national alliance for medical image computing project half week january 10/12, 2007 held in...

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

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)


Structural Analysis1. ITK Spherical Wavelet Transform Filter2. UNC shape analysis with Spherical Wavelet Features 3. EMSegmenter Software Development4. Data assimilation for NAMIC5. Parallelization of ITK for deformable registration6. Integrating KWMeshVisu into Slicer7. Group-wise Registration of Medical Images8. Genus Zero Slicer3 Module9. Thickness Slicer3 Module

Diffusion Image Analysis1. Finsler Tractography2. Finsler Levelsets3. Tensor estimation and Monte-Carlo simulation 4. Rician Noise Removal in Diffusion Tensor MRI 5. ITK implementation of POIStat, and Integration into Slicer3 6. Image Format issues in application of POIStats to Dartmouth data 7. ITK Stochastic Tractography Filter

NA-MIC Kit 1. Slicer3:Architecture/Features2. Slicer3: Data Model / libMRML3. 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 Integration8. LONI Pipeline for UNC Shape Analysis9. Slicer3: Grid Integration10. Slicer3:Performance Analysis 11. Matlab-Slicer3 pipeline enhancement

Project Half Week January 10/12, 2007

NCBC Collaboration: Hexahedral Voxel Meshing Slicer31. 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 Preparation1. Nonhuman Primate slicer Module (Alcohol Exposure)

External Collaborations:1. Slicer3 Module for HPC deformable registration 2. Slicer3: IGT, Trackers3. IGT Workflow for Slicer3: Interventional Imaging4. Radiology Workstation Module for Slicer3 5. vmtk module for Slicer

Non-Medical Collaboration1. Slicer Enhancements for Astronomical Data

Cubes


Structural Analysis

Structural Analysis1. ITK Spherical Wavelet Transform Filter2. UNC shape analysis with Spherical Wavelet Features 3. EMSegmenter Software Development4. Data assimilation for NAMIC5. Parallelization of ITK for deformable registration6. Integrating KWMeshVisu into Slicer7. Group-wise Registration of Medical Images8. Genus Zero Slicer3 Module9. Thickness Slicer3 Module


ITK Spherical Wavelet Transform Filter:Develop algorithm and ITK software module for Spherical Wavelet computation

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

Plan/Expected Challenges/PublicationTeam

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

.

SWFSignal to Coeffs Filter

Coeffs to Signal FilterSWF

Paper: •To write: ITK Insight journal to be completed by the end of the week.

2007 Project Half Week

Theme: Structural Analysis


Scripts to combine UNC Shape Analysis with Spherical Wavelet Features

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 coefficientsOUTPUT: 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




EMSegmenter Software Development:Integrate EMSegmenter from Slicer 2 to Slicer 3

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 directionsBegan integrating rules into wizardAdded panel-specific helpIntinsity distribution widget: nearly completedBug fixeshttp://www.na-mic.org/Wiki/index.php/Slicer3:EM




NA-MIC Data Assimilation:Centralize the archival, analysis, and access of NA-MIC tutorial data and select project data.

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).


MIDAS



ITK Registration Parallelization:Develop implementations of ITK registration methods to take advantage of multi-core and multi-processor systems.

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.


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

Expected Date for Insight Journal Publication: August, 2007




Integrating KWMeshVisu into Slicer:

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.



We have successfully integrated KWMeshVisu into Slicer3 as a command line tool.




Group-wise Registration of Medical Images:Develop algorithm for group-wise non-rigid registration of medical images.

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.



-Incorporated B-Splines into the registration framework-Implemented multiresolution registration

Mean Images before: after:

Expected Date for Insight Journal Publication:




Genus 0 Slicer3 Module: Develop Slicer3 Module for the topological correction of labelmaps.

Marc Niethammer, BWH (contact)Sylvain Bouix, BWHSteve Pieper, Isomics

based on work bySteve Haker, BWHMichael Rabes, BWH

Algorithms: finish Slicer3 topology correction module. Fix orientation issues for model output.



Implemented command line moduleand fixed various orientation issues.




Thickness Measurement Slicer3 Module:Develop simple Slicer3 Module for thickness measurement of label maps.

Marc Niethammer, BWH (contact)Sylvain Bouix, BWHSteve Pieper, Isomics

Algorithms: Finish a simple module for thickness measurement based on boundary conditions given by a labelmap. Improve user interface.



Created command line module for slicer 3.




Diffusion Image Analysis

Diffusion Image Analysis1. Finsler Tractography2. Finsler Levelsets3. Tensor estimation and Monte-Carlo simulation 4. Rician Noise Removal in Diffusion Tensor MRI 5. ITK implementation of POIStat, and Integration into Slicer3 6. Image Format issues in application of POIStats to Dartmouth data 7. ITK Stochastic Tractography Filter


Finsler Tractography:Develop ITK filter for Finsler Tractography.

John Melonakos, GT (algorithms) (contact)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.


Accomplished by end of Programming Week-Created the itkImageDirectionalIteratorWithIndex

Expected Date for Insight Journal Publication: April 2007

Is this a continuation of a previous programming week project? If so, please include that slide as well. - NO -

Luis Ibanez, Kitware (software)

Marc Niethammer, PNL (clinical)Marek Kubicki, PNL (clinical)

-Created the itkFastSweepingImageFilter

-Created the itkFinslerTractographyImageFilter

-This project is still under development...

...


Theme: Diffusion Image Analysis


Finsler Levelsets:Develop ITK software module for levelset-based directional segmentation framework in arbitrary dimension.

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.

Clinical: Validation of neural tract segmentation.


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)

Expected Date for Insight Journal Publication: April 2007

Is this a continuation of a previous programming week project? If so, please include that slide as well. - NO -


Luis Ibanez, Kitware (software)

Marc Niethammer, PNL (clinical)Marek Kubicki, PNL (clinical)



DTI monte-carlo simulation and tensor estimation:Develop algorithm and software for monte-carlo simulation of noise effect on tensor estimation

Casey Goodlett, UNC (algorithms) (contact)Ran Tao, Utah (algorithms)Tom Fletcher, Utah (algorithms)

(software)

(clinical)

Algorithms: Compare existing existing algorithms for tensor estimation.

Software: MATLAB simulation. ITK filters for non-linear least squares, weighted least, maximum likelihood estimation.

Clinical: Validation of results in real scans



• ITK filters for tensor estimation routines• Simulated/Experimental comparison of estimationmethods


Linear Non-linear Weighted



Rician Noise Removal in DTI:Develop ITK and Slicer module for Rician noise removal in DTI.

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.




Added method for automatic threshold ofair voxels to find the Rician noise sigma.

Created Slicer plug-in module to run the filter.


Jim Miller (software)

Noisy data Filtered data



Poistats, Slicer, and ITK Integration:Further develop algorithm for integration into ITK and Slicer.

Dennis Jen, MGH (algorithms) (contact)Steve Pieper, Isomics (software)

Algorithms: Continue c++ development and adjust API as needed for integration.

Software: Compatibility with Slicer and ITK.Clinical: Validation of results.


Accomplished by end of Programming Week- wrote xml for command line interface- set Slicer path to look for poistats filter and load Poistats GUI- Slicer runs poistats!

Expected Date for Insight Journal Publication: 3/1/2007


ROIs

Path



Applying Poistats to Dartmouth Data:Generalize poistats for applying to Dartmouth data.

Dennis Jen, MGH (algorithms) (contact)

Steve Pieper, Isomics (software)Luis Ibanez, Kitware (software)

John West, Dartmouth (clinical)Andy Saykin, Dartmouth (clinical)

Algorithms: Develop current version of poistats so Darthmouth data can be run successfully.

Software: Image format incompatibility with current version of poistats.



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.

Expected Date for Insight Journal Publication: 3/1/2006




Stochastic Tractography:Develop an ITK filter to generate region connectivity probabilities.

Tri Ngo, MIT (contact)C-F Westin, LMIPolina Golland, MIT

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 resultsand enable detection of tracts which pass through regions of lowanisotropy.




Based on work by:Ola Friman and Raul San Jose

Expected Date for Insight Journal Publication: February 2007

•Finished first Implementation of Filter (results shown in left image)•Finished Slicer3 Command Line Module with GUI interface (right image)



NA-MIC Kit

NA-MIC Kit 1. Slicer3:Architecture/Features2. Slicer3: Data Model / libMRML3. 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 Integration8. LONI Pipeline for UNC Shape Analysis9. Slicer3: Grid Integration10. Slicer3:Performance Analysis 11. Matlab-Slicer3 pipeline enhancement


Slicer 3 Architecture:Allow components of Slicer 3 project to work well together.

Steve PieperBill LorensenRon KikinisMike HalleNoby HataWith Slicer 3 Team

•Plan for 3.0 Release•Improving the Stability and Performance•Completing Remaining Features•Fixing Bugs



•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


Theme: NA-MIC Kit


Data Model / libMRML:

Alex YarmarkovichSteve PieperWith Slicer 3 Team

•Collect Feedback from Developers•Identify Outstanding Bugs/Issues



• Feedback sessions were very helpful• Next focus will be on supporting DTI module with its requirements for diffusion volumes and tract bundles


Theme: NA-MIC Kit


MRML Hierarchies

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.



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.


Theme: NA-MIC Kit


Interface Design and Usability for Slicer3

Wendy Plesniak, BWHSebastien Barre, KitwareYumin Yuan, Kitware

GUI: Present and describe user interface for Slicer; Work toward completing View Control GUI functionality;Refine features according to feedback;



• Disseminated information about interface and GUI development infrastructure.• Collected feedback from users.• Prototyped View Control GUI elements (shown right) and worked on stabilizing code.


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.

Theme: NA-MIC Kit


Tractography in Slicer3:Develop Slicer software module for tractography.

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.



•MRML infrastructure for tractography.•Load/Save framework for tractography.•Initial display capabilities.•Increased understanding of slicer3 platform.

Expected Date for Insight Journal Publication: May 2007


Theme: NA-MIC Kit


DTI in Slicer3:Develop core functionality to support DTI processing and display.

Raul San Jose, BWH/LMI

Steve Pieper, Alex Yarmarkovik, IsomicsWendy Plesniak, BWHSebastien Barre, Kitware

Software: Currently supported: DTI and DWI can be I/O and MRMLnodes can be created. Redesign Volumes GUI classes to support different volumetypes with different display needs.Develop Geometry Layer infrastructure to allow therepresentation of glyphs, and in general models, in the resliced view.



Goals are:Display and interact with DWI and DTI images.Estimate DTI from DWI.Design of the Geometry Layer.

Expected Date for Insight Journal Publication: May 2007


DWI Volume loaded in the Slicer

Theme: NA-MIC Kit


Slicer3 Editor:

Steve Pieper

Sylvain BouixJohn West

•Experiment with current implementation•Identify and characterize bugs•Define needed improvements



• 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


Theme: NA-MIC Kit


Transition of Slicer2.x Modules to Slicer3: Colors

Nicole Aucoin, BWH (contact)Sebastien Barre, KitwareYumin Yuan, Kitware


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.


Plan: Subclass the vtkMRMLColorNode to create Proceduraland PieceWise colour nodes, subclass the Procedural node tocreate a FreeSurfer node. Update the ColorsGUI to handleall subclasses.

Expected Challenges: Generalising the colour nodes for easyextensibility


Theme: NA-MIC Kit


Transition of Slicer2.x Modules to Slicer3: Fiducials

Nicole Aucoin, BWH (contact)Steve Pieper, Isomics Software: Implement placing Fiducials in 3D.

Discuss how to integrate display styles.



Various picking strategies were explored for placing fiducials in 3D, but a final selectionis reliant on some architecture reorganisation to integrate event handling. Completionis projected to occur by mid-February.


Theme: NA-MIC Kit


Transition of Slicer2.x Modules to Slicer3: FreeSurferIntegration of FreeSurfer scalar overlays and colour lookup tables into Slicer3.

Nicole Aucoin, BWH (contact)Software: Extend MRML color nodes to include FreeSurfercolours. Support scalar overlays on models.



This project didn't get time devoted to it during programming week, it's been rescheduledto February/07.


Theme: NA-MIC Kit


Transition of Slicer2.x Modules to Slicer3: ModelMakerExtend ModelMaker to use MRML Color nodes.

Nicole Aucoin, BWH (contact)Bill Lorensen, GE (consultation) Software: Pass in a colour node to the ModelMaker

command line program, name models and colour themaccording to the look up table.



This project didn't get time devoted to it during programming week. Reloading a directory of models requires modification of the CLI architecture.

This is a continuation of a previous programming week project, see next slide.


Theme: NA-MIC Kit


Packaging and deployment of NA-MIC Kit

Andy Cedilnik, KitwareKatie Hayes, BWH

Packaging: Improve current packaging of Slicer and NA-MIC kitto better support the target platforms, which are Linux, Windows,and Mac OSX.



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


Deployment: Improve Slicer download web-site to better supportdownloading appropriate packages.

Theme: NA-MIC Kit


Slicer3 Launch and Pack:Setting up an efficient and workable deployment solution for Slicer3

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…



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

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


Theme: NA-MIC Kit


Slicer3 and LONI Pipeline Integration

Jagadeeswaran Rajendiran, UCLA (Core 2) ([email protected])

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.





• 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

Theme: NA-MIC Kit


LONI pipeline for UNC shape analysis:Developing LONI pipelines for UNC shape analysis ready for clinicians

Martin Styner, UNC

Michael Pan, LONIJagadeeswaran Rajendiran, LONI

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.

Software: Training, Extension of LONI software if needed.




LONI pipeline for full processing createdBug fixing and considerable feature request issuedTop-level view encapsulating details from usersNearly ready for Core 3 and training core

Open Issues: Full encapsulation, job distribution, Visualization of Quality Control data and results,Validation of Results


Theme: NA-MIC Kit


Grid Interface for Slicer3:Make Slicer 3 work on a set of clusters.

(algorithms)

Neil Jones, UCSD (software) (contact)Jeff Grethe, UCSD (software)Steve Pieper, Isomics (Slicer)Bill Lorenson, GE (CLI)Jim Miller, GE (CLI)

(clinical)

Algorithms:

Define Slicer/Gwiz interface, calling protocol, polling interfaceIdentify 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 scheduleDeliverables: UML for SPI, XML schemas, project plan with milestones

Clinical:



Accomplished by end of Programming WeekDiscussed using BatchMake as an underlying grid execution technologyAgreed on an overall workflow for running tasks on a gridCode improvements to GridWizard

Slicer

XML work descriptor

Execution model

Grid+

Theme: NA-MIC Kit


Slicer3 Performance Analysis:

Katie HayesWith Slicer 3 Team


Accomplished as a result of Programming Week

•Collect feedback about which areas are a priority for optimization•Use profiling tools to locate inefficient areas of Slicer•Collect feature requests

•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 =>


Theme: NA-MIC Kit


Matlab-Slicer3 pipeline enhancement:Generalize data type handling and extend to DWI and tensor data

Katharina Quintus, BWH (contact)Sylvain Bouix, BWHSteve Pieper, IsomicsMarc Niethammer, BWHMahnaz Maddah, MIT


Accomplished by 01/31/2007


Software: Extend the existing pipeline to handle more data types. Modify pipeline to handle DWI and tensor data.

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.

Theme: NA-MIC Kit


External Collaborations

NCBC Collaboration: Hexahedral Voxel Meshing Slicer31. 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 Preparation1. Nonhuman Primate slicer Module (Alcohol Exposure)

External Collaborations:1. Slicer3 Module for HPC deformable registration 2. Slicer3: IGT, Trackers3. IGT Workflow for Slicer3: Interventional Imaging4. Radiology Workstation Module for Slicer3 5. vmtk module for Slicer

Non-Medical Collaboration1. Slicer Enhancements for Astronomical Data Cubes


Slicer3 Module for HPC deformable registration

Daniel Goldberg-Zimring, BWHJim Miller, GEBill Lorensen, GE

Algorithms: Implementation/development of ITK based rigid and non-rigid registration algorithms for surgery planning in neurosurgery brain tumor resections cases.

Software: Computational speed, need for real time non-rigid registration.



Accomplished by end of Programming WeekIdentification 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).



Preop Intraop Registered Preop

Theme: External Collaboration


Interventional Imaging:Develop a demonstration of real-time image display for IGT applications.

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 linkexternal libraries (opentracker, IGSTK)




Created IGT library (Slicer3/Libs/IGT), which is shared by IGT modulesMRAblation module is back on the module list in Slicer3NeuroNav module is working with opentrackerNeuroNav gets tracking data from GENavNeuroNav gets linked with IGSTK



Interventional Imaging:Develop a demonstration of real-time image display for IGT applications.

Raimundo Sierra, BWH Simon DiMaio, BWHHaiying Liu, BWHNoby 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 demomodule 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].


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.

Expected Date for Insight Journal Publication: n/a




A Translation Workstation:Integrate 3D Slicer within a radiology clinical workstation.

Pat Mongkolwat, Northwestern UniversitySkip Talbot, Northwestern UniversityAlex Kogan, Northwestern University

Software: •Integration of Slicer 3 functionality into clinical workstation•Modification of Slicer 3 GUI for clinical efficiency



Better understanding of Slicer 3 GUI components and integration techniques

Expected Date for RSNA: November 2007




vmtk Slicer module:Integrate vmtk (Vascular Modeling Toolkit) functionality within Slicer.

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



Any vmtk command line can now be convertedto a Slicer3 CLI module automatically.

Interactive vmtk scripts have been extended touse command-line specified fiducials.

A collection of vmtk Slicer3 modules will be includedin the main vmtk distributions as soon as Slicer3 is released

Expected Date for Insight Journal Publication: July 2007




Bone Meshing:Integrate voxel based meshing tool into Slicer3 as an execution model.

Vincent Magnotta, IowaRitesh Bafna, Iowa Nicole Grosland, Iowa

Steve Pieper, Isomics (software)Curt Lisle, Isomics (software)

Algorithms: Convert a standard command line voxel mesh tool into a Slicer3 module using the execution model.



Basic voxel meshing can now be run in the Slicer3 execution model framework.

Remaining issues:1. Verify Anatomical Position of Mesh2. Need to modify temporary directory used by Slicer33. Unstructured grids that result do not load into Slicer3, currently extracting exterior faces using vtkGeometryFilter()




Mesh Quality Visualization:Discuss additional features required for mesh and mesh quality visualization.

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 thesample meshes available.



• 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




Mapped Hexahedral Mesh Generation:Discuss the manipulation of bounding box structure and the implementation of the same in Slicer3.

Nicole Grosland, Univ of IowaVincent Magnotta, Univ of Iowa Kiran Shivanna, Univ of Iowa

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.



Discussed the implementation of the above mentioned algorithms in Slicer3. Diagrams illustrate the steps involved in mapped meshing.


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Tetrahedral Mesh Generation Methods in VTKDiscuss the various methods available in vtk and implementation of same in IaFeMesh

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 generationDelaunay 3D, Ordered Triangulator , Sliver removal and Mesh optimization methods.

Software: Discuss methods to Modify/Extend existing classes necessary forTetrahedral mesh generation.




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.



Mapped Hexahedral Meshing:Evaluate the use of multi-resolution itk::fem registration for mapped meshing

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.



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




Nonhuman Primate slicer Module:Adapt EM Segmentation algorithm and ITK/Slicer software module for analysis of nonhuman primate structural MRI.

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



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.





Slicer Enhancements for Astronomical Data Cubes

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.



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.

Expected Date for Insight Journal Publication: TBD.

This is a continuation of a project from the June 2006 Project Week.



national alliance for medical image computing project half week january 10/12, 2007 held in...

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