Structural and functional connectivity reconstruction with CATO - A Connectivity Analysis TOolbox

Abstract We describe a Connectivity Analysis TOolbox (CATO) for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging and resting-state functional MRI data. CATO is an integrative and modular software package that enables researchers to run end-to-end reconstructions from MRI data to structural and functional connectome maps, customize their analysis and utilize different software packages during the data preprocessing. The structural and functional connectome maps can be reconstructed with respect to user-defined (sub)cortical atlases providing aligned connectivity matrices for integrative multimodal analyses. We outline the structural and functional processing pipelines in CATO, the implementation in MATLAB and associated stand-alone application, and the calibration of performance with respect to simulated diffusion weighted imaging data and resting-state functional MRI data from the ICT2015 challenge and the Human Connectome Project. CATO is free open-source software and available at www.dutchconnectomelab.nl/CATO.