Allows the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. FreeSurfer proposes a suite of tools that provide extensive and automated analysis of key features in the human brain. This includes skull stripping, image registration, subcortical segmentation, cortical surface reconstruction, cortical segmentation, cortical thickness estimation, longitudinal processing, fMRI analysis, tractography, FreeView Visualization GUI, etc... FreeSurfer is freely available, runs on a wide variety of hardware and software platforms, and is open source.
Computes high-dimensional mappings to capture the statistics of brain structure and function. ANTs allows users to organize, visualize and statistically explore large biomedical image sets. It integrates imaging modalities and related information in space and time, and works across species or organ systems with minimal customization. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute. ANTs can be used paired with ANTsR, an emerging tool supporting standardized multimodality image analysis. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.
Automates regional behavioral analysis of human brain images. Mango provides analysis tools and a user interface to navigate image volumes. The tool is ease to use, multi-platform Java application and extensive region of interest tools. It has the ability to add and update software as a plugin module and offers full access to a suite of image viewing and processing features. The software is able to rapidly determine regionally specific behaviors for researchers’ brain studies.
Allows detailed investigation and evaluation of multidimensional biomedical images. AnalyzePro can serve for magnetic resonance imaging, radionuclide emission tomography, ultrasound tomography, and 3-D imaging modalities based on x-ray computed tomography. It contains features for interactive display, manipulation and measurement of multidimensional image data.
Provides a high-resolution in vivo magnetic resonance imaging template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, maps of tissue segmentation and cortical thickness were generated. Surface reconstructions and transformations to previously published digital brain atlases are also provided. An analysis pipeline using the NMT automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies.
Offers an assortment of utilities for 3D mesh tasks. iso2mesh is a toolbox including functionalities for: (i) surface mesh extraction; (ii) surface mesh repairing; (iii) sub-region labeling and hole specifications; (iv) generation of water-tight surfaces; (v) surface mesh smoothing and (vi) volumetric mesh generation and adaptative resolution. This application aims to ease multi-modal analysis with a focus on structural and functional image fusion.
Provides a surface mesh renderer. MRIcros is a standalone application intending to be used as a complement for the SPM software. It can be used to: (i) visualize meshes, connectome data and track files; (ii) basic features allowing users to parameter wireframe, desired rotation, color and transparency of images; (iii) display region of interest (ROI) nodes and connectivity links; (iv) get surface meshes from voxel images.
Hosts heterogeneous tools dedicated to neuroimaging research. BrainVISA aims to help researchers in developing new neuroimaging tools, sharing data and distributing software. It offers a way to define viewers which may use any visualization software. Thanks to its data management functions, the tool can define the data types handled by the software, associate key attributes for indexation, and filename patterns to make the link between the filesystem and the database schema.
Allows users to display multiplanar, orthogonal views, volume and surface renderings with thresholding-based tissue segmentation. 3DimViewer is a lightweight 3D viewer of medical digital imaging and communications in medicine (DICOM) datasets. It contains several features such as: distance and density measuring, high quality volume rendering for direct 3D visualization, surface reconstruction of any segmented tissue, or 3D surface rendering.
Provides a software environment for comprehensively processing 3D image data (MRI, CT, micro-CT, FIB-SEM…). Simpleware ScanIP offers powerful image visualisation, analysis, segmentation, and quantification tools. It includes video recording features and options to export surface models/meshes from segmented data for CAD and 3D printing. Additional modules are available for exporting CAE meshes, integrating image data and CAD, exporting NURBS and calculating effective material properties from scans.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Creates interactive surface plots from all image types. Interactive 3D Surface Plot assists in interpreting the luminance of an image, and in viewing the position of the plot. The plugin has several modes for displaying surface plots: (1) drawing mode; (2) display colors; (3) axes; and (4) invert. It allows users to realize 3D projection.
Serves for the creation and visualization of surface reconstructions of the cerebral and cerebellar cortex. Caret provides several features such as viewing and manipulation of experimental data on surfaces and volumes. It has a graphical and interactive interface but provides also a command line option containing up to 200 command-line operations that permits batch processing of neuroimaging data.
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