BrainCAT - Brain Connectivity Analysis Tool

Combined functional Magnetic Resonance Imaging (fMRI) and Diffusion Tensor Imaging (DTI) studies gained increasing popularity in recent years. These studies mainly focus on finding which white matter tracts reconstructed from DTI tractography interconnect the clusters of resting state networks extracted from resting state fMRI data through Independent Component Analysis (ICA).

However, several difficulties limit the use this multimodal approach, especially for newcomers to the neuroimaging field. The amount of generated data, the lack of standardized procedures for multimodal analysis, the amount of tools to be used and parameters to be set as well as the need for manual interventions are just some examples of such difficulties.

We developed a new Mac OS application called BrainCAT (Brain Connectivity Analysis Tool) as a simple and user-friendly application that enables the user to perform such analysis in a fully automated way, from raw data to results, pipelining tools from previously installed software packages. With BrainCAT, the user can preprocess diffusion-weighted and fMRI images, run ICA on fMRI data, extract resting state networks’ clusters and filter the white matter pathways that interconnect those clusters. Moreover, several statistics about both analyses are outputted.


  • Paulo César Gonçalves Marques
  • José Miguel Montenegro Soares
  • Victor Manuel Rodrigues Alves
  • Nuno Jorge Carvalho Sousa