Skip to main content

Currently supported Software:

FiberViewerLight logo
Go to the FiberViewerLight webpage Fiber ViewerLight is an open-source C++ application to analyze fiber bundles. It provides:
Several methods for clustering
arrow.gif 3D fibers visualization
arrow.gif 3D plane selection
dtiatlasfiberanalyzer-logo-v2 Go to the DTIAtlasFiberAnalyzer (DTI Fiber Tract Statistics) webpage DTIAtlasFiberAnalyzer is an open-source C++ application that applies an atlas fiber to all individual subjects from a dataset, extracts fiber profiles, gathers and plots related information (FA map…)


DTI-Reg Go to the DTI-Reg webpage DTI-Reg is an open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration.


Tractograpy with unscented Kalman Filter Go to the UKF webpage We present a framework which uses an unscented Kalman filter to perform tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods.
DTIAtlasBuilderIcon Go to the DTIAtlasBuilder webpage This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps :
arrow.gif Affine Registration with BRAINSFit
arrow.gif Non Linear Registration with GreedyAtlas
A final step will apply the transformations to the original DTI images so that the final average can be computed.
DTI Process Toolkit Go to the DTI Process webpage DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess…


CCSeg logo

Go to the CCSeg webpage CCSeg is an open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum.

Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.

NIRAL Utilities Logo

Go to the NIRAL Utilities webpage NIRAL Utilities are open-source C++ based command line applications that allow image analysis and processing using ITK or VTK libraries
ShapeWorks logo
Go to the ShapeWorks webpage ShapeWorks software is an open-source distribution (initially developped by the SCI Institute) 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:
Data preprocessing
Group-wise particle-based shape correspondence
Data visualization

DTIPrep logo

Go to the DTIPrep webpage DTIPrep performs a “Study-specific Protocol” based automatic pipeline for DWI/DTI quality control and preparation:
Image/diffusion information check
Interlace-wise and gradient-wise intensity and motion check
Head motion and Eddy current artifact correction
DTI computation

AutoSeg logo

Go to the AutoSeg webpage AutoSeg is an end-to-end application that performs automatic brain tissue classification and structural segmentation:
Atlas-based EM tissue segmentation
Atlas-based subcortical structure segmentation and lobar parcellation
Regional histogram analysis


Go to the GAMBIT webpage GAMBIT is an end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements:
Voxel-based cortical thickness
White matter cortical surface creation and inflation
Group-wise shape correspondence using ShapeWorks


Go to the ARCTIC webpage ARCTIC (Automatic Regional Cortical ThICkness) is a cross-platform end-to-end application allowing individual analysis of cortical thickness. It can be run within Slicer3 as an external module or directly as a command line:
Brain tissue segmentation
Lobar cortical thickness analysis
White and gray matter mesh creation


Go to the NITRC SPHARM-PDM page The SPHARM shape analysis toolset is used for doing local statistical shape analysis. ITK based.


Go to the NITRC MriWatcher page MriWatcher is a vizualisation tool for MRI images (.gipl,.mha,.hdr).
arrow.gif Coupled cursors to show the differences between images
arrow.gif Load an overlay images
arrow.gif Screenshot


Go to the HeadCircumference webpage Program which compute head circumference based on a 3D image
arrow.gif Use Fourier harmonics to parametrize the contour
arrow.gif Embedded tutorial
arrow.gif Store results in an excel spreadsheet automatically


Go to the MakeAtlasScripts – Rodent webpage Sets of BatchMake scripts to process rodent images

arrow.gif Perform alignment, skullstripping, average computation, parcellation, region based statistics

Non-supported Software:

NeuroLib download page

Other deprecated software

CCSeg is an open-source C++-based application developed at UNC-Chapel Hill that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation