Difference between revisions of "NA-MIC Internal Collaborations"
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(New page: == Diffusion Image Analysis == === Fiber Tract Extraction and Analysis === ====Continued from 2006==== # Fiber Tract Statistics (Utah, UNC) # [[Project...) |
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=== Fiber Tract Extraction and Analysis === | === Fiber Tract Extraction and Analysis === | ||
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# [[Projects:FiberTractStatistics|Fiber Tract Statistics]] (Utah, UNC) | # [[Projects:FiberTractStatistics|Fiber Tract Statistics]] (Utah, UNC) | ||
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# [[Projects:DWMRIGeodesicActiveContours|Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation]] (Georgia Tech, BWH) | # [[Projects:DWMRIGeodesicActiveContours|Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation]] (Georgia Tech, BWH) | ||
# [[Projects:CorpusCallosumFiberTractography|Corpus Callosum Fiber Tractography in Schizophrenia]] (Dartmouth, BWH, MIT) | # [[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) | #[[Projects:DTINoiseStatistics|Tensor estimation and Monte-Carlo simulation]] (UNC, Utah) | ||
#[[Projects:DTIStochasticTractography|ITK Stochastic Tractography Filter]] (MIT, BWH) | #[[Projects:DTIStochasticTractography|ITK Stochastic Tractography Filter]] (MIT, BWH) | ||
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=== Fractional Anisotropy Analysis === | === Fractional Anisotropy Analysis === | ||
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# [[Projects:CorpusCallosumRegionalFAAnalysis|Corpus Callosum Regional FA analysis in Schizophrenia]] (BWH, UNC, Dartmouth) | # [[Projects:CorpusCallosumRegionalFAAnalysis|Corpus Callosum Regional FA analysis in Schizophrenia]] (BWH, UNC, Dartmouth) | ||
# [[Projects:FractionalAnisotropyOfTheCorpusCallosumAndAnteriorCommissure|Fractional Anisotropy of the Corpus Callosum and Anterior Commissure]] (BWH, MIT, Dartmouth) | # [[Projects:FractionalAnisotropyOfTheCorpusCallosumAndAnteriorCommissure|Fractional Anisotropy of the Corpus Callosum and Anterior Commissure]] (BWH, MIT, Dartmouth) | ||
# [[Projects:FractionalAnisotrophyInTheUncinateFasciculus|Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study]] (Dartmouth, BWH) | # [[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) | # [[Projects:DWMRIGeodesicActiveContours|Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation]] (Georgia Tech, BWH) | ||
# [[Projects:ProbabilisticCorpusCallosumAnalysis|Corpus Callosum Probabilistic Subdivision and FA Analysis]] (BWH, UNC) | # [[Projects:ProbabilisticCorpusCallosumAnalysis|Corpus Callosum Probabilistic Subdivision and FA Analysis]] (BWH, UNC) | ||
=== Path of Interest Analysis === | === Path of Interest Analysis === | ||
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#[[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis]] (Dartmouth, MGH, Isomics, BWH) | #[[Projects:IntegrityOfFrontoTemporalCircuitry|Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis]] (Dartmouth, MGH, Isomics, BWH) | ||
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#[[AHM_2006:ProjectsDTIPathOfInterest|ITK implementation of POIStats, and Integration into Slicer3]] (MGH, Isomics), | #[[AHM_2006:ProjectsDTIPathOfInterest|ITK implementation of POIStats, and Integration into Slicer3]] (MGH, Isomics), | ||
#[[AHM_2006:ProjectsDTIPathOfInterest|Dartmouth Data Image Format Compatibility in Application of POIStats]] (MGH, Isomics, Kitware, Dartmouth) | #[[AHM_2006:ProjectsDTIPathOfInterest|Dartmouth Data Image Format Compatibility in Application of POIStats]] (MGH, Isomics, Kitware, Dartmouth) | ||
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=== Validation === | === Validation === | ||
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# [[Projects:DTIValidation|DTI Validation]] (UCI, MGH, UNC, MIT) | # [[Projects:DTIValidation|DTI Validation]] (UCI, MGH, UNC, MIT) | ||
=== Algorithm/Software Infrastructure === | === Algorithm/Software Infrastructure === | ||
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# [[Projects:DTISoftwareAndAlgorithmInfrastructure|DTI Software/Algorithm Infrastructure]] (Utah, UNC) | # [[Projects:DTISoftwareAndAlgorithmInfrastructure|DTI Software/Algorithm Infrastructure]] (Utah, UNC) | ||
# [[Projects:TensorBasedStatistics|Tensor based statistics]] (BWH, Utah) | # [[Projects:TensorBasedStatistics|Tensor based statistics]] (BWH, Utah) | ||
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# [[Projects:NonRigidEPIRegistration|Non-rigid EPI Registration]] (MGH, Kitware, Dartmouth) | # [[Projects:NonRigidEPIRegistration|Non-rigid EPI Registration]] (MGH, Kitware, Dartmouth) | ||
# [[Projects:FiberToolsSlicerIntegration|Fiber Tools Integration with Slicer 3]] (UNC, GE, Isomics) | # [[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) | # [[Projects:DTIRicianNoiseRemoval|Rician Noise Remvoal in Diffusion Tensor MRI]] (Utah) | ||
# [[Projects:DWMRIGeodesicActiveContours|Finsler Tractography in ITK]] (Georgia Tech, Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]] | # [[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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=== Image Segmentation === | === Image Segmentation === | ||
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# [[Projects:KnowledgeBasedBayesianSegmentation|Knowledge-Based Bayesian Classification and Segmentation]] (Georgia Tech, Kitware) | # [[Projects:KnowledgeBasedBayesianSegmentation|Knowledge-Based Bayesian Classification and Segmentation]] (Georgia Tech, Kitware) | ||
# [[Projects:InterleavedSegmentationAndRegistration|Brain Tissue Classification and Subparcellation of Brain Structures]] (BWH, MIT, Kitware) | # [[Projects:InterleavedSegmentationAndRegistration|Brain Tissue Classification and Subparcellation of Brain Structures]] (BWH, MIT, Kitware) | ||
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# [[Projects:StatisticalSegmentationSlicer2|Statistical/PDE methods for Segmentation]] (Georgia Tech) | # [[Projects:StatisticalSegmentationSlicer2|Statistical/PDE methods for Segmentation]] (Georgia Tech) | ||
# [[Projects:AutomaticFullBrainSegmentation|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] (MGH) | # [[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]] | # [[Projects:EMSegmenterSoftwareDevelopment| EMSegmenter Software Development]] (BWH, MIT, Kitware) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] | ||
# 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) | # 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) | ||
=== Image Registration === | === Image Registration === | ||
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# [[Projects:OptimalMassTransportRegistration|Optimal Mass Transport for Registration]] (Georgia Tech, BWH) | # [[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]] | #[[Projects:NonRigidRegistration|Parallelization of ITK for deformable registration]] (Kitware, GE, Utah), [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]] | ||
#[[Projects:GroupwiseRegistration|Group-wise Registration of Medical Images]] (MIT, BWH, MGH), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]] | #[[Projects:GroupwiseRegistration|Group-wise Registration of Medical Images]] (MIT, BWH, MGH), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]] | ||
=== Morphometric Measures and Shape Analysis === | === 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) | # [[Projects:ShapeAnalysisOfCaudateAndCorpusCallosum|Shape Analysis for the caudate and corpus callosum data]] (BWH, UNC, Georgia Tech, Dartmouth) | ||
# [[Projects:ShapeAnalysisOfHippocampus|Shape Analysis of the hippocampus]] (Dartmouth, UNC, BWH) | # [[Projects:ShapeAnalysisOfHippocampus|Shape Analysis of the hippocampus]] (Dartmouth, UNC, BWH) | ||
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# [[Projects:CorticalSurfaceShapeAnalysisUsingSphericalWavelets|Cortical Surface Shape Analysis Based on Spherical Wavelets]] (MGH) | # [[Projects:CorticalSurfaceShapeAnalysisUsingSphericalWavelets|Cortical Surface Shape Analysis Based on Spherical Wavelets]] (MGH) | ||
# [[Projects:TopologyCorrectionNonSeparatingLoops|Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops]] (MGH) | # [[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]] | # [[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]] | ||
# [[Projects:MultiscaleShapeAnalysis|UNC shape analysis with Spherical Wavelet Features]] (GaTech, UNC): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]] | # [[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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=== Functional Activation Analysis === | === Functional Activation Analysis === | ||
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# [[Projects:NeuralSubstratesOfWorkingMemoryInSchizophrenia|Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study]] (Dartmouth, Harvard) | # [[Projects:NeuralSubstratesOfWorkingMemoryInSchizophrenia|Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study]] (Dartmouth, Harvard) | ||
# [[Projects:BrainActivationDuringContinuousVerbalEncodingAndRecognitionTaskInSchizophrenia|Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia]] (Dartmouth, Harvard) | # [[Projects:BrainActivationDuringContinuousVerbalEncodingAndRecognitionTaskInSchizophrenia|Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia]] (Dartmouth, Harvard) | ||
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=== Algorithm and Software Infrastructure === | === Algorithm and Software Infrastructure === | ||
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# [[Projects:fMRIStatisticsSoftwareInfrastructure|fMRI Statistics Software Infrastructure]] (GE, Isomics, Kitware, MIT) | # [[Projects:fMRIStatisticsSoftwareInfrastructure|fMRI Statistics Software Infrastructure]] (GE, Isomics, Kitware, MIT) | ||
# [[Projects:SpatialRegularizationForfMRIDetection|Spatial Regularization for fMRI Detection]] (MIT, Harvard) | # [[Projects:SpatialRegularizationForfMRIDetection|Spatial Regularization for fMRI Detection]] (MIT, Harvard) | ||
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=== NAMIC Software Process === | === NAMIC Software Process === | ||
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# [[NA-MIC/Projects/NA-MIC_Kit/CMake_-_NAMIC_Kit_Building|CMake - NAMIC Kit Building]] (Kitware) | # [[NA-MIC/Projects/NA-MIC_Kit/CMake_-_NAMIC_Kit_Building|CMake - NAMIC Kit Building]] (Kitware) | ||
# [[NA-MIC/Projects/NA-MIC_Kit/CPack_-_NAMIC_Kit_Distribution|CPack - NAMIC Kit Distribution]] (Kitware) | # [[NA-MIC/Projects/NA-MIC_Kit/CPack_-_NAMIC_Kit_Distribution|CPack - NAMIC Kit Distribution]] (Kitware) | ||
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=== Software Infrastructure === | === Software Infrastructure === | ||
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# [[NA-MIC/Projects/NA-MIC_Kit/Slicer3|Slicer 3]] (Isomics, GE, Kitware, UCSD, UCLA) | # [[NA-MIC/Projects/NA-MIC_Kit/Slicer3|Slicer 3]] (Isomics, GE, Kitware, UCSD, UCLA) | ||
## [[NA-MIC/Projects/NA-MIC_Kit/MRML|MRML]] (Isomics, Kitware, GE) | ## [[NA-MIC/Projects/NA-MIC_Kit/MRML|MRML]] (Isomics, Kitware, GE) |
Revision as of 15:58, 17 October 2007
Home < NA-MIC Internal CollaborationsContents
Diffusion Image Analysis
Fiber Tract Extraction and Analysis
- Fiber Tract Statistics (Utah, UNC)
- Diffusion measures alongs fiber tracts of the cingulum bundle (BWH, MIT, UNC)
- Clustering of anatomically distinct fiber tracts (BWH, MIT)
- Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
- Corpus Callosum Fiber Tractography in Schizophrenia (Dartmouth, BWH, MIT)
- Tensor estimation and Monte-Carlo simulation (UNC, Utah)
- ITK Stochastic Tractography Filter (MIT, BWH)
- Volumetric White Matter Connectivity (Utah)
- DTI Atlas-Building (UNC, BWH)
- Inferior Frontotemporal Connections in Schizophrenia (BWH, MIT)
- Automatic Clustering of Corpus Callosum and FA Analysis (BWH, MIT)
- FA Analysis of Fornix Tractography in Schizophrenia (BWH, MIT)
- A Diffusion Tensor Imaging and Genetics Study of Psychosis Across the Lifespan - Project in Recruitment Phase (Toronto, BWH)
Fractional Anisotropy Analysis
- Corpus Callosum Regional FA analysis in Schizophrenia (BWH, UNC, Dartmouth)
- Fractional Anisotropy of the Corpus Callosum and Anterior Commissure (BWH, MIT, Dartmouth)
- Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study (Dartmouth, BWH)
- Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
- Corpus Callosum Probabilistic Subdivision and FA Analysis (BWH, UNC)
Path of Interest Analysis
- Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis (Dartmouth, MGH, Isomics, BWH)
- ITK implementation of POIStats, and Integration into Slicer3 (MGH, Isomics),
- Dartmouth Data Image Format Compatibility in Application of POIStats (MGH, Isomics, Kitware, Dartmouth)
- Anatomical Connectivity of Regions of Functional Activation (BWH)
Validation
- DTI Validation (UCI, MGH, UNC, MIT)
Algorithm/Software Infrastructure
- DTI Software/Algorithm Infrastructure (Utah, UNC)
- Tensor based statistics (BWH, Utah)
- Diffusion tensor image filtering (Utah, BWH)
- Non-rigid EPI Registration (MGH, Kitware, Dartmouth)
- Fiber Tools Integration with Slicer 3 (UNC, GE, Isomics)
- Rician Noise Remvoal in Diffusion Tensor MRI (Utah)
- Finsler Tractography in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
- Finsler Levelsets in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
- Restoration of DWI data using a Rician LMMSE Estimator (BWH)
Structural Image Analysis
Image Segmentation
- Knowledge-Based Bayesian Classification and Segmentation (Georgia Tech, Kitware)
- Brain Tissue Classification and Subparcellation of Brain Structures (BWH, MIT, Kitware)
- Rule based segmentation: Striatum (Georgia Tech, BWH, Isomics, Kitware)
- Rule based segmentation: DLPFC (Georgia Tech, UCI, Isomics, Kitware)
- Multiscale Shape Segmentation Techniques (Georgia Tech, BWH)
- Stochastic Methods for Segmentation (Georgia Tech)
- Statistical/PDE methods for Segmentation (Georgia Tech)
- Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms (MGH)
- EMSegmenter Software Development (BWH, MIT, Kitware) 4-block PPT Jan 2007
- 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)
Image Registration
- Optimal Mass Transport for Registration (Georgia Tech, BWH)
- Parallelization of ITK for deformable registration (Kitware, GE, Utah), 4-block PPT Jan 2007
- Group-wise Registration of Medical Images (MIT, BWH, MGH), 4-block PPT Jan 2007
Morphometric Measures and Shape Analysis
- Shape Analysis for the caudate and corpus callosum data (BWH, UNC, Georgia Tech, Dartmouth)
- Shape Analysis of the hippocampus (Dartmouth, UNC, BWH)
- Multiscale Shape Analysis applied to Caudate and Hippocampus (Georgia Tech, BWH, UNC)
- UNC Shape Analysis with LONI pipeline for clinical investigators (UNC, UCLA)
- Population Studies (UNC, GE)
- Multi-site morphometry in Mild Cognitive Impairment (UCI, mBIRN?)
- Multi-site morphometry in Schizophrenia (UCI, FBIRN)
- Automated shape model construction (Utah, BWH)
- Neural substrates of apathy in schizophrenia (Dartmouth, Isomics)
- Cortical Surface Shape Analysis Based on Spherical Wavelets (MGH)
- Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops (MGH)
- ITK Spherical Wavelet Transform Filter (Georgia Tech,GE, Kitware): 4-block PPT Summer 2006, 4-block PPT Jan 2007
- UNC shape analysis with Spherical Wavelet Features (GaTech, UNC): 4-block PPT Jan 2007
- Integrating KWMeshVisu into Slicer (UNC, Kitware), 4-block PPT Jan 2006, 4-block PPT Jan 2007
- Integrating UNC Shape Analysis into Slicer (UNC, Kitware)
- Correspondence of complex structures using (Curvature + Location) MDL (UNC)
- Qdec - a GUI front-end tool for GLM-based group analysis of Freesurfer-processed subject morphometry data (MGH): Freesurfer wiki page
- Adaptive, Particle-Based Sampling for Shapes and Complexes (Utah, UNC)
- Thickness Slicer3 Module (BWH, Isomics)
- Genus Zero Slicer3 Module (BWH, Isomics)
- Morphometry of Frontal circuitry in patients with schizophrenia with and without co-occurring substance use disorder (Dartmouth, Isomics)
fMRI Analysis
Functional Activation Analysis
- Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study (Dartmouth, Harvard)
- Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia (Dartmouth, Harvard)
- Fronto-Temporal Connectivity in Schizophrenia during Semantic Memory (Dartmouth, Harvard)
- Imaging Phenotypes in Schizophrenics and Controls (UCI, Toronto)
- Attentional Circuits in Schizophrenia as revealed by fMRI and PET (UCI)
- Serotonergic / dopaminergic genes and processing of threatening stimuli in panic disorder: an imaging genetics study (Toronto)
Algorithm and Software Infrastructure
- fMRI Statistics Software Infrastructure (GE, Isomics, Kitware, MIT)
- Spatial Regularization for fMRI Detection (MIT, Harvard)
- Conformal Flattening for fMRI Visualization (Georgia Tech, Harvard)
NA-MIC Kit
NAMIC Software Process
- CMake - NAMIC Kit Building (Kitware)
- CPack - NAMIC Kit Distribution (Kitware)
- Dart 2 and CTest - Software Quality (GE, Kitware)
Software Infrastructure
- Slicer 3 (Isomics, GE, Kitware, UCSD, UCLA)
- MRML (Isomics, Kitware, GE)
- Coordinate Systems (GE, Isomics)
- IO Unification (GE, Isomics)
- Execution Model (GE)
- Grid Computing (UCSD, GE, Kitware, Isomics)
- Licenses Unification (Kitware, Isomics)
- Toolkits
Training & Dissemination
Continued from 2006
- Training Material and Workshops for NA-MIC Kit (MGH, BWH)
- Dissemination for NA-MIC (Isomics, Kitware, Harvard)