CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data

Abstract

A large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing the field of human brain mapping. Here we introduce the Computational Anatomy Toolbox (CAT) - a powerful suite of tools for morphometric analyses with an intuitive graphical user interface, but also usable as a shell script. CAT is suitable for beginners, casual users, experts, and developers alike providing a comprehensive set of analysis options, workflows, and integrated pipelines. The available analysis streams - illustrated on an example dataset - allow for voxel-based, surface-based, as well as region-based morphometric analyses. Importantly, CAT includes various quality control options and covers the entire analysis workflow, from cross-sectional or longitudinal data processing, to the statistical analysis, and visualization of results. The overarching aim of this article is to provide a complete description of CAT, while, at the same time, offering a citable standard reference.

Auditory driven gamma synchrony is associated with cortical thickness in widespread cortical areas

“…Segmentation/reconstruction and labeling, as well as estimation of cortical thickness of the anatomical MRI, were performed with the CAT12 toolbox for MATLAB implemented in the Brainstorm toolbox, applying default parameters ( Gaser and Dahnke, 2016 ). For the quality control assurance checks, we relied on the control metrics generated by CAT12.…”

An investigation of the cognitive and neural correlates of semantic memory search related to creative ability

“…In the last step of the preprocessing, the data were co-registered on the T1-weighted structural image using the Statistical Parametric Mapping (SPM) 12 package running in Matlab (Matlab R2017b, The MathWorks, Inc., USA) and normalized to the Montreal Neurological Institute (MNI) template. To spatially normalize the fMRI data, we used the transformation matrix computed from the normalization of the T1-weighted structural image, using with the default settings of the computational anatomy toolbox (CAT 12; http://dbm.neuro.unijena.de/cat/) 153 implemented in SPM 12.…”

Gray matter volumetric correlates of attention deficit and hyperactivity traits in emerging adolescents

“…Quality check of images was performed visually and quantitatively with tools available in the CAT12 toolbox 69 . One axial slice (z = 0) per subject was plotted and visually checked (option “Display slices”), and outliers were detected by computing the voxel-wise cross-correlation of GM density across subjects (option “Check sample homogeneity”).…”