Research > Software


LONI is a leader in the development of advanced computational algorithms and software for the comprehensive and quantitative mapping of brain structure and function. LONI aims to encourage communication between users and LONI software engineers in order to improve the effectiveness of our software and to promote its use by researchers worldwide. We have expanded our software website to include more tools, training and support. Be sure to visit LONI Forums and discuss our tools with other end-users as well as our dedicated LONI staff.

LONI Webapps allow users to analyze, visualize and interact with neuroscience data directly from their web browser.

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Data Management
Surface Modeling
Shape Analysis
Image Processing
Statistical Analysis
A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple and yet extensive API that provides the core functionality of 2-D image presentation needed by most imaging applications.
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.
Brain Surface Extraction: Designed to automatically extract the brain from a set of T1 weighted Magnetic Resonance (MR) images of the human head.
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.
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.
An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.
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.
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.
ConvexHull is a Java based tool that computes the convex hull of a given shape. The convex hull is the minimal convex set that contains the vertices of the given shape. Similarly, the convex hull is the intersection of all convex sets that contain the given shape.
DuffOffTranslator is an application that converts between the Duff (*.dfs) and Off (*.off) surface formats with a minimal loss of data.
GeodesicPath is an application that finds the shortest path between two vertices on a surface. Two types of shortest paths the application can find are the Dijkstra path and the Geodesic path.
ImageToShape is an application that creates a shape file that encodes the intensity data of a planar slice of a volume image.
The SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications.
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.
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.
MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model.
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.
The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file.
The ShapeCurvature application allows researchers to calculate the curvature of a surface mesh that is stored in a shape file. These curvature values may be written to disk files in a variety of file formats.
The ShapeToDX application is a Java application that translates data files that can be read by the ShapeTools library into an OpenDX "genreal format" data file.
The VirtualFileSystemBrowser is an interoperable replacement for the Java JFileChooser. It supports most JFileChooser methods and functionality for local file systems, and extends this functionality to remote file systems supporting the sFtp and ssh protocols.
The FFT library is used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms.
A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model. The program automatically segments all the vessels with connected components until no further vascular trees are observed.
CFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data.
IO Plugins
Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.
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.
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.
BrainSuite is a suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools.<br><br><div style="border:1px solid #666; padding:10px; background-color:#eee; color:#ff0000; font-weight:bold;font-size:11px; font-family:arial;">Please note that we have released a new version of BrainSuite, which you can download here: <a href=""></a>.</div>
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.
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.
InterpolateUCF is a Java based tool that interpolates contour vertices and data attributes in a UCF file. UCF file contours typically contain widely varying numbers of sample points. The analysis of these files often requires that the contours of the files be re-sampled into a regular grid, which allows groups of UCF files to be meaningfully compared.
The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines.
ShapeDistance allows the point-by-point comparison of two shapes or surface meshes. The distance between comparable vertices at each point of the two shapes compared is calculated and stored in an output file.
The DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files.
Pygr is an open source software project used to develop graph database interfaces.
ShapeViewer Applet enables a three dimensional view of these structures to be easily embedded into a web page. This view may be rotated and zoomed by the user.
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.
The Morphometric Atlasing Statistical Toolkit is a collection of tools which deals with the general problem of creating statistical maps of data from populations of subjects.
The ShapeTransform application applies a linear coordinate transformation to the vertex coordinates of a shape file. This makes it possible to move a shape file from one coordinate system to another, and reduces the number of separate programs needed to manage coordinate system transformations.
FDRShape is an application that performs a False Discovery Rate procedure on the p-values associated with the vertices of a shape.
iTools offers a graphical interface for perusing meta-data information about software tools, databases and material resources freely provided by NCBC funded institutions. iTools is built upon the XML framework prescribed by, for generating and disseminating resource descriptions.
For a given shape defined by a set of contours, MedialDistance computes and stores the distance from the vertices of a shape to a polygon passing through the centers of each of the contours.
ShapeToObj converts an arbitrary ShapeTools-compatible surface file to a Minc Obj surface file.
UcfReorder will perform several useful re-orderings of the vertices of a LONI Ucf file.
GAMIXTURE is a collection of software for solving complex finite mixture model parameter estimation problems in neuroimaging. At the moment, the Matlab package for the FMM parameter estimation is available.
The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.
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).
Analysis tool to extract geometric and contrast informmation from ADNI phantom scans
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.
NI Provenance
The LONI Neuroimaging Provenance XSD is an XML schema Document for validating and describing .prov data provenance description files
InterpolateContour interpolates the vertices and data attributes of a contour file.
MLS is an algorithm and application for skull-stripping magnetic resonance.
The BrainGraph Editor is a JAVA based tool that allows researchers to create taxonomies or hierarchies to classify and organize information such as anatomy, connectivity, and developmental stages.
The goal of the MBAT is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases.
A collection of applications based on the various ShapeTools libraries.
REM registers N-D image pairs that may contain topological differences. It produces an output reconstructed image and both a geometric and intensity transformation as a N-D vector field.
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.
This web resource provides an online framework for evaluating the results of skull-stripping algorithms. Users may browse the results produced by others, or they may download the test data, segment it with their own algorithm, and upload it to have it evaluated.
DIRAC is a collection of tools for rapid and robust processing of diffusion-weighted imaging (DWI) data. Programs are included for both diffusion tensor and HARDI reconstruction and analysis.
The LONI Pipeline Web Start (PWS) has all of the features and functionality of the stand-alone Pipeline software application. Users can run PWS directly from their web browser. There is no need to register, download or install anything. You have immediate and direct access to the LONI Pipeline servers. As soon as you allow the program to launch, your workflow will start.
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.
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.