Software and Data

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Research Themes

• Brain Atlas
• Registration
• Diffusion Analysis
• Segmentation
• Longitudinal Analysis
• Shape Analysis
• Microscopy
• Simulation

Research Projects

• Alzheimer's Disease Neuroimaging Initiative
• Autism Centers of Excellence
• Early brain development in infants at risk for mental illness
• CAMID Neurobiological and Behavioral Consequences of Cocaine Use in Mother-Infant Dyads
• National Center for Biomedical Computing NA-MIC
• Image Analysis of Pathological changes
• Brain Lesion Modeling and Segmentation
• 4D Analysis of White Matter Diffusion
• 4D Modeling of Image Appearance Changes
• Time varying shape analysis
• Meshing Biological Models
• Long Range Connectivity Reconstruction
• Connectomics with Electron Microscopy
• Neuroanatomical Shape Analysis
• Diffusion Tensor Analysis
• Brain Population Analysis with Manifold Models
• Non-parametric Models for Brain Image Analysis
• Statistical Analysis of Ensembles of Nonregular Shapes

Shapeworks

The ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

TumorSim

The simulation software that generates pathological ground truth from the adult healthy ground truth (e.g., the BrainWeb data) is available for download for the Linux and Windows platforms. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc). An example input directory that is generated from subject 04 of the BrainWeb Twenty Normals Database is available for download.

3D Slicer and FiberView

3D Slicer is an comprehensive, integrated, open-source environment for medical image visualization and analysis developed as part of the national alliance for medical image computing (NA-MIC) funded as a national center for biomedical computing (NCBC) through the NIH Roadmap for Medical Research. Slicer includes modules for segmentation, registration, diffusion tensor image (DTI) analysis, and many other features. DTI analysis software from the NeuroLib library for neuroimage processing (www.ia.unc.edu/dev) such as FiberViewer has been made compatible with Slicer in order to allow an integrated analysis process. Clinical users are able to load diffusion weighted images into Slicer to perform preprocessing, tensor estimation, and fiber tracking. Data exported from Slicer can then be loaded into the FiberViewer tool to enable the study of diffusion statistics along fiber bundles of interest. This provides a complete environment for end users to process DTI data for clinical studies.

AtlasWerks

AtlasWerks is an open-source (BSD license) software package for medical image atlas generation. Such atlases are a widely-used tool for image segmentation, and deformations generated using these techniques are used for statistical analysis of brain shape to identify patterns of change related to disease progression. The AtlasWerks software package provides efficient CPU and GPU implementations of nonlinear deformation algorithms based on the Large Deformation Diffeomorphic Metric Mapping (LDMM) framework for single machines and clusters, command line frontends for atlas and deformation generation, and a number of utility programs for handling 3D medical image data. ...more

NCR Toolset

NCR Toolset is a collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data. This toolset includes Iris, Ir-mosaic, Ir-tweak, and Ir-tools.

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