Software installed in Lin4Neuro 12.04

Below is the list of Neuroimagin Softweare Packages included in Lin4Neuro 12.04 as of 13 Mar 2014;

  • 3D Slicer
    Tools for the segmentation, registration, and three-dimensional visualization of multi-modal image data. The package includes image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging, and image-guided therapy.

  • AFNI
    An environment for processing and displaying functional MRI data. It provides a complete analysis tool chain, including 3D cortical surface models and mapping of volumetric data (SUMA).

  • UCL Camino Diffusion MRI Toolkit
    Camino is an open-source software toolkit for diffusion MRI processing. The toolkit implements standard techniques, such as diffusion tensor fitting, mapping fractional anisotropy and mean diffusivity, deterministic and probabilistic tractography. It also contains more specialized and cutting-edge techniques, such as Monte-Carlo diffusion simulation, multi-fibre and HARDI reconstruction techniques, multi-fibre PICo, compartment models, and axon density and diameter estimation.

  • Caret
    A tool which enables the user to create, view, and manipulate surface reconstructions of the cerebral and cerebellar cortex. It also displays experimental data on surfaces and volumes.

  • Connectome Analyzer
    a complete set of tools to analyze connectomes from any source (DSI, DTI, QBall, rs-fMRI, etc…) at different scales (global, subnetworks and local).

  • Connectome Viewer
    The Connectome Viewer connects Multi-Modal Multi-Scale Neuroimaging and Network Datasets For Analysis and Visualization in Python.

  • DSI Studio 
    A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization.

  • FSL
    A comprehensive library of image analysis and statistical tools for fMRI, MRI, and DTI brain imaging data. Implementation of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis.

  • Ginkgo CADx
    An extensible multi-platform Open Source Medical Imaging software which provides a complete DICOM Viewer solution.

  • ITK-Snap
    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.

  • Minc toolkit

    Tools to manipulate MINC files.

  • MITK
    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.

  • MITK Diffusion
    A selection of image analysis algorithms for the processing of diffusion-weighted MR images. It encompasses the research of the Neuroimaging Group in the Division Medical and Biological Informatics at the German Cancer Research Center (dkfz).

  • MRIConvert
    A medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager, and MetaImage volume formats.

    Somehow MRIConvert doesn’t work fine now…

  • MRIcron
    A GUI-based visualization and analysis tool for (functional) MRI. It can also draw anatomical regions-of-interest (ROI), or lesion mapping, as well as basic analysis of functional time series. In addition to ‘mricron’, the package also provides ‘dcm2nii’, which supports converting DICOM and PAR/REC images into the NIfTI format and ‘npm’ for non-parametric data analysis.

  • MRtrix
    MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.

  • Virtual MRI (3.2.14)
    A realistic simulation of an MRI scanner. For the user it should be possible to change all the relevant settings of the virtual scanner and to adapt them to the expected pathology.