Download Software
Currently supported Software:
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Go to the FiberViewerLight webpage | Fiber ViewerLight is an open-source C++ application to analyze fiber bundles. It provides: Several methods for clustering 3D fibers visualization 3D plane selection |
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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…)
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| 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.
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| 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. |
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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 : Affine Registration with BRAINSFit 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…
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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. |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Go to the NITRC SPHARM-PDM page | The SPHARM shape analysis toolset is used for doing local statistical shape analysis. ITK based. |
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Go to the NITRC MriWatcher page | MriWatcher is a vizualisation tool for MRI images (.gipl,.mha,.hdr). Coupled cursors to show the differences between images Load an overlay images Screenshot |
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Go to the HeadCircumference webpage | Program which compute head circumference based on a 3D image Use Fourier harmonics to parametrize the contour Embedded tutorial Store results in an excel spreadsheet automatically |
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Go to the MakeAtlasScripts – Rodent webpage | Sets of BatchMake scripts to process rodent images
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Non-supported Software:
NeuroLib download page
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