Software installed or to be installed in Lin4Neuro 18.04

Below is the list of Neuroimaging Softweare Packages included in Lin4Neuro 18.04 as of 17 May 2020;

  • 3D Slicer (4.10.2) (can be installed from installer)
    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 (the latest version can be installed from installer)
    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).

  • Advanced Normalization Tools: ANTs (compiled on 02 Feb 2020)

  • Convert3d (1.0)
    Convert3d is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling. The tool can also be used to obtain information about image files.

  • DSI Studio (compiled on 9 Mar 2019)
    A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization.

  • FreeSurfer (Version 6.0/7.1 can be installed from installer)
    An open source software suite for processing and analyzing (human) brain MRI images.

  • FSL (the latest version can be installed from installer)
    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.

  • HCP connectome workbench (1.4.2: You need to install FreeSurfer and FSL beforehand to use workbench)
    An open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualiation platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data. wb_command is necessary for running HCP data processing pipelines.

  • ITK-Snap (3.8.0)
    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.

  • Mango (V4.1)
    A viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.

  • MRIConvert (2.0.8 build 416)
    A medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager, and MetaImage volume formats.

  • MRIcroGL (31-Mar-2020)
    A program designed to display 3D medical imaging.
    By using computer’s graphics card, MRIcroGL can allow real-time interactive rendering.

  • MRIcron (12OCT2016)
    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 (the latest version can be installed from installer)
    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.

  • Robust Brain Extraction (ROBEX) (1.2)
    ROBEX is an automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping).
    ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.

  • 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.

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