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Laboratory of Neuro Imaging Resource

Arthur W. Toga, Ph.D.
P41EB015922
Active

Center Overview

The Laboratory of Neuro Imaging Resource (LONIR) develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.

Impact on Human Health

The mission of the Laboratory of Neuro Imaging (LONI) is to improve understanding of the human brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for comprehensive and quantitative mapping of brain structure and function.

To provide powerful tools to study brain diseases, research at LONI goes beyond just atlases and maps of the brain with static morphology. It develops frameworks and tools for three-dimensional reconstruction and visualization at different time points of a specific study. This enables rigorous evaluation of dynamic changes during brain development, aging, and progression of specific diseases.

LONI is a key partner in many national and international collaborations. One important ongoing collaboration at LONI is to serve as the Informatics Core for the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, funded by NIH. ADNI leverages infrastructures and tools developed at LONI for receiving, archiving, and displaying all MRI and PET data.

Tags

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
BGE - Brain Graph Editor
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
CFMBIS - Charged Fluid Model for Brain Image Segmentation
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Unix, Windows N/A N/A
DiD - LONI De-identification Debablet
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
DIRAC - Diffusion Imaging Reconstruction and Analysis Collection
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
DPS - LONI Distributed Pipeline Server Installation Utility
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux N/A N/A
DSM - DualSurfaceMin
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Unix Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
FFT Library
Laboratory of Neuro Imaging Resource
NIBIB

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

Linux, Mac OSX, Windows N/A N/A
GAMIXTURE Matlab toolbox
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows Matlab N/A N/A
jViewbox
Laboratory of Neuro Imaging Resource
NIBIB

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.

Irix, Linux, Mac OSX, Unix, Windows N/A N/A
LONI Brain Parser
Laboratory of Neuro Imaging Resource
NIBIB

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.

Windows N/A N/A
LONI Debabeler
Laboratory of Neuro Imaging Resource
NIBIB

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 researcher's needs.

Irix, Linux, Mac OSX, Unix, Windows N/A N/A
LONI ICE - It's Close Enuf
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
LONI Inspector
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows AFNI, Analyze (.hdr), Analyze...(more) N/A N/A
LONI Java Image I/O Plugins
Laboratory of Neuro Imaging Resource
NIBIB

Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.

Linux, Mac OSX, Windows AFNI, Analyze (.hdr), Analyze...(more) N/A N/A
LOVE
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Unix, Windows N/A N/A
MAST - Morphometric Atlasing Statistical Toolkit
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows CCBBM, Duff, MINC, Minc...(more) N/A N/A
MBAT - Mouse BIRN Atlasing Toolkit
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
MLS - Model-based Level Set
Laboratory of Neuro Imaging Resource
NIBIB

MLS is an algorithm and application for skull-stripping magnetic resonance.

MRI N/A N/A
MRFSEG+GAMIXTURE Software Bundle
Laboratory of Neuro Imaging Resource
NIBIB

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).

Linux N/A N/A
MultiPhase-SEG
Laboratory of Neuro Imaging Resource
NIBIB

MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model.

Linux, Mac OSX, Windows N/A N/A
Neuroimaging Provenance XSD
Laboratory of Neuro Imaging Resource
NIBIB

The LONI Neuroimaging Provenance XSD is an XML schema Document for validating and describing .prov data provenance description files

Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
Pipeline - LONI Pipeline Processing Environment
Laboratory of Neuro Imaging Resource
NIBIB

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.

N/A N/A
Provenance Editor
Laboratory of Neuro Imaging Resource
NIBIB

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.

Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
PWS - LONI Pipeline Web Start
Laboratory of Neuro Imaging Resource
NIBIB

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.

Web-Based N/A N/A
REM - Registration using Embedded Maps
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
ShapeTools
Laboratory of Neuro Imaging Resource
NIBIB

The LONI 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.

Linux, Mac OSX, Windows N/A N/A
ShapeTools Applications
Laboratory of Neuro Imaging Resource
NIBIB

A collection of applications based on the various ShapeTools libraries.

Linux, Mac OSX, Windows Minc OBJ, OFF, PLY,...(more) N/A N/A
ShapeViewer
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Unix, Windows GIFTI, Minc OBJ, OFF,...(more) N/A N/A
SHIVA - Synchronized Histological Image Viewing Architecture
Laboratory of Neuro Imaging Resource
NIBIB

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.

N/A N/A
SurfaceWarpTools
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows N/A N/A
SVT - Sub-Volume Thresholding Analysis
Laboratory of Neuro Imaging Resource
NIBIB

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.

Irix N/A N/A
WAIR - Wavelet Analysis of Image Registration
Laboratory of Neuro Imaging Resource
NIBIB

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.

Irix N/A N/A
Public Anonymized Dataset (PAD)
Laboratory of Neuro Imaging Resource
NIBIB

Public anonymized MRI dataset.

MRI N/A