Project Half Week January 10/12, 2007
Held 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)
National Alliance for Medical Image Computing
http://na-mic.org
Project Half Week January 10/12, 2007
Structural Analysis
1.
2.
3.
4.
5.
6.
7.
8.
9.
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:
1.
Slicer3 Module for HPC deformable registration
2.
Slicer3: IGT, Trackers
3.
IGT Workflow for Slicer3: Interventional Imaging
4.
Radiology Workstation Module for Slicer3
5.
vmtk module for Slicer
Diffusion Image Analysis
1.
2.
3.
4.
5.
6.
7.
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
NA-MIC Kit
1.
Slicer3:Architecture/Features
2.
Slicer3: Data Model / libMRML
3.
Slicer3: Interface Design and Usability
4.
Slicer3: Modules for DTMRI,Tractography,Editor, Colors,
Fiducials, FreeSurfer, ModelMaker
5.
Build/Test/Deploy System
6.
Slicer3 launch and deployment issues
7.
Slicer3: LONI Pipeline Integration
8.
LONI Pipeline for UNC Shape Analysis
9.
Slicer3: Grid Integration
10.
Slicer3:Performance Analysis
11.
Matlab-Slicer3 pipeline enhancement
National Alliance for Medical Image Computing
http://na-mic.org
NCBC Collaboration: Hexahedral Voxel Meshing Slicer3
1.
Voxel meshing as an execuation module in Slicer3
2.
Mesh Quality Visualization Development
3.
Bounding Box Projection Meshing
4.
Tetrahedral Mesh Generation Tools in VTK
5.
Mapped Meshing Using ITK
NCBC Collaboration in Preparation
1.
Nonhuman Primate slicer Module (Alcohol Exposure)
Non-Medical Collaboration
1.
Slicer Enhancements for Astronomical Data
Cubes
Structural Analysis
Structural Analysis
1.
2.
3.
4.
5.
6.
7.
8.
9.
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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
ITK Spherical Wavelet Transform Filter:
Develop algorithm and ITK software module for Spherical Wavelet computation
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Delphine Nain, GT (algorithms)
Yi Gao, GT (algorithms)
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.
Luis Ibanez, Kitware (software)
Jim Miller, GE (software)
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
Coeffs to Signal Filter
National Alliance for Medical Image Computing
http://na-mic.org
SWF
2007 Project Half Week
Scripts to combine UNC Shape Analysis with Spherical Wavelet
Features
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
National Alliance for Medical Image Computing
http://na-mic.org
EMSegmenter
Software Development:
Integrate EMSegmenter from Slicer 2 to Slicer 3
2007 Project Half Week
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Kilian Pohl, BWH-MIT (algorithms) (contact)
Brad Davis, Kitware (software) (contact)
Sebastien Bare, Kitware (software)
Yumin Yuan, Kitware (software)
Marc Niethammer , BWH (clinical)
Algorithm: Work on user interface of
EMSegmenter in Slicer3 including bug
fixes and new functionality.
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-mic.org/Wiki/index.php/Slicer3:EM
National Alliance for Medical Image Computing
http://na-mic.org
NA-MIC Data Assimilation:
2007 Project Half Week
Centralize the archival, analysis, and access of NA-MIC tutorial data and select project data.
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Stephen Aylward, Kitware (Data/Software) (contact)
Steve Pieper, Isomics (Data)
Julien Jomier, Kitware (software)
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.
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 Pohl’s MR/MR head registration data
• Killian Pohl’s CT/CT abdominal registration data
• Steve Pieper’s 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).
National Alliance for Medical Image Computing
http://na-mic.org
MIDAS
ITK Registration Parallelization:
2007 Project Half Week
Develop implementations of ITK registration methods to take advantage of multi-core and multi-processor systems.
Theme: Structural Analysis
Team
Plan/Expected Challenges/Publication
Stephen Aylward, Kitware (Algorithms/Software) (contact) Algorithms: Identify ITK registration methods, specify component
Jim Miller, GE (Algorithms)
tests, collect test data. Challenge: Test speed and maintain accuracy
Ross Whitaker, Utah (Algorithms)
Software: Identify/develop cross-platform timing system, implement
Luis Ibanez, Kitware (Algorithms/Software)
component tests, centralize data and results, identify bottlenecks,
Driving problems:
parallelize and re-test. Challenge: Cross-platform multi-threaded timing
Kilian Pohl, BWH-MIT (Inter-subject mapping)
Driving Problem: Validation of results.
Steve Pieper, Isomics (fMRI to high-res MRI)
Sandy Wells, MIT (EPI/MRI)
Expected Date for Insight Journal Publication: August, 2007
Sylvain Bouix, BWH (DTI component registration)
Accomplished by end of Programming Week
•
•
•
•
•
Driving problem will be Killian Pohl’s 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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Integrating KWMeshVisu into Slicer:
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Ipek Oguz, UNC (algorithms) (contact)
Martin Styner, UNC (algorithms)
Sebastien Barre, Kitware (software)
Jim Miller, GE (software)
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
MICCAI’06 issue.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Group-wise Registration of Medical Images:
Develop algorithm for group-wise non-rigid registration of medical images.
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Serdar K Balci, MIT (algorithms)
Polina Golland, MIT (algorithms)
Mert R Sabuncu, MIT (algorithms)
Lilla Zollei, MIT (collaborator)
Sandy Wells, MIT (algorithms)
Luis Ibanez, Kitware (software)
Algorithms: Apply non-rigid and multi-resolution registration currently
available in ITK to group-wise registration framework.
Software: computational speed, parallel
programming.
Clinical: Validation of results.
Expected Date for Insight Journal Publication:
Accomplished by end of Programming Week
-Incorporated B-Splines into the
registration framework
-Implemented multiresolution registration
National Alliance for Medical Image Computing
http://na-mic.org
Mean Images
before:
after:
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
Marc Niethammer, BWH (contact)
Sylvain Bouix, BWH
Steve Pieper, Isomics
Algorithms: finish Slicer3 topology correction module. Fix orientation
issues for model output.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Thickness Measurement Slicer3 Module:
Develop simple Slicer3 Module for thickness measurement of label maps.
Theme: Structural Analysis
Plan/Expected Challenges/Publication
Team
Marc Niethammer, BWH (contact)
Sylvain Bouix, BWH
Steve Pieper, Isomics
Algorithms: Finish a simple module for thickness measurement based
on boundary conditions given by a labelmap. Improve user interface.
Accomplished by end of Programming Week
Created command line module for slicer 3.
National Alliance for Medical Image Computing
http://na-mic.org
Diffusion Image Analysis
Diffusion Image Analysis
1.
2.
3.
4.
5.
6.
7.
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
National Alliance for Medical Image Computing
http://na-mic.org
Finsler Tractography:
Develop ITK filter for Finsler Tractography.
2007 Project Half Week
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Luis Ibanez, Kitware (software)
Algorithms: Dynamical programming formulation of directional open
curve segmentation using a Finsler metric.
Software: Incorporation into an ITK filter. Addition of
itkImageDirectionalIteratorWithIndex to ITK.
Clinical: Validation of neural tract segmentation.
Marc Niethammer, PNL (clinical)
Marek Kubicki, PNL (clinical)
Is this a continuation of a previous programming week project? If so,
please include that slide as well. - NO -
John Melonakos, GT (algorithms) (contact)
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...
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Finsler Levelsets:
Develop ITK software module for levelset-based directional segmentation framework in arbitrary dimension.
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Vandana Mohan, GT (algorithms) (contact)
John Melonakos, GT (algorithms)
Algorithms: Directional levelset segmentation of DWI datasets using a
surface evolution.
Software: Incorporation into ITK for arbitrary dimensions.
Luis Ibanez, Kitware (software)
Clinical: Validation of neural tract segmentation.
Marc Niethammer, PNL (clinical)
Marek Kubicki, PNL (clinical)
Is this a continuation of a previous programming week project? If so,
please include that slide as well. - NO 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)
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
DTI monte-carlo simulation and tensor estimation:
Develop algorithm and software for monte-carlo simulation of noise effect on tensor estimation
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Casey Goodlett, UNC (algorithms) (contact)
Ran Tao, Utah (algorithms)
Tom Fletcher, Utah (algorithms)
(software)
Algorithms: Compare existing existing algorithms for tensor
estimation.
Software: MATLAB simulation. ITK filters for non-linear least squares,
weighted least, maximum likelihood estimation.
(clinical)
Clinical: Validation of results in real scans
Accomplished by end of Programming Week
• ITK filters for tensor estimation routines
• Simulated/Experimental comparison of estimation
methods
National Alliance for Medical Image Computing
http://na-mic.org
Linear
Non-linear
Weighted
2007 Project Half Week
Rician Noise Removal in DTI:
Develop ITK and Slicer module for Rician noise removal in DTI.
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Tom Fletcher, Utah (algorithms) (contact)
McKay Davis, Utah (algorithms)
Algorithm: DTI Rician noise removal as described in Basu, et al
MICCAI 2006. Add method to compute noise sigma from data.
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
National Alliance for Medical Image Computing
http://na-mic.org
Filtered data
2007 Project Half Week
Poistats, Slicer, and ITK Integration:
Further develop algorithm for integration into ITK and Slicer.
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Algorithms: Continue c++ development and adjust API as needed for
integration.
Software: Compatibility with Slicer and ITK.
Clinical: Validation of results.
Expected Date for Insight Journal Publication: 3/1/2007
Dennis Jen, MGH (algorithms) (contact)
Steve Pieper, Isomics (software)
Accomplished by end of Programming We
- wrote xml for command line interface
- set Slicer path to look for poistats filter and load
Poistats GUI
- Slicer runs poistats!
ROIs
Path
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Applying Poistats to Dartmouth Data:
Generalize poistats for applying to Dartmouth data.
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Dennis Jen, MGH (algorithms) (contact)
Algorithms: Develop current version of poistats so Darthmouth data
can be run successfully.
Steve Pieper, Isomics (software)
Luis Ibanez, Kitware (software)
Software: Image format incompatibility with current version of poistats.
John West, Dartmouth (clinical)
Andy Saykin, Dartmouth (clinical)
Clinical: Validation of results.
Expected Date for Insight Journal Publication: 3/1/2006
Accomplished by end of Programming Week
- Poistats reads in tensors stored symmetrically, as team/tend outputs them
- John trained on poistats usage, expected input, output, etc.
National Alliance for Medical Image Computing
http://na-mic.org
Stochastic Tractography:
Develop an ITK filter to generate region connectivity probabilities.
2007 Project Half Week
Theme: Diffusion Image Analysis
Plan/Expected Challenges/Publication
Team
Tri Ngo, MIT (contact)
C-F Westin, LMI
Polina Golland, MIT
Based on work by:
Ola Friman and Raul San Jose
Algorithms: Calculate the probability that two brain regions are
connected via a fiber tract given the measurements in a DWI dataset.
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.
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)
National Alliance for Medical Image Computing
http://na-mic.org
NA-MIC Kit
NA-MIC Kit
1. Slicer3:Architecture/Features
2.
Slicer3: Data Model / libMRML
3.
Slicer3: Interface Design and Usability
4.
Slicer3: Modules for DTMRI,Tractography,Editor, Colors, Fiducials,
FreeSurfer, ModelMaker
5.
Build/Test/Deploy System
6. Slicer3 launch and deployment issues
7.
Slicer3: LONI Pipeline Integration
8.
LONI Pipeline for UNC Shape Analysis
9.
Slicer3: Grid Integration
10. Slicer3:Performance Analysis
11. Matlab-Slicer3 pipeline enhancement
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Slicer 3 Architecture:
Allow components of Slicer 3 project to work well together.
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
•Much debugging was done as part of programming week
•The program is proving to be pretty stable
National Alliance for Medical Image Computing
http://na-mic.org
in June (3.1)
2007 Project Half Week
Data Model / libMRML:
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
diffusion volumes and tract bundles
National Alliance for Medical Image Computing
http://na-mic.org
for
2007 Project Half Week
MRML Hierarchies
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Alex Yarmarkovich (Isomics),
Lauren O’Donnell (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
O’Donnell). 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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Interface Design and Usability for Slicer3
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Tractography in Slicer3:
Develop Slicer software module for tractography.
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Lauren O’Donnell, BWH/LMI/MIT (algorithms/software)
(contact)
Steve Pieper, Isomics (software)
Alex Yarmarkovitch, BWH (software)
Wendy Plesniak, BWH (software)
Alex Golby, Marek Kubicki, BWH (clinical)
Algorithms: Tractography module in future can provide a base for
algorithmic experimentation.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
DTI in Slicer3:
Develop core functionality to support DTI processing and display.
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Raul San Jose, BWH/LMI
Steve Pieper, Alex Yarmarkovik, Isomics
Wendy Plesniak, BWH
Sebastien Barre, Kitware
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.
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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Slicer3 Editor:
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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Transition of Slicer2.x Modules to Slicer3: Colors
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Nicole Aucoin, BWH (contact)
Sebastien Barre, Kitware
Yumin Yuan, Kitware
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
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Transition of Slicer2.x Modules to Slicer3: Fiducials
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Transition of Slicer2.x Modules to Slicer3: FreeSurfer
Integration of FreeSurfer scalar overlays and colour lookup tables into Slicer3.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Transition of Slicer2.x Modules to Slicer3: ModelMaker
Extend ModelMaker to use MRML Color nodes.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Packaging and deployment of NA-MIC Kit
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
National Alliance for Medical Image Computing
http://na-mic.org
Slicer3 Launch and Pack:
Setting up an efficient and workable deployment solution for Slicer3
2007 Project Half Week
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Steve Pieper, Will Schroeder, Sebastien Barre, Jim
Miller, Bill Lorensen, Andy Cedilnik
Define details of slicer3’s 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…
Accomplished by end of Programming Week
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
National Alliance for Medical Image Computing
http://na-mic.org
Plan:
• a starpack solution like slicer2 uses will be
put 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
2007 Project Half Week
Slicer3 and LONI Pipeline Integration
Theme: NA-MIC Kit
Plan/Expected Challenges/Publication
Team
Jagadeeswaran Rajendiran, UCLA (Core 2)
(r.jagadeeswaran@loni.ucla.edu)
Martin Styner, UNC (Algorithms)
Steve Pieper, Isomics (Core 2)
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
. 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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
LONI pipeline for UNC shape analysis:
Developing 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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Grid Interface for Slicer3:
Make Slicer 3 work on a set of clusters.
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)
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:
(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
XML work descriptor
Slicer
+
Execution model
National Alliance for Medical Image Computing
http://na-mic.org
Grid
2007 Project Half Week
Slicer3 Performance Analysis:
Theme: NA-MIC Kit
Team
Plan/Expected Challenges/Publication
•Collect feedback about which areas are a priority for optimization
•Use profiling tools to locate inefficient areas of Slicer
•Collect feature requests
Katie Hayes
With Slicer 3 Team
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
<= Mantis
KCachegrind =>
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Matlab-Slicer3 pipeline enhancement:
Generalize data type handling and extend to DWI and tensor data
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.
National Alliance for Medical Image Computing
http://na-mic.org
External Collaborations
External Collaborations:
1.
Slicer3 Module for HPC deformable registration
2. Slicer3: IGT, Trackers
3.
IGT Workflow for Slicer3: Interventional Imaging
4.
Radiology Workstation Module for Slicer3
5.
vmtk module for Slicer
NCBC Collaboration: Hexahedral Voxel Meshing Slicer3
1. Voxel meshing as an execuation module in Slicer3
2.
Mesh Quality Visualization Development
3.
Bounding Box Projection Meshing
4.
Tetrahedral Mesh Generation Tools in VTK
5.
Mapped Meshing Using ITK
NCBC Collaboration in Preparation
1.
Nonhuman Primate slicer Module (Alcohol Exposure)
Non-Medical Collaboration
1.
Slicer Enhancements for Astronomical Data Cubes
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Slicer3 Module for HPC deformable registration
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
Daniel Goldberg-Zimring, BWH
Jim Miller, GE
Bill Lorensen, GE
Algorithms: Implementation/development of ITK based rigid and nonrigid registration algorithms for surgery planning in neurosurgery brain
tumor resections cases.
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. Gee’s Lab at UPENN).
National Alliance for Medical Image Computing
http://na-mic.org
Preop
Intraop
Registered Preop
Interventional Imaging:
Develop a demonstration of real-time image display for IGT applications.
Team
2007 Project Half Week
Theme: External Collaboration
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 Brainlabbased 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
National Alliance for Medical Image Computing
http://na-mic.org
Interventional Imaging:
Develop a demonstration of real-time image display for IGT applications.
2007 Project Half Week
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
Raimundo Sierra, BWH
Simon DiMaio, BWH
Haiying Liu, BWH
Noby Hata, BWH
Stephen Aylward, Kitware
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.
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.
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
A Translation Workstation:
Integrate 3D Slicer within a radiology clinical workstation.
Team
Theme: External Collaboration
Plan/Expected Challenges/Publication
Pat Mongkolwat, Northwestern University
Skip Talbot, Northwestern University
Alex Kogan, Northwestern University
Software:
•Integration of Slicer 3 functionality into clinical workstation
•Modification of Slicer 3 GUI for clinical efficiency
Expected Date for RSNA: November 2007
Accomplished by end of Programming Week
Better understanding of Slicer 3 GUI components and
integration techniques
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
vmtk Slicer module:
Integrate vmtk (Vascular Modeling Toolkit) functionality within Slicer.
Team
Theme: External Collaboration
Plan/Expected Challenges/Publication
Luca Antiga, Mario Negri Institute
Jim Miller, GE
Software:
•automatic generation of Slicers modules from vmtk pipes using Slicer’s
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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Bone Meshing:
Integrate voxel based meshing tool into Slicer3 as an execution model.
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
Vincent Magnotta, Iowa
Ritesh Bafna, Iowa
Nicole Grosland, Iowa
Algorithms: Convert a standard command line voxel mesh tool into a
Slicer3 module using the execution model.
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()
National Alliance for Medical Image Computing
http://na-mic.org
Mesh Quality Visualization:
Discuss additional features required for mesh and mesh quality visualization.
2007 Project Half Week
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
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)
Algorithms: Mesh quality measures that could be implemented are
edge angles, volume etc.,
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
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Mapped Hexahedral Mesh Generation:
Discuss the manipulation of bounding box structure and the implementation of the same in Slicer3.
Theme: External Collaboration
a
Plan/Expected Challenges/Publication
Team
Nicole Grosland, Univ of Iowa
Vincent Magnotta, Univ of Iowa
Kiran Shivanna, Univ of Iowa
b
Steve Pieper, Isomics Inc (software)
Curtis Lisle, Isomics Inc (software)
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.
Software: Discussion of the implementation of the above mentioned
C++ classes in Slicer3.
c
Accomplished by end of Programming Week
d
Discussed the implementation of the
above mentioned algorithms in Slicer3.
Diagrams illustrate the steps involved in
mapped meshing.
e
National Alliance for Medical Image Computing
http://na-mic.org
2007 Project Half Week
Tetrahedral Mesh Generation Methods in VTK
Discuss the various methods available in vtk and implementation of same in IaFeMesh
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
Nicole Grosland, Univ of Iowa (contact)
Vincent Magnotta, Univ of Iowa (algorithms)
Srinivas Tadepalli, Univ of Iowa (algorithms)
Algorithms: Algorithms available in vtk for tetrahedral mesh generation
Delaunay 3D, Ordered Triangulator , Sliver removal and Mesh
optimization methods.
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.
National Alliance for Medical Image Computing
http://na-mic.org
Mapped Hexahedral Meshing:
Evaluate the use of multi-resolution itk::fem 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
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.
Bill Lorensen, GE (software)
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
National Alliance for Medical Image Computing
http://na-mic.org
After Registration
2007 Project Half Week
Nonhuman Primate slicer Module:
Adapt EM Segmentation algorithm and ITK/Slicer software module for analysis of nonhuman primate structural MRI.
Theme: External Collaboration
Plan/Expected Challenges/Publication
Team
Kilian Pohl, MIT (algorithms) (contact)
Chris Wyatt, VT (algorithms)
Sandy Wells, BWH (algorithms consultant)
Algorithms: start with the EM Segmentation algorithm currently
available in slicer3, and refine as necessary.
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
National Alliance for Medical Image Computing
http://na-mic.org
Place your picture/movie here.
2007 Project Half Week
Slicer Enhancements for Astronomical Data Cubes
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 itk::ImageIOBase’s incompatibility with CFITSIO’s “extended filename syntax”.
Identified compatibility issues present with the alpha version of Slicer 3.
Devised plan for passing a FITS WCS itk::Transform 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.
National Alliance for Medical Image Computing
http://na-mic.org