Software installed or to be installed in Lin4Neuro

Below is the list of Neuroimaging Softweare Packages included in Lin4Neuro as of 24 Sep 2022;

* installed in Lin4Neuro minimal
** installed in Lin4Neuro standard
*** installer is provided

• 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).

• Aliza MS**
  A cross-platform DICOM viewer with various useful functions.

• Advanced Normalization Tools: ANTs**

• Convert3d aka c3d*
  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.

• CONN toolbox***
  CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). I provide a standalone running on matlab runtime.

• 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.

• FreeSurfer***
  An open source software suite for processing and analyzing (human) brain MRI images.

• 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.

• HCP connectome 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**
  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*
  A viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.

• MRIcroGL*
  A program designed to display 3D medical imaging.
  By using computer’s graphics card, MRIcroGL can allow real-time interactive rendering.
  This also includes dcm2niix, a dicom to nifti converter.

• 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.

• MRtrix3**
  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.

• 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 a free and open source software that is called SPM.
  I provide a standalone running on Matlab Runtime

• Virtual MRI*
  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.