National Alliance for Medical Image Computing 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 Structural Analysis 1.ITK Spherical Wavelet Transform FilterITK Spherical Wavelet Transform Filter 2.UNC shape analysis with Spherical Wavelet FeaturesUNC shape analysis with Spherical Wavelet Features 3.EMSegmenter Software DevelopmentEMSegmenter Software Development 4.Data assimilation for NAMICData assimilation for NAMIC 5.Parallelization of ITK for deformable registrationParallelization of ITK for deformable registration 6.Integrating KWMeshVisu into SlicerIntegrating KWMeshVisu into Slicer 7.Group-wise Registration of Medical ImagesGroup-wise Registration of Medical Images 8.Genus Zero Slicer3 ModuleGenus Zero Slicer3 Module 9.Thickness Slicer3 ModuleThickness Slicer3 Module Diffusion Image Analysis 1.Finsler TractographyFinsler Tractography 2.Finsler LevelsetsFinsler Levelsets 3.Tensor estimation and Monte-Carlo simulationTensor estimation and Monte-Carlo simulation 4.Rician Noise Removal in Diffusion Tensor MRIRician Noise Removal in Diffusion Tensor MRI 5.ITK implementation of POIStat, and Integration into Slicer3ITK implementation of POIStat, and Integration into Slicer3 6.Image Format issues in application of POIStats to Dartmouth dataImage Format issues in application of POIStats to Dartmouth data 7.ITK Stochastic Tractography FilterITK Stochastic Tractography Filter NA-MIC Kit 1.Slicer3:Architecture/FeaturesSlicer3:Architecture/Features 2.Slicer3: Data Model / libMRMLSlicer3: Data Model / libMRML 3.Slicer3: Interface Design and UsabilitySlicer3: Interface Design and Usability 4.Slicer3: Modules for DTMRI,Tractography,Editor, Colors, Fiducials, FreeSurfer, ModelMakerDTMRITractographyEditorColors FiducialsFreeSurfer ModelMaker 5.Build/Test/Deploy SystemBuild/Test/Deploy System 6.Slicer3 launch and deployment issuesSlicer3 launch and deployment issues 7.Slicer3: LONI Pipeline IntegrationSlicer3: LONI Pipeline Integration 8.LONI Pipeline for UNC Shape AnalysisLONI Pipeline for UNC Shape Analysis 9.Slicer3: Grid IntegrationSlicer3: Grid Integration 10.Slicer3:Performance AnalysisSlicer3:Performance Analysis 11.Matlab-Slicer3 pipeline enhancementMatlab-Slicer3 pipeline enhancement Project Half Week January 10/12, 2007 NCBC Collaboration: Hexahedral Voxel Meshing Slicer3 1.Voxel meshing as an execuation module in Slicer3Voxel meshing as an execuation module in Slicer3 2.Mesh Quality Visualization DevelopmentMesh Quality Visualization Development 3.Bounding Box Projection MeshingBounding Box Projection Meshing 4.Tetrahedral Mesh Generation Tools in VTKTetrahedral Mesh Generation Tools in VTK 5.Mapped Meshing Using ITKMapped Meshing Using ITK NCBC Collaboration in Preparation 1.Nonhuman Primate slicer Module (Alcohol Exposure)Nonhuman Primate slicer Module (Alcohol Exposure) External Collaborations: 1.Slicer3 Module for HPC deformable registrationSlicer3 Module for HPC deformable registration 2.Slicer3: IGT, TrackersSlicer3: IGT, Trackers 3.IGT Workflow for Slicer3: Interventional ImagingIGT Workflow for Slicer3: Interventional Imaging 4.Radiology Workstation Module for Slicer3Radiology Workstation Module for Slicer3 5.vmtk module for Slicervmtk module for Slicer Non-Medical Collaboration 1.Slicer Enhancements for Astronomical Data CubesSlicer Enhancements for Astronomical Data Cubes

National Alliance for Medical Image Computing Structural Analysis 1.ITK Spherical Wavelet Transform FilterITK Spherical Wavelet Transform Filter 2.UNC shape analysis with Spherical Wavelet FeaturesUNC shape analysis with Spherical Wavelet Features 3.EMSegmenter Software DevelopmentEMSegmenter Software Development 4.Data assimilation for NAMICData assimilation for NAMIC 5.Parallelization of ITK for deformable registrationParallelization of ITK for deformable registration 6.Integrating KWMeshVisu into SlicerIntegrating KWMeshVisu into Slicer 7.Group-wise Registration of Medical ImagesGroup-wise Registration of Medical Images 8.Genus Zero Slicer3 ModuleGenus Zero Slicer3 Module 9.Thickness Slicer3 ModuleThickness Slicer3 Module

National Alliance for Medical Image Computing 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/Publication Team 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 SWF Paper: To write: ITK Insight journal to be completed by the end of the week Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing 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 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 Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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) Project Half Week MIDAS Theme: Structural Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/PublicationTeam 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, Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week We have successfully integrated KWMeshVisu into Slicer3 as a command line tool Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week -Incorporated B-Splines into the registration framework -Implemented multiresolution registration Mean Images before: after: Expected Date for Insight Journal Publication: 2007 Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing Genus 0 Slicer3 Module: Develop Slicer3 Module for the topological correction of labelmaps. Marc Niethammer, BWH (contact) Sylvain Bouix, BWH Steve Pieper, Isomics based on work by Steve Haker, BWH Michael Rabes, BWH Algorithms: finish Slicer3 topology correction module. Fix orientation issues for model output. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week Implemented command line module and fixed various orientation issues Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing Thickness Measurement Slicer3 Module: Develop simple Slicer3 Module for thickness measurement of label maps. 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. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week Created command line module for slicer Project Half Week Theme: Structural Analysis

National Alliance for Medical Image Computing Diffusion Image Analysis 1.Finsler TractographyFinsler Tractography 2.Finsler LevelsetsFinsler Levelsets 3.Tensor estimation and Monte-Carlo simulationTensor estimation and Monte-Carlo simulation 4.Rician Noise Removal in Diffusion Tensor MRIRician Noise Removal in Diffusion Tensor MRI 5.ITK implementation of POIStat, and Integration into Slicer3ITK implementation of POIStat, and Integration into Slicer3 6.Image Format issues in application of POIStats to Dartmouth dataImage Format issues in application of POIStats to Dartmouth data 7.ITK Stochastic Tractography FilterITK Stochastic Tractography Filter

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 Project Half Week Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 Project Half Week Luis Ibanez, Kitware (software) Marc Niethammer, PNL (clinical) Marek Kubicki, PNL (clinical) Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing 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 Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week ITK filters for tensor estimation routines Simulated/Experimental comparison of estimation methods 2007 Project Half Week Linear Non-linearWeighted Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing 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 Add method to compute noise sigma from data. Software: Integration into Slicer. Clinical: Validation of results. Plan/Expected Challenges/Publication Team 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 Project Half Week Jim Miller (software) Noisy data Filtered data Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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/ Project Half Week ROIs Path Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing 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. Clinical: Validation of results. Plan/Expected Challenges/Publication Team 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/ Project Half Week Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing Stochastic Tractography: Develop an ITK filter to generate region connectivity probabilities. Tri Ngo, MIT (contact) C-F Westin, LMI Polina 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 results and enable detection of tracts which pass through regions of low anisotropy. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week 2007 Project Half Week 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) Theme: Diffusion Image Analysis

National Alliance for Medical Image Computing NA-MIC Kit 1.Slicer3:Architecture/FeaturesSlicer3:Architecture/Features 2.Slicer3: Data Model / libMRMLSlicer3: Data Model / libMRML 3.Slicer3: Interface Design and UsabilitySlicer3: Interface Design and Usability 4.Slicer3: Modules for DTMRI,Tractography,Editor, Colors, Fiducials, FreeSurfer, ModelMakerDTMRITractographyEditorColorsFiducials FreeSurfer ModelMaker 5.Build/Test/Deploy SystemBuild/Test/Deploy System 6.Slicer3 launch and deployment issuesSlicer3 launch and deployment issues 7.Slicer3: LONI Pipeline IntegrationSlicer3: LONI Pipeline Integration 8.LONI Pipeline for UNC Shape AnalysisLONI Pipeline for UNC Shape Analysis 9.Slicer3: Grid IntegrationSlicer3: Grid Integration 10.Slicer3:Performance AnalysisSlicer3:Performance Analysis 11.Matlab-Slicer3 pipeline enhancementMatlab-Slicer3 pipeline enhancement

National Alliance for Medical Image Computing Slicer 3 Architecture: Allow components of Slicer 3 project to work well together. 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 Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Data Model / libMRML: Alex Yarmarkovich Steve Pieper With Slicer 3 Team Collect Feedback from Developers Identify Outstanding Bugs/Issues Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Interface Design and Usability for Slicer3 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; Plan/Expected Challenges/Publication Team 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 Project Half Week 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

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week MRML infrastructure for tractography. Load/Save framework for tractography. Initial display capabilities. Increased understanding of slicer3 platform. Expected Date for Insight Journal Publication: May Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing DTI in Slicer3: Develop core functionality to support DTI processing and display. 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. Plan/Expected Challenges/Publication Team 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. Expected Date for Insight Journal Publication: May Project Half Week DWI Volume loaded in the Slicer Theme: NA-MIC Kit

National Alliance for Medical Image Computing Slicer3 Editor: Steve Pieper Sylvain Bouix John West Experiment with current implementation Identify and characterize bugs Define needed improvements Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Transition of Slicer2.x Modules to Slicer3: Colors Nicole Aucoin, BWH (contact) Sebastien Barre, Kitware Yumin Yuan, Kitware Plan/Expected Challenges/Publication Team 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 Project Half Week 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 Theme: NA-MIC Kit

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Transition of Slicer2.x Modules to Slicer3: FreeSurfer Integration of FreeSurfer scalar overlays and colour lookup tables into Slicer3. Nicole Aucoin, BWH (contact) Software: Extend MRML color nodes to include FreeSurfer colours. Support scalar overlays on models. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week This project didn't get time devoted to it during programming week, it's been rescheduled to February/ Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Transition of Slicer2.x Modules to Slicer3: ModelMaker Extend 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 them according to the look up table. Plan/Expected Challenges/Publication Team 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. This is a continuation of a previous programming week project, see next slide Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Packaging and deployment of NA-MIC Kit 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. Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Deployment: Improve Slicer download web-site to better support downloading appropriate packages. Theme: NA-MIC Kit

National Alliance for Medical Image Computing 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… Plan/Expected Challenges/Publication Team 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 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 Theme: NA-MIC Kit

National Alliance for Medical Image Computing Slicer3 and LONI Pipeline Integration Jagadeeswaran Rajendiran, UCLA (Core 2) 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. Clinical: Validation of results. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week 2007 Project Half Week 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

National Alliance for Medical Image Computing LONI pipeline for UNC shape analysis : Developing LONI pipelines for UNC shape analysis ready for clinicians Martin Styner, UNC Michael Pan, LONI Jagadeeswaran 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. Clinical: Validation of results. Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing 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 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: Plan/Expected Challenges/Publication Team 2007 Project Half Week 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 Slicer XML work descriptor Execution model Grid + Theme: NA-MIC Kit

National Alliance for Medical Image Computing Slicer3 Performance Analysis: Katie Hayes With Slicer 3 Team Plan/Expected Challenges/Publication 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 => 2007 Project Half Week Theme: NA-MIC Kit

National Alliance for Medical Image Computing Matlab-Slicer3 pipeline enhancement: Generalize data type handling and extend to DWI and tensor data Katharina Quintus, BWH (contact) Sylvain Bouix, BWH Steve Pieper, Isomics Marc Niethammer, BWH Mahnaz Maddah, MIT Plan/Expected Challenges/Publication Team Accomplished by 01/31/ Project Half Week 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

National Alliance for Medical Image Computing External Collaborations NCBC Collaboration: Hexahedral Voxel Meshing Slicer3 1.Voxel meshing as an execuation module in Slicer3Voxel meshing as an execuation module in Slicer3 2.Mesh Quality Visualization DevelopmentMesh Quality Visualization Development 3.Bounding Box Projection MeshingBounding Box Projection Meshing 4.Tetrahedral Mesh Generation Tools in VTKTetrahedral Mesh Generation Tools in VTK 5.Mapped Meshing Using ITKMapped Meshing Using ITK NCBC Collaboration in Preparation 1.Nonhuman Primate slicer Module (Alcohol Exposure)Nonhuman Primate slicer Module (Alcohol Exposure) External Collaborations: 1.Slicer3 Module for HPC deformable registrationSlicer3 Module for HPC deformable registration 2.Slicer3: IGT, TrackersSlicer3: IGT, Trackers 3.IGT Workflow for Slicer3: Interventional ImagingIGT Workflow for Slicer3: Interventional Imaging 4.Radiology Workstation Module for Slicer3Radiology Workstation Module for Slicer3 5.vmtk module for Slicervmtk module for Slicer Non-Medical Collaboration 1.Slicer Enhancements for Astronomical Data CubesSlicer Enhancements for Astronomical Data Cubes

National Alliance for Medical Image Computing Slicer3 Module for HPC deformable registration Daniel Goldberg-Zimring, BWH Jim Miller, GE Bill 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. Clinical: Validation of results. Plan/Expected Challenges/Publication Team 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). Expected Date for Insight Journal Publication: 2007 Project Half Week PreopIntraop Registered Preop Theme: External Collaboration

National Alliance for Medical Image Computing 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 link external libraries (opentracker, IGSTK) Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week 2007 Project Half 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 Theme: External Collaboration

National Alliance for Medical Image Computing 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 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]. Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing A Translation Workstation: Integrate 3D Slicer within a radiology clinical workstation. 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 Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week Better understanding of Slicer 3 GUI components and integration techniques Expected Date for RSNA: November Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing 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 Plan/Expected Challenges/Publication Team 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 Expected Date for Insight Journal Publication: July Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing Bone Meshing: Integrate voxel based meshing tool into Slicer3 as an execution model. Vincent Magnotta, Iowa Ritesh 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. Plan/Expected Challenges/Publication Team 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() 2007 Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing 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 the sample meshes available. Plan/Expected Challenges/Publication Team 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 2007 Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing Mapped Hexahedral Mesh Generation: Discuss the manipulation of bounding box structure and the implementation of the same in Slicer3. 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: 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. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week Discussed the implementation of the above mentioned algorithms in Slicer3. Diagrams illustrate the steps involved in mapped meshing Project Half Week a b c d e Theme: External Collaboration

National Alliance for Medical Image Computing Tetrahedral Mesh Generation Methods in VTK Discuss 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 generation Delaunay 3D, Ordered Triangulator, Sliver removal and Mesh optimization methods. Software: Discuss methods to Modify/Extend existing classes necessary for Tetrahedral mesh generation. Plan/Expected Challenges/Publication Team Accomplished by end of Programming Week 2007 Project Half 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. Theme: External Collaboration

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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 RegistrationAfter Registration 2007 Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing 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 Plan/Expected Challenges/Publication Team 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. Expected Date for Insight Journal Publication: 2007 Project Half Week Theme: External Collaboration

National Alliance for Medical Image Computing 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. Plan/Expected Challenges/Publication Team 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. Expected Date for Insight Journal Publication: TBD. This is a continuation of a project from the June 2006 Project Week Project Half Week Theme: External Collaboration