NA-MIC Internal Collaborations

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Diffusion Image Analysis

Fiber Tract Extraction and Analysis

1. Fiber Tract Statistics (Utah, UNC)
2. Diffusion measures alongs fiber tracts of the cingulum bundle (BWH, MIT, UNC)
3. Clustering of anatomically distinct fiber tracts (BWH, MIT)
4. Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
5. Corpus Callosum Fiber Tractography in Schizophrenia (Dartmouth, BWH, MIT)
6. Tensor estimation and Monte-Carlo simulation (UNC, Utah)
7. ITK Stochastic Tractography Filter (MIT, BWH)
8. Volumetric White Matter Connectivity (Utah)
9. DTI Atlas-Building (UNC, BWH)
10. Inferior Frontotemporal Connections in Schizophrenia (BWH, MIT)
11. Automatic Clustering of Corpus Callosum and FA Analysis (BWH, MIT)
12. FA Analysis of Fornix Tractography in Schizophrenia (BWH, MIT)
13. A Diffusion Tensor Imaging and Genetics Study of Psychosis Across the Lifespan - Project in Recruitment Phase (Toronto, BWH)

Fractional Anisotropy Analysis

1. Corpus Callosum Regional FA analysis in Schizophrenia (BWH, UNC, Dartmouth)
2. Fractional Anisotropy of the Corpus Callosum and Anterior Commissure (BWH, MIT, Dartmouth)
3. Fractional Anisotrophy in the Uncinate Fasciculus in Schizophrenia and Bipolar I Disorder--replication and extension of Kubicki study (Dartmouth, BWH)
4. Geodesic Active Contours for Fiber Tractography and Fiber Bundle Segmentation (Georgia Tech, BWH)
5. Corpus Callosum Probabilistic Subdivision and FA Analysis (BWH, UNC)

Path of Interest Analysis

1. Integrity of Fronto-Temporal Circuitry in Schizophrenia using Path of Interest Analysis (Dartmouth, MGH, Isomics, BWH)
2. ITK implementation of POIStats, and Integration into Slicer3 (MGH, Isomics),
3. Dartmouth Data Image Format Compatibility in Application of POIStats (MGH, Isomics, Kitware, Dartmouth)
4. Anatomical Connectivity of Regions of Functional Activation (BWH)

Validation

1. DTI Validation (UCI, MGH, UNC, MIT)

Algorithm/Software Infrastructure

1. DTI Software/Algorithm Infrastructure (Utah, UNC)
2. Tensor based statistics (BWH, Utah)
3. Diffusion tensor image filtering (Utah, BWH)
4. Non-rigid EPI Registration (MGH, Kitware, Dartmouth)
5. Fiber Tools Integration with Slicer 3 (UNC, GE, Isomics)
6. Rician Noise Remvoal in Diffusion Tensor MRI (Utah)
7. Finsler Tractography in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
8. Finsler Levelsets in ITK (Georgia Tech, Kitware): 4-block PPT Jan 2007
9. Restoration of DWI data using a Rician LMMSE Estimator (BWH)

Structural Image Analysis

Image Segmentation

1. Knowledge-Based Bayesian Classification and Segmentation (Georgia Tech, Kitware)
2. Brain Tissue Classification and Subparcellation of Brain Structures (BWH, MIT, Kitware)
3. Rule based segmentation: Striatum (Georgia Tech, BWH, Isomics, Kitware)
4. Rule based segmentation: DLPFC (Georgia Tech, UCI, Isomics, Kitware)
5. Multiscale Shape Segmentation Techniques (Georgia Tech, BWH)
6. Stochastic Methods for Segmentation (Georgia Tech)
7. Statistical/PDE methods for Segmentation (Georgia Tech)
8. Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms (MGH)
9. EMSegmenter Software Development (BWH, MIT, Kitware) 4-block PPT Jan 2007 ‎
10. 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

1. Optimal Mass Transport for Registration (Georgia Tech, BWH)
2. Parallelization of ITK for deformable registration (Kitware, GE, Utah), 4-block PPT Jan 2007
3. Group-wise Registration of Medical Images (MIT, BWH, MGH), 4-block PPT Jan 2007

Morphometric Measures and Shape Analysis

1. Shape Analysis for the caudate and corpus callosum data (BWH, UNC, Georgia Tech, Dartmouth)
2. Shape Analysis of the hippocampus (Dartmouth, UNC, BWH)
3. Multiscale Shape Analysis applied to Caudate and Hippocampus (Georgia Tech, BWH, UNC)
4. UNC Shape Analysis with LONI pipeline for clinical investigators (UNC, UCLA)
5. Population Studies (UNC, GE)
6. Multi-site morphometry in Mild Cognitive Impairment (UCI, mBIRN?)
7. Multi-site morphometry in Schizophrenia (UCI, FBIRN)
8. Automated shape model construction (Utah, BWH)
9. Neural substrates of apathy in schizophrenia (Dartmouth, Isomics)
10. Cortical Surface Shape Analysis Based on Spherical Wavelets (MGH)
11. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops (MGH)
12. ITK Spherical Wavelet Transform Filter (Georgia Tech,GE, Kitware): 4-block PPT Summer 2006, 4-block PPT Jan 2007
13. UNC shape analysis with Spherical Wavelet Features (GaTech, UNC): 4-block PPT Jan 2007
14. Integrating KWMeshVisu into Slicer (UNC, Kitware), 4-block PPT Jan 2006, 4-block PPT Jan 2007
15. Integrating UNC Shape Analysis into Slicer (UNC, Kitware)
16. Correspondence of complex structures using (Curvature + Location) MDL (UNC)
17. Qdec - a GUI front-end tool for GLM-based group analysis of Freesurfer-processed subject morphometry data (MGH): Freesurfer wiki page
18. Adaptive, Particle-Based Sampling for Shapes and Complexes (Utah, UNC)
19. Thickness Slicer3 Module (BWH, Isomics)
20. Genus Zero Slicer3 Module (BWH, Isomics)
21. Morphometry of Frontal circuitry in patients with schizophrenia with and without co-occurring substance use disorder (Dartmouth, Isomics)

fMRI Analysis

Functional Activation Analysis

1. Neural Substrates of Working Memory in Schizophrenia: A Parametric 3-Back Study (Dartmouth, Harvard)
2. Brain Activation during a Continuous Verbal Encoding and Recognition Task in Schizophrenia (Dartmouth, Harvard)
3. Fronto-Temporal Connectivity in Schizophrenia during Semantic Memory (Dartmouth, Harvard)
4. Imaging Phenotypes in Schizophrenics and Controls (UCI, Toronto)
5. Attentional Circuits in Schizophrenia as revealed by fMRI and PET (UCI)
6. Serotonergic / dopaminergic genes and processing of threatening stimuli in panic disorder: an imaging genetics study (Toronto)

Algorithm and Software Infrastructure

1. fMRI Statistics Software Infrastructure (GE, Isomics, Kitware, MIT)
2. Spatial Regularization for fMRI Detection (MIT, Harvard)
3. Conformal Flattening for fMRI Visualization (Georgia Tech, Harvard)

NA-MIC Kit

NAMIC Software Process

1. CMake - NAMIC Kit Building (Kitware)
2. CPack - NAMIC Kit Distribution (Kitware)
3. Dart 2 and CTest - Software Quality (GE, Kitware)

Software Infrastructure

1. Slicer 3 (Isomics, GE, Kitware, UCSD, UCLA)
   1. MRML (Isomics, Kitware, GE)
   2. Coordinate Systems (GE, Isomics)
   3. IO Unification (GE, Isomics)
   4. Execution Model (GE)
   5. Grid Computing (UCSD, GE, Kitware, Isomics)
2. Licenses Unification (Kitware, Isomics)
3. Toolkits
   1. KWWidgets (Kitware)
   2. Teem (Harvard/BWH)

Training & Dissemination

1. Training Material and Workshops for NA-MIC Kit (MGH, BWH)
2. Dissemination for NA-MIC (Isomics, Kitware, Harvard)

Other Projects

1. Non-Rigid Registration
2. FreeSurfer NRRD IO
3. FreeSurfer Numerical Recipies Replacement
4. Slicer3 Fluorescence and Electron Microscopy Support