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| − | Back to [[NA-MIC_Collaborations:New]] | + | Back to [[NA-MIC_Collaborations|NA-MIC Collaborations]] |
| | + | __NOTOC__ |
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| − | == Diffusion Image Analysis == | + | <gallery Caption="NA-MIC Collaborative Projects" > |
| | | | |
| − | === Fiber Tract Extraction and Analysis ===
| + | Image:Arcuate_new.png|[[DBP2:Harvard:Brain_Segmentation_Roadmap|<big>Stochastic Tractography for VCSF</big>]] |
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| − | # [[Projects:FiberTractStatistics|Fiber Tract Statistics]] (Utah, UNC)
| + | Image:TRProstateBiopsyRobot.jpg|[[DBP2:JHU:Roadmap|<big>Prostate Biopsy Needle Positioning Robot Integration</big>]] |
| − | # [[Projects:DiffusionMeasuresAlongFiberTracts|Diffusion measures alongs fiber tracts of the cingulum bundle]] (BWH, MIT, UNC)
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| − | # [[Projects:ClusteringOfAnatomicallyDistinctFiberTracts|Clustering of anatomically distinct fiber tracts]] (BWH, MIT)
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| − | # [[Projects:DWMRIGeodesicActiveContours|Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation]] (Georgia Tech, BWH)
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| − | # [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography in Schizophrenia]] (Dartmouth, BWH, MIT)
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| − | #[[Projects:DTINoiseStatistics|Tensor estimation and Monte-Carlo simulation]] (UNC, Utah)
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| − | #[[Projects:DTIStochasticTractography|ITK Stochastic Tractography Filter]] (MIT, BWH)
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| − | #[[Projects:DTIVolumetricWhiteMatterConnectivity|Volumetric White Matter Connectivity]] (Utah)
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| − | #[[Projects:DTIPopulationAnalysis|DTI Atlas-Building]] (UNC, BWH)
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| − | #[[Projects:InferiorFrontotemporalConnections|Inferior Frontotemporal Connections in Schizophrenia]] (BWH, MIT)
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| − | #[[Projects:CorpusFiberClustering|Automatic Clustering of Corpus Callosum and FA Analysis]] (BWH, MIT)
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| − | #[[Projects:FornixTractography|FA Analysis of Fornix Tractography in Schizophrenia]] (BWH, MIT)
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| − | #[[Projects:DiffusionImageAnalysisGenetics|A Diffusion Tensor Imaging and Genetics Study of Psychosis Across the Lifespan - Project in Recruitment Phase]] (Toronto, BWH)
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| | | | |
| − | === Fractional Anisotropy Analysis ===
| + | Image:Lupus.png|[[DBP2:MIND:Roadmap|<big>Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus</big>]] |
| − | # [[Projects:CorpusCallosumRegionalFAAnalysis|Corpus Callosum Regional FA analysis in Schizophrenia]] (BWH, UNC, Dartmouth)
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| − | # [[Projects:FractionalAnisotropyOfTheCorpusCallosumAndAnteriorCommissure|Fractional Anisotropy of the Corpus Callosum and Anterior Commissure]] (BWH, MIT, Dartmouth)
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| − | # [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study]] (Dartmouth, BWH)
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| − | # [[Projects:DWMRIGeodesicActiveContours|Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation]] (Georgia Tech, BWH)
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| − | # [[Projects:ProbabilisticCorpusCallosumAnalysis|Corpus Callosum Probabilistic Subdivision and FA Analysis]] (BWH, UNC)
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| | | | |
| − | === Path of Interest Analysis ===
| + | Image:BrainDevelopment.jpg|[[DBP2:UNC:Cortical_Thickness_Roadmap|<big>Cortical Thickness for Autism</big>]] |
| − | #[[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis]] (Dartmouth, MGH, Isomics, BWH)
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| − | #[[Projects:DTIPathOfInterest|ITK implementation of POIStats, and Integration into Slicer3]] (MGH, Isomics),
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| − | #[[Projects:DTIPathOfInterest|Dartmouth Data Image Format Compatibility in Application of POIStats]] (MGH, Isomics, Kitware, Dartmouth)
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| − | #[[Projects:ConnectingRegionsOfFunctionalActivation|Anatomical Connectivity of Regions of Functional Activation]] (BWH)
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| | | | |
| − | === Validation ===
| + | Image:Slicer3-11-2007.jpg|[[NA-MIC-Kit|<big>NA-MIC Kit</big>]] |
| − | # [[Projects:DTIValidation|DTI Validation]] (UCI, MGH, UNC, MIT)
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| | | | |
| − | === Algorithm/Software Infrastructure ===
| + | Image:CingulumAllSubjectsFibers.png|[[NA-MIC_Internal_Collaborations:DiffusionImageAnalysis|<big>Diffusion Image Analysis</big>]] |
| − | # [[Projects:DTISoftwareAndAlgorithmInfrastructure|DTI Software/Algorithm Infrastructure]] (Utah, UNC)
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| − | # [[Projects:TensorBasedStatistics|Tensor based statistics]] (BWH, Utah)
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| − | # [[Projects:DiffusionTensorImageFiltering|Diffusion tensor image filtering]] (Utah, BWH)
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| − | # [[Projects:NonRigidEPIRegistration|Non-rigid EPI Registration]] (MGH, Kitware, Dartmouth)
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| − | # [[Projects:FiberToolsSlicerIntegration|Fiber Tools Integration with Slicer 3]] (UNC, GE, Isomics)
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| − | # [[Projects:DTIRicianNoiseRemoval|Rician Noise Remvoal in Diffusion Tensor MRI]] (Utah)
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| − | # [[Projects:DWMRIGeodesicActiveContours|Finsler Tractography in ITK]] (Georgia Tech, Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
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| − | # [[Projects:DWMRIGeodesicActiveContours|Finsler Levelsets in ITK]] (Georgia Tech, Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
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| − | # [[Projects:LMMSERicianDWINoiseRemoval|Restoration of DWI data using a Rician LMMSE Estimator]] (BWH)
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| | | | |
| − | == Structural Image Analysis ==
| + | Image:Sulcaldepth.png|[[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|<big>Structural Image Analysis</big>]] |
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| | + | Image:Mit_fmri_clustering_parcellation2_xsub.png|[[NA-MIC_Internal_Collaborations:fMRIAnalysis|<big>fMRI Analysis </big>]] |
| | | | |
| − | === Image Segmentation ===
| + | </gallery> |
| − | # [[Projects:KnowledgeBasedBayesianSegmentation|Knowledge-Based Bayesian Classification and Segmentation]] (Georgia Tech, Kitware)
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| − | # [[Projects:InterleavedSegmentationAndRegistration|Brain Tissue Classification and Subparcellation of Brain Structures]] (BWH, MIT, Kitware)
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| − | # [[Projects:RuleBasedSegmentation|Rule based segmentation: Striatum]] (Georgia Tech, BWH, Isomics, Kitware)
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| − | # [[Projects:RuleBasedSegmentation|Rule based segmentation: DLPFC]] (Georgia Tech, UCI, Isomics, Kitware)
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| − | # [[Projects:MultiscaleShapeSegmentation|Multiscale Shape Segmentation Techniques]] (Georgia Tech, BWH)
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| − | # [[Projects:StochasticMethodsSegmentation|Stochastic Methods for Segmentation]] (Georgia Tech)
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| − | # [[Projects:StatisticalSegmentationSlicer2|Statistical/PDE methods for Segmentation]] (Georgia Tech)
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| − | # [[Projects:AutomaticFullBrainSegmentation|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] (MGH)
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| − | # [[Projects:EMSegmenterSoftwareDevelopment| EMSegmenter Software Development]] (BWH, MIT, Kitware) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]]
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| − | # Expanded neuroanatomy training for algorithm development at GA Tech, to expand the rules set for semiautomated segmmentation/shape analysis of frontal cortex (UCI, Georgia Tech)
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| | | | |
| − | === Image Registration ===
| + | Click [[NA-MIC_Internal_Collaborations:Old|here]] for old links to internal collaborations. |
| − | # [[Projects:OptimalMassTransportRegistration|Optimal Mass Transport for Registration]] (Georgia Tech, BWH)
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| − | #[[Projects:NonRigidRegistration|Parallelization of ITK for deformable registration]] (Kitware, GE, Utah), [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
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| − | #[[Projects:GroupwiseRegistration|Group-wise Registration of Medical Images]] (MIT, BWH, MGH), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
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| − | | |
| − | === Morphometric Measures and Shape Analysis ===
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| − | # [[Projects:ShapeAnalysisOfCaudateAndCorpusCallosum|Shape Analysis for the caudate and corpus callosum data]] (BWH, UNC, Georgia Tech, Dartmouth)
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| − | # [[Projects:ShapeAnalysisOfHippocampus|Shape Analysis of the hippocampus]] (Dartmouth, UNC, BWH)
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| − | # [[Projects:MultiscaleShapeAnalysis|Multiscale Shape Analysis applied to Caudate and Hippocampus]] (Georgia Tech, BWH, UNC)
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| − | # [[Projects:Shape AnalysisUsingLONIPipeline|UNC Shape Analysis with LONI pipeline for clinical investigators]] (UNC, UCLA)
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| − | # [[Projects:GenericPopulationStudies|Population Studies]] (UNC, GE)
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| − | # [[Projects:MorphometricMeasuresForMildCognitiveImpairment|Multi-site morphometry in Mild Cognitive Impairment]] (UCI, mBIRN?)
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| − | # [[Projects:MultiSiteMorphometry|Multi-site morphometry in Schizophrenia]] (UCI, FBIRN)
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| − | # [[Projects:AutomatedShapeModelConstruction|Automated shape model construction]] (Utah, BWH)
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| − | # [[Projects:NeuralSubstratesOfApathy|Neural substrates of apathy in schizophrenia]] (Dartmouth, Isomics)
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| − | # [[Projects:CorticalSurfaceShapeAnalysisUsingSphericalWavelets|Cortical Surface Shape Analysis Based on Spherical Wavelets]] (MGH)
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| − | # [[Projects:TopologyCorrectionNonSeparatingLoops|Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops]] (MGH)
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| − | # [[Projects:SphericalWaveletsInITK|ITK Spherical Wavelet Transform Filter]] (Georgia Tech,GE, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
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| − | # [[Projects:MultiscaleShapeAnalysis|UNC shape analysis with Spherical Wavelet Features]] (GaTech, UNC): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
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| − | # [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM| Integrating KWMeshVisu into Slicer]] (UNC, Kitware), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
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| − | # [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM| Integrating UNC Shape Analysis into Slicer]] (UNC, Kitware)
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| − | # [[Projects:PopulationBasedCorrespondence | Correspondence of complex structures using (Curvature + Location) MDL]] (UNC)
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| − | # Qdec - a GUI front-end tool for GLM-based group analysis of Freesurfer-processed subject morphometry data (MGH): [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Freesurfer wiki page]
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| − | # [[Projects:ParticlesForShapesAndComplexes| Adaptive, Particle-Based Sampling for Shapes and Complexes]] (Utah, UNC)
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| − | # [[Projects:ThicknessSlicer3Module| Thickness Slicer3 Module]] (BWH, Isomics)
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| − | # [[Projects:GenusZeroSlicer3Module| Genus Zero Slicer3 Module]] (BWH, Isomics)
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| − | # [[Projects:MorphometryFrontalCircuitry|Morphometry of Frontal circuitry in patients with schizophrenia with and without co-occurring substance use disorder]] (Dartmouth, Isomics)
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| − | | |
| − | == fMRI Analysis ==
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| − | | |
| − | === Functional Activation Analysis ===
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| − | # [[Projects:NeuralSubstratesOfWorkingMemoryInSchizophrenia|Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study]] (Dartmouth, Harvard)
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| − | # [[Projects:BrainActivationDuringContinuousVerbalEncodingAndRecognitionTaskInSchizophrenia|Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia]] (Dartmouth, Harvard)
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| − | # [[Projects:FrontoTemporalConnectivityInSchizophreniaDuringSemanticMemory|Fronto-Temporal Connectivity in Schizophrenia during Semantic Memory]] (Dartmouth, Harvard)
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| − | # [[Projects:ImagingPhenotypesInSchizophrenicsAndControls|Imaging Phenotypes in Schizophrenics and Controls]] (UCI, Toronto)
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| − | # [[Projects:AttentionalCircuitsInSchizophreniaInfMRIAndPET|Attentional Circuits in Schizophrenia as revealed by fMRI and PET]] (UCI)
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| − | # [[Projects:fMRIAnalysisAnxietyDisorder| Serotonergic / dopaminergic genes and processing of threatening stimuli in panic disorder: an imaging genetics study]] (Toronto)
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| − | | |
| − | === Algorithm and Software Infrastructure ===
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| − | # [[Projects:fMRIStatisticsSoftwareInfrastructure|fMRI Statistics Software Infrastructure]] (GE, Isomics, Kitware, MIT)
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| − | # [[Projects:SpatialRegularizationForfMRIDetection|Spatial Regularization for fMRI Detection]] (MIT, Harvard)
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| − | # [[Projects:ConformalFlatteningRegistration|Conformal Flattening for fMRI Visualization]] (Georgia Tech, Harvard)
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| − | | |
| − | == NA-MIC Kit ==
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| − | | |
| − | === NAMIC Software Process ===
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/CMake_-_NAMIC_Kit_Building|CMake - NAMIC Kit Building]] (Kitware)
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/CPack_-_NAMIC_Kit_Distribution|CPack - NAMIC Kit Distribution]] (Kitware)
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/Dart_2_and_CTest_-_Software_Quality|Dart 2 and CTest - Software Quality]] (GE, Kitware)
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| − | | |
| − | === Software Infrastructure ===
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/Slicer3|Slicer 3]] (Isomics, GE, Kitware, UCSD, UCLA)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/MRML|MRML]] (Isomics, Kitware, GE)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/Coordinate_Systems|Coordinate Systems]] (GE, Isomics)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/IO_Unification|IO Unification]] (GE, Isomics)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/Execution_Model|Execution Model]] (GE)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/Grid_Computing|Grid Computing]] (UCSD, GE, Kitware, Isomics)
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/Licenses_Unification|Licenses Unification]] (Kitware, Isomics)
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| − | # Toolkits
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/KWWidgets|KWWidgets]] (Kitware)
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| − | ## [[NA-MIC/Projects/NA-MIC_Kit/Teem|Teem]] (Harvard/BWH)
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| − | | |
| − | === Training & Dissemination ===
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/Training_Material_and_Workshops_for_NA-MIC_Kit|Training Material and Workshops for NA-MIC Kit]] (MGH, BWH)
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| − | # [[NA-MIC/Projects/NA-MIC_Kit/Dissemination|Dissemination for NA-MIC]] (Isomics, Kitware, Harvard)
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| − | | |
| − | == Other Projects ==
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| − | | |
| − | # [[Non_Rigid_Registration|Non-Rigid Registration]]
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| − | # [[NA-MIC/Projects/Diffusion_Image_Analysis/FreeSurfer_NRRD_IO|FreeSurfer NRRD IO]]
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| − | # [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|FreeSurfer Numerical Recipies Replacement]]
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| − | # [[Slicer3:Fluorescence and Electron Microscopy Support | Slicer3 Fluorescence and Electron Microscopy Support]]
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