expected Date for Insight Journal Publication
May 2007
Accomplished by end of Programming Week
Goals are Display and interact with DWI and DTI
images. Estimate DTI from DWI. Design of the
Geometry Layer.
DWI Volume loaded in the Slicer
28
Slicer3 Editor
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Steve Pieper Sylvain Bouix John West
  • Experiment with current implementation
  • Identify and characterize bugs
  • Define needed improvements

Accomplished by end of Programming Week
  • Got Core3 feedback from Dartmouth
  • Found some bugs that seem to depend on what
    dataset is loaded
  • Goal is to get the Editor working for a March
    release of the Base

29
Transition of Slicer2.x Modules to Slicer3 Colors
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Plan Subclass the vtkMRMLColorNode to create
Procedural and PieceWise colour nodes, subclass
the Procedural node to create a FreeSurfer node.
Update the ColorsGUI to handle all
subclasses. Expected Challenges Generalising
the colour nodes for easy extensibility
Nicole Aucoin, BWH (contact) Sebastien Barre,
Kitware Yumin Yuan, Kitware
Accomplished by end of Programming Week
Got some feedback from application users, sped
up display of colour tables. Got feedback from
application developers, drafted a plan to
integrate tractography needs into the MRML color
hierarchy.
30
Transition of Slicer2.x Modules to Slicer3
Fiducials
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Nicole Aucoin, BWH (contact) Steve Pieper,
Isomics
Software Implement placing Fiducials in 3D.
Discuss how to integrate display styles.
Accomplished by end of Programming Week
Various picking strategies were explored for
placing fiducials in 3D, but a final selection is
reliant on some architecture reorganisation to
integrate event handling. Completion is projected
to occur by mid-February.
31
Transition of Slicer2.x Modules to Slicer3
FreeSurferIntegration of FreeSurfer scalar
overlays and colour lookup tables into Slicer3.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Nicole Aucoin, BWH (contact)
Software Extend MRML color nodes to include
FreeSurfer colours. Support scalar overlays on
models.
Accomplished by end of Programming Week
This project didn't get time devoted to it during
programming week, it's been rescheduled to
February/07.
32
Transition of Slicer2.x Modules to Slicer3
ModelMakerExtend ModelMaker to use MRML Color
nodes.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Nicole Aucoin, BWH (contact) Bill Lorensen, GE
(consultation)
Software Pass in a colour node to the ModelMaker
command line program, name models and colour
them according to the look up table.
This is a continuation of a previous programming
week project, see next slide.
Accomplished by end of Programming Week
This project didn't get time devoted to it during
programming week. Reloading a directory of
models requires modification of the CLI
architecture.
33
Packaging and deployment of NA-MIC Kit
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Andy Cedilnik, Kitware Katie Hayes, BWH
Packaging Improve current packaging of Slicer
and NA-MIC kit to better support the target
platforms, which are Linux, Windows, and Mac OSX.
Deployment Improve Slicer download web-site to
better support downloading appropriate packages.
Accomplished by end of Programming Week
Packaging on Mac improved to facilitate easy
uninstallation Decided on a directory hierarchy
to support Slicer2 and Slicer3
downloads Graphical upload tool to easily put
files on the server for download
34
Slicer3 Launch and PackSetting up an efficient
and workable deployment solution for Slicer3
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Define details of slicer3s launcher (order from
the current chaos). Issues quick startup,
cross-platform maintainability, finding modules,
error detection/feedback Options static builds,
C launcher, Tcl Launcher, BAT/Shell Scripts
Steve Pieper, Will Schroeder, Sebastien Barre,
Jim Miller, Bill Lorensen, Andy Cedilnik
Accomplished by end of Programming Week
  • Plan
  • a starpack solution like slicer2 uses will
    beput in place (Steve)
  • this is a fully-static executable that can be
    programmed in tcl/tk to set up the environment
    and launch/monitor the Slicer3-real process
  • Meeting took place on Friday everyone was in
    attendance.
  • Consensus
  • cannot build static since plugins may require
    any/all of vtk/itk/slicer
  • dynamic builds require launcher to find shared
    libraries
  • launcher has other benefits
  • quick splash screen
  • catch errors/crashes

35
Slicer3 and LONI Pipeline Integration
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Algorithms, Software Development Create a
workflow in LONI pipeline that wraps around a new
set of UNC shape analysis executables. Develop,
provide interface for executing the workflow on
the LONI grid. Continuation of last programming
week. Discuss Slicer3 integration, eg Pipeline
v4 batch mode operation .
Jagadeeswaran Rajendiran, UCLA (Core 2)
(r.jagadeeswaran_at_loni.ucla.edu) Martin Styner,
UNC (Algorithms) Steve Pieper, Isomics (Core 2)
Software computational speed. Intuitive user
interface.
Accomplished by end of Programming Week
Clinical Validation of results.
  • Pipeline batch mode completed, workflows can be
    executed without GUI
  • Capability to execute both locally (on your
    laptop) and on the grid completed
  • Worked on client-server, testing for scalability
    in progress
  • Worked with Martin, discussed possible
    enhancements to the data model
  • Pipeline available for alpha-testing

36
2007 Project Half Week
LONI pipeline for UNC shape analysisDeveloping
LONI pipelines for UNC shape analysis ready for
clinicians
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Algorithms create LONI pipeline modules and
network for new set of shape analysis
executables, as well as interface for running UNC
shape analysis in LONI as simple as possible.
Continuation of last programming week.
Martin Styner, UNC Michael Pan,
LONI Jagadeeswaran Rajendiran, LONI
Software Training, Extension of LONI software if
needed.
Clinical Validation of results.
Accomplished by end of Programming Week
LONI pipeline for full processing created Bug
fixing and considerable feature request
issued Top-level view encapsulating details from
users Nearly ready for Core 3 and training
core Open Issues Full encapsulation, job
distribution, Visualization of Quality Control
data and results, Validation of Results
37
Grid Interface for Slicer3Make Slicer 3 work on
a set of clusters.
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Algorithms
(algorithms) Neil Jones, UCSD (software)
(contact) Jeff Grethe, UCSD (software) Steve
Pieper, Isomics (Slicer) Bill Lorenson, GE
(CLI) Jim Miller, GE (CLI) (clinical)
Define Slicer/Gwiz interface, calling protocol,
polling interface Identify necessary changes to
Slicer3 (e.g., password collection?) Work on
existing code-level issues (e.g., code
redesign) Identify minimum protocol set (e.g.,
GSI, ssh keys, condor, sge) Agree on delivery
schedule Deliverables UML for SPI, XML schemas,
project plan with milestones
Clinical
Accomplished by end of Programming Week
Discussed using BatchMake as an underlying grid
execution technology Agreed on an overall
workflow for running tasks on a grid Code
improvements to GridWizard
Grid
XML work descriptor
Slicer

Execution model
38
Slicer3 Performance Analysis
2007 Project Half Week
Theme NA-MIC Kit
Team
Plan/Expected Challenges/Publication
Katie Hayes With Slicer 3 Team
  • Collect feedback about which areas are a priority
    for optimization
  • Use profiling tools to locate inefficient areas
    of Slicer
  • Collect feature requests

Accomplished as a result of Programming Week
  • Defined immediate goals for optimization with
    Steve, including file I/O
  • Collect feedback from developers about which
    areas are a priority for optimization
  • Compiled feature requests in Mantis for tracking
    performance issues
  • Work continues on code profiling

lt Mantis KCachegrind gt
39
Matlab-Slicer3 pipeline enhancementGeneralize
data type handling and extend to DWI and tensor
data
2007 Project Half Week
Theme NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Katharina Quintus, BWH (contact) Sylvain Bouix,
BWH Steve Pieper, Isomics Marc Niethammer,
BWH Mahnaz Maddah, MIT
Software Extend the existing pipeline to handle
more data types. Modify pipeline to handle DWI
and tensor data.
Accomplished by 01/31/2007
The involved scripts have been extended to handle
data types char, unsigned char, unsigned short,
signed int32, unsigned int32, float, and
double. Working on extending to tensor data.
40
External Collaborations
  • External Collaborations
  • Slicer3 Module for HPC deformable registration
  • Slicer3 IGT, Trackers
  • IGT Workflow for Slicer3 Interventional Imaging
  • Radiology Workstation Module for Slicer3
  • vmtk module for Slicer
  • NCBC Collaboration Hexahedral Voxel Meshing
    Slicer3
  • Voxel meshing as an execuation module in Slicer3
  • Mesh Quality Visualization Development
  • Bounding Box Projection Meshing
  • Tetrahedral Mesh Generation Tools in VTK
  • Mapped Meshing Using ITK
  • NCBC Collaboration in Preparation
  • Nonhuman Primate slicer Module (Alcohol Exposure)
  • Non-Medical Collaboration
  • Slicer Enhancements for Astronomical Data Cubes

41
Slicer3 Module for HPC deformable registration
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms Implementation/development of ITK
based rigid and non-rigid registration algorithms
for surgery planning in neurosurgery brain tumor
resections cases.
Daniel Goldberg-Zimring, BWH Jim Miller, GE Bill
Lorensen, GE
Software Computational speed, need for real time
non-rigid registration.
Clinical Validation of results.
Expected Date for Insight Journal Publication
Accomplished by end of Programming Week
Identification and testing of the parts of the
pipeline already implemented in slicer 3 rigid
registration and b-splines non-rigid
registration. These parts worked fine with the
test case. Identification of the parts of the
pipleline not yet implemented in slicer 3
geometry distortion correction and a more robust
deformable registration algorithm, perhaps
ADMIRA which is already implemented in ITK
(from J. Gees Lab at UPENN).
Preop
Intraop
Registered Preop
42
Interventional ImagingDevelop a demonstration
of real-time image display for IGT applications.
2007 Project Half Week
Theme External Collaboration
Team
Plan/Expected Challenges/Publication
Raimundo Sierra, BWH Simon DiMaio, BWH Haiying
Liu, BWH Noby Hata, BWH Stephen Aylward,
Kitware
Base Design and develop IGTBaseLogic (MRML
logging...) Lib design classes for sensor
(image, tracker, robot), patient-to-image
registration, tool calibration Module finalize
MRAblation module for MRI-guided ablation
therapy, and Neurosurgery to connect to GE- and
Brainlab- based navigation system Challenge
Design sustainable design for Lib, Strategy to
link external libraries (opentracker, IGSTK)
Accomplished by end of Programming Week
Created IGT library (Slicer3/Libs/IGT), which is
shared by IGT modules MRAblation module is back
on the module list in Slicer3 NeuroNav module is
working with opentracker NeuroNav gets tracking
data from GENav NeuroNav gets linked with IGSTK
43
Interventional ImagingDevelop a demonstration
of real-time image display for IGT applications.
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms spatio-temporal compression of a
stream of image frames for efficient
communication and display of real-time
interventional images in Slicer3 for IGT
applications.
Raimundo Sierra, BWH Simon DiMaio, BWH Haiying
Liu, BWH Noby Hata, BWH Stephen Aylward,
Kitware
Software gain understanding of Slicer3
architecture, develop demo module for real-time
imaging, drive MRML image node from incoming
image stream, source image streams via
opentracker protocol, codec transforms to
implement compression algorithms.
Clinical extend for use in Neurosugery demo
module Liu, Hata.
Expected Date for Insight Journal Publication n/a
Accomplished by end of Programming Week
  • Learned how to develop a Slicer3 module,
  • Learned how to manipulate pixel data in a
    volume,
  • Constructed module to demonstrate continuous
    image update from an OpenTracker source,
  • Identified update latencies between GUI image
    frames that need to be investigated further,
  • The screen snapshot on the right shows a
    real-time MRI image of a fiducial frame that was
    streamed using the OpenTracker library.
  • To be integrated with the IGT Library.

44
A Translation WorkstationIntegrate 3D Slicer
within a radiology clinical workstation.
2007 Project Half Week
Theme External Collaboration
Team
Plan/Expected Challenges/Publication
  • Software
  • Integration of Slicer 3 functionality into
    clinical workstation
  • Modification of Slicer 3 GUI for clinical
    efficiency

Pat Mongkolwat, Northwestern University Skip
Talbot, Northwestern University Alex Kogan,
Northwestern University
Expected Date for RSNA November 2007
Accomplished by end of Programming Week
Better understanding of Slicer 3 GUI components
and integration techniques
45
vmtk Slicer moduleIntegrate vmtk (Vascular
Modeling Toolkit) functionality within Slicer.
2007 Project Half Week
Theme External Collaboration
Team
Plan/Expected Challenges/Publication
Luca Antiga, Mario Negri Institute Jim Miller, GE
  • Software
  • automatic generation of Slicers modules from vmtk
    pipes using Slicers execution model
  • potential inclusion of selected vmtk classes into
    Slicer

Expected Date for Insight Journal Publication
July 2007
Accomplished by end of Programming Week
Any vmtk command line can now be converted to a
Slicer3 CLI module automatically. Interactive
vmtk scripts have been extended to use
command-line specified fiducials. A collection
of vmtk Slicer3 modules will be included in the
main vmtk distributions as soon as Slicer3 is
released
46
Bone MeshingIntegrate voxel based meshing tool
into Slicer3 as an execution model.
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms Convert a standard command line voxel
mesh tool into a Slicer3 module using the
execution model.
Vincent Magnotta, Iowa Ritesh Bafna, Iowa Nicole
Grosland, Iowa Steve Pieper, Isomics
(software) Curt Lisle, Isomics (software)
Accomplished by end of Programming Week
Basic voxel meshing can now be run in the Slicer3
execution model framework. Remaining issues 1.
Verify Anatomical Position of Mesh 2. Need to
modify temporary directory used by Slicer3 3.
Unstructured grids that result do not load into
Slicer3, currently extracting exterior faces
using vtkGeometryFilter()
47
Mesh Quality VisualizationDiscuss additional
features required for mesh and mesh quality
visualization.
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms Mesh quality measures that could be
implemented are edge angles, volume etc.,
Nicole Grosland, Univ of Iowa Vincent Magnotta,
Univ of Iowa Kiran Shivanna, Univ of Iowa
Steve Pieper, Isomics Inc (software) Curtis
Lisle, Isomics Inc (software)
Software Discussion of the Implementation of
mesh visualization capabilities available in
Abaqus Viewer into Slicer3. Adding a new Hex
element quality test and evaluating it against
the sample meshes available.
Accomplished by end of Programming Week
  • Initial FE Mesh Quality viewer using KWWidgets
    was developed
  • Tested viewer with new vtkMeshQuality filter to
    implement multiple tests for Hex element meshes
    (see colored meshes representing different
    quality tests)
  • Tested integration between Mesh Quality class and
    Univ. of Iowa Mesh Editor application

48
Mapped Hexahedral Mesh GenerationDiscuss the
manipulation of bounding box structure and the
implementation of the same in Slicer3.
2007 Project Half Week
Theme External Collaboration
a
Plan/Expected Challenges/Publication
Team
Algorithms Algorithms to manipulate the bounding
box structure used in mapped mesh generation have
already been developed. All the code has been
done in VTK compatible C classes.
Nicole Grosland, Univ of Iowa Vincent Magnotta,
Univ of Iowa Kiran Shivanna, Univ of Iowa Steve
Pieper, Isomics Inc (software) Curtis Lisle,
Isomics Inc (software)
Software Discussion of the implementation of the
above mentioned C classes in Slicer3.
b
c
Accomplished by end of Programming Week
Discussed the implementation of the above
mentioned algorithms in Slicer3. Diagrams
illustrate the steps involved in mapped meshing.
d
e
49
Tetrahedral Mesh Generation Methods in
VTKDiscuss the various methods available in vtk
and implementation of same in IaFeMesh
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms Algorithms available in vtk for
tetrahedral mesh generation Delaunay 3D, Ordered
Triangulator , Sliver removal and Mesh
optimization methods.
Nicole Grosland, Univ of Iowa (contact) Vincent
Magnotta, Univ of Iowa (algorithms) Srinivas
Tadepalli, Univ of Iowa (algorithms)
Software Discuss methods to Modify/Extend
existing classes necessary for Tetrahedral mesh
generation.
Accomplished by end of Programming Week
Discussed methods available in VTK for
tetrahedral mesh generation. Delaunay 3D works
for some cases but cannot avoid slivers on the
surface. Ordered triangulator is not useful in
tet mesh generation.
50
Mapped Hexahedral MeshingEvaluate the use of
multi-resolution itkfem registration for mapped
meshing
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Ritesh Bafna, Iowa Nicole Grosland, Iowa
Vincent Magnotta, Iowa Bill Lorensen, GE
(software)
Implement a multi-resolution mapped mesh
algorithm using the ITK fem framework. The
driving force will be the distance from the
template mesh to the subject surface following
the normal direction.
Accomplished by end of Programming Week
Multi-resolution was implemented using a
thin-plate spline to initialize the next level of
registration. Initial working implementation
supported two levels and has been generalized to
support N levels of refinement. Work is
continuing to develop this into a Slicer3
execution module
Before Registration
After Registration
51
Nonhuman Primate slicer ModuleAdapt EM
Segmentation algorithm and ITK/Slicer software
module for analysis of nonhuman primate
structural MRI.
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Algorithms start with the EM Segmentation
algorithm currently available in slicer3, and
refine as necessary.
Kilian Pohl, MIT (algorithms) (contact) Chris
Wyatt, VT (algorithms) Sandy Wells, BWH
(algorithms consultant)
Software
Clinical Apply to images from longitudinal
alcohol exposure study
Expected Date for Insight Journal Publication
Accomplished by end of Programming Week
Image to the left shows skull-stripping with
current technology available to Chris Wyatt. Our
goal is to generate segmentations with greater
anatomical detail. Accomplishments - discussed
general framework for primate segmentation-
conference call with PIs from Wake Forrest
Place your picture/movie here.
52
Slicer Enhancements for Astronomical Data Cubes
2007 Project Half Week
Theme External Collaboration
Plan/Expected Challenges/Publication
Team
Douglas Alan, Harvard IIC (software)
(contact) Mike Halle, BWH/IIC (software) Bill
Lorensen, GE (software) Jim Miller, GE
(software) Wendy Plesniak, BWH (software)
Software Address some of the outstanding issues
with the planned software enhancements required
to make Slicer a good quantitative tool for
visualization of astronomical data cubes.
This is a continuation of a project from the June
2006 Project Week.
Expected Date for Insight Journal Publication
TBD.
Accomplished by end of Programming Week
  • Solved problem of itkImageIOBases
    incompatibility with CFITSIOs extended filename
    syntax.
  • Identified compatibility issues present with the
    alpha version of Slicer 3.
  • Devised plan for passing a FITS WCS
    itkTransform object from the FITS ITK reader to
    the resulting VTK image in Slicer.
  • Planned incorporation of the ITK FITS reader into
    Slicer as a Slicer execution module.
  • Planned incorporation of the ITK FITS reader into
    Slicer as a dynamically loading module.
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