A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.
BrainSuite13 is a collection of image analysis tools designed to process magnetic resonance images (MRI) of the human brain. BrainSuite13 provides an automatic sequence to extract cortical surface mesh models from the MRI, tools to register these to a labeled atlas to define anatomical regions of interest, and tools for processing diffusion imaging data including coregistration to anatomical data, ODF and tensor fitting and tractography. BrainSuite13 also contains visualization tools for exploring these data, and can produce interactive maps of regional connectivity.
The dualsurfacemin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images.
Brain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.
A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files. Removal of this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.
The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats. Its visual programming environment provides an intuitive and easy way to modify a variety of existing translations to meet researchers' needs.
DPS is a utility that streamlines the process of setting up an independent Pipeline environment. The interface walks a user through several steps, providing default preferences along the way, but also gives the user flexibility in configuring the resulting system. As a result, this tool is designed to be used by neuroscientists, bioinformaticians, and system administrators alike.
LONI ICE is a Java application that generates seed points for other image processing applications. ICE stands for "It's Close Enuf" and implies that the seed points it generates are "close enough" to be useful.
The LONI Pipeline is a free workflow application primarily aimed at Neuroimaging Researchers. With the LONI Pipeline, users can create workflows that take advantage of all the greatest Neuroimaging tools available, quickly.
The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.
The LONI ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java, it can run on a wide variety of computers.
MBAT provides a workflow environment bringing together online resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. MBAT is written in java so it is platform independent and is extensible through its plugin architecture.
MRFSEG+GAMIXTURE is a collection of tools implementing a flexible voxel classification framework. The framework is based on a novel genetic algorithm based finite mixture model (GAMIXTURE) and a standard 3-D Markov random field (MRF) based on the iterative conditional modes (ICM) algorithm (MRFSEG).
MultiTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.
SVT is a tool for the Statistical Analysis of Stereotactic Functional Brain Data. The series of 'C' subroutines which comprise the SVT library can be easily incorporated into the user's site specific programs adapted to their particular needs.
The Surface Warping protocol warps a collection of shapes to an atlas, using sets of sulcal contours to guide the warp. The atlas is computed from the contours provided by the user, and the resulting shapes will have anatomically homologous vertices.
The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets.
A tool for the quantitative analysis of various n-dimensional (n-D) image registration techniques. The series of 'C' subroutines which comprise the WAIR library can be easily incorporated into the user's site specific programs and adapted to their particular needs.