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 | VTK The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. BSD license |
 | ITK ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. Apache 2.0 license |
 | FSL FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). license |
 | SPM Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. GPL license |
 | GIMIAS GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development. GIMIAS has functionalities for manual and automatic segmentation, visualization, mesh editing and electro mechanical and CFD simulation among others. BSD license |
 | 3D Slicer Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. BSD license |
 | MIA MIA is a general purpose image processing toolbox written in C++ that puts its focus on 2D and 3D gray scale medical image analysis. It is designed around a plug-in infrastructure that makes adding new functionality easy, uses a test-driven development to ensure reliability of the implementation, and provides command line tools as a means for algorithmic prototyping based on interactive execution of image processing tasks and their combination in shell scripts. GPLv3+ license |
Registration
 | NiftyReg This project, developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation. BSD license |
 | elastix elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. BSD license and contains some GNU Lesser Public Licence dependancies |
 | ANTS The ANTS package is designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). BSD license |
Segmentation
 | NiftySeg This project, developed at University College London, contains programs to perform EM based segmentation of nifti or analyse images. It also contains a package of label fusion algorithms (MV, STAPLE, SBA) with different types of ranking strategies. BSD license |
Visualisation
 | ITK-Snap SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. GPL license |
 | MITK The Medical Imaging Interaction Toolkit (MITK) is a free open-source software system for development of interactive medical image processing software. MITK combines the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) with an application framework. As a toolkit, MITK offers those features that are relevant for the development of interactive medical imaging software covered neither by ITK nor VTK. BSD-style license |
Reconstruction
 | NiftyRec This project, developed at UCL London, provides code for tomographic reconstruction. The software is written in C and comes with Python and Matlab (mex) interfaces. Computationally intensive functions have a GPU accelerated version based on CUDA. BSD license |
Simulation
 | NiftySim Nifty Sim is a high-performance nonlinear finite element solver, developed at University College London. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages. BSD license |
Diffusion
 | Camino Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. Artistic license 2.0 |
 | DTI-TK DTI-TK is a spatial normalization and atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. GPL license |
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