Image segmentation software tools | Magnetic resonance imaging analysis
Image segmentation is one of the most important tasks in medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, image segmentation is commonly used for measuring and visualizing the brain’s anatomical structures, for analyzing brain changes, for delineating pathological regions, and for surgical planning and image-guided interventions.
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 for instance skull stripping, image registration, subcortical segmentation, cortical surface reconstruction, cortical segmentation, cortical thickness estimation, longitudinal processing, fMRI analysis or tractography.
Offers a digital imaging and communications in medicine (DICOM) solution. OsiriX is an image processing software that provides displaying, reviewing, interpreting and post-processing image files. It supports DICOM standard for a complete integration in a workflow environment and in a picture archiving and communication system (PACS).
Allows users to segment structures in 3D medical images. ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. It is an application providing a method to extract structures in 3D image data of different modalities and from different anatomical regions. Moreover, it permits users to link cursor for 3D navigation or to post-process the segmentation results.
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.
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.
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.
Segments structural magnetic resonance imaging (MRI) data. IBASPM aims to complement the SPM software by providing an atlas registration approach. It offers a set of features dedicated to: (i) spatial normalization; (ii) segments gray/white matter and cerebral spinal fluid tissues; (iii) labellisation; (iv) generate atlases, statistical probability anatomy maps (SPAMs) and MaxProb atlases; (v) compute statistics and individual brain volumes and (vi) visualize results. This program is compatible with SPM2 et SPM5.