The Computational Anatomy Toolbox (CAT) is a powerful suite of tools for brain morphometric analyses, offering an intuitive graphical user interface and the ability to be used as a shell script. It is suitable for users of all levels, providing a comprehensive set of analysis options, workflows, and integrated pipelines. CAT supports voxel-based, surface-based, and region-based morphometric analyses, including preprocessing of cross-sectional and longitudinal data, statistical analysis, and visualization of results. It incorporates multiple quality control options and covers the entire analysis workflow. CAT is designed to work with SPM12 and is compatible with MATLAB versions 7.4 and later. It is free and distributed under the GNU General Public License. CAT can be started through SPM, from the MATLAB command window, from a shell, or as a standalone version. It provides a user interface for easy access to all analysis options and functions, along with graphical output windows for interactive help. CAT's processing pipeline includes two main streams: voxel-based processing for voxel-based morphometry (VBM) and surface-based processing for surface-based morphometry (SBM). VBM involves tissue segmentation and spatial registration, while SBM includes surface creation and registration. Both streams can be extended to include region-based processing and region-based morphometry (RBM). Voxel-based processing involves tissue segmentation and spatial registration. Tissue segmentation uses a spatially adaptive nonlocal means denoising filter and SPM's standard unified segmentation. Spatial registration uses geodesic shooting to register individual tissue segments to standardized templates. VBM also includes adjustments for volume changes due to registration and convolution with a 3D Gaussian kernel. Surface-based processing includes surface creation and registration. Surface creation uses a projection-based thickness method, while surface registration uses a 2D version of the DARTEL approach. SBM includes surface-based morphometry, such as cortical thickness, cortical folding, and cortical complexity. CAT provides region-based processing and morphometry, allowing for regional analyses via region-based morphometry (RBM). It supports both voxel-based and surface-based ROIs, using standardized atlases. CAT has been evaluated and proven to be accurate, sensitive, reliable, and robust, outperforming other common neuroimaging tools. It supports longitudinal processing, quality control, mapping onto the cortical surface, and threshold-free cluster enhancement (TFCE). It allows for visualization of results and is suitable for both small and large datasets. CAT is compatible with various operating systems and programming languages, and it supports the Brain Imaging Data Structure (BIDS) standards. It is a valuable alternative to other neuroimaging tools and is suitable for structural, functional, diffusion, and quantitative MRI data analysis.The Computational Anatomy Toolbox (CAT) is a powerful suite of tools for brain morphometric analyses, offering an intuitive graphical user interface and the ability to be used as a shell script. It is suitable for users of all levels, providing a comprehensive set of analysis options, workflows, and integrated pipelines. CAT supports voxel-based, surface-based, and region-based morphometric analyses, including preprocessing of cross-sectional and longitudinal data, statistical analysis, and visualization of results. It incorporates multiple quality control options and covers the entire analysis workflow. CAT is designed to work with SPM12 and is compatible with MATLAB versions 7.4 and later. It is free and distributed under the GNU General Public License. CAT can be started through SPM, from the MATLAB command window, from a shell, or as a standalone version. It provides a user interface for easy access to all analysis options and functions, along with graphical output windows for interactive help. CAT's processing pipeline includes two main streams: voxel-based processing for voxel-based morphometry (VBM) and surface-based processing for surface-based morphometry (SBM). VBM involves tissue segmentation and spatial registration, while SBM includes surface creation and registration. Both streams can be extended to include region-based processing and region-based morphometry (RBM). Voxel-based processing involves tissue segmentation and spatial registration. Tissue segmentation uses a spatially adaptive nonlocal means denoising filter and SPM's standard unified segmentation. Spatial registration uses geodesic shooting to register individual tissue segments to standardized templates. VBM also includes adjustments for volume changes due to registration and convolution with a 3D Gaussian kernel. Surface-based processing includes surface creation and registration. Surface creation uses a projection-based thickness method, while surface registration uses a 2D version of the DARTEL approach. SBM includes surface-based morphometry, such as cortical thickness, cortical folding, and cortical complexity. CAT provides region-based processing and morphometry, allowing for regional analyses via region-based morphometry (RBM). It supports both voxel-based and surface-based ROIs, using standardized atlases. CAT has been evaluated and proven to be accurate, sensitive, reliable, and robust, outperforming other common neuroimaging tools. It supports longitudinal processing, quality control, mapping onto the cortical surface, and threshold-free cluster enhancement (TFCE). It allows for visualization of results and is suitable for both small and large datasets. CAT is compatible with various operating systems and programming languages, and it supports the Brain Imaging Data Structure (BIDS) standards. It is a valuable alternative to other neuroimaging tools and is suitable for structural, functional, diffusion, and quantitative MRI data analysis.