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.
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.
Conducts surface registration from multiple sources of information. MSM represents displacement of each surface vertex in form of a discrete set of possible rotations. It offers a regularization term method specially created for the spherical surface. This tool is based on penalising the geodesic distance between rotation matrices. It has a reduced sensitivity to local minima and includes a multivariate mutual-information measure.
Manages task-based and resting-state functional magnetic resonance imaging (fMRI) for analysis. FMRIPrep is divided into anatomical and functional preprocessing tasks which are both composed of modules that can be merged differently according to the user input data. It encompasses several features such as voxel-based, resting-state connectivity or surface-based analysis. The software can also be run through the OpenNeuro platform or the Singularity container.
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).
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