FATCAT: (an efficient) Functional and Tractographic Connectivity Analysis Toolbox

Brain Connect. 2013;3(5):523-35. doi: 10.1089/brain.2013.0154.


We present a suite of software tools for facilitating the combination of functional magnetic resonance imaging (FMRI) and diffusion-based tractography from a network-focused point of view. The programs have been designed for investigating functionally derived gray matter networks and related structural white matter networks. The software comprises the Functional and Tractographic Connectivity Analysis Toolbox (FATCAT), now freely distributed with AFNI. This toolbox supports common file formats and has been designed to integrate as easily as possible with existing standard FMRI pipelines and diffusion software, such as AFNI, FSL, and TrackVis. The programs are efficient, run by commandline for facilitating group processing, and produce several visualizable outputs. Here, we present the programs and their underlying methods, and we also provide a test example of resting-state FMRI analysis combined with tractography. Tractography results are compared with existing methods, showing significantly reduced runtime and generally similar connectivity, but with important differences such as more circumscribed tract regions and more physiologically identifiable paths produced between several region-of-interest pairs. Currently, FATCAT uses only diffusion tensor-based tractography (one direction per voxel), but higher-order models will soon be included.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Brain Mapping / methods*
  • Brain* / anatomy & histology
  • Brain* / physiology
  • Diffusion Tensor Imaging / methods*
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Magnetic Resonance Imaging / methods
  • Nerve Net* / anatomy & histology
  • Nerve Net* / physiology
  • Neural Pathways / anatomy & histology
  • Neural Pathways / physiology
  • Reproducibility of Results
  • Rest / physiology
  • Software*