Using functional magnetic resonance imaging (fMRI) data to analyze human brain is an effective way to explore brain function and structure in medicine. We have developed a MATLAB toolbox called Intelligent Analysis of Brain Connectivity (IABC) Toolbox for extracting and analyzing brain functional networks and related measures from large-scale fMRI data. Our previous work group-information guided independent component analysis (GIG-ICA), NeuroMark and splitting-merging assisted reliable ICA (SMARTICA) make great progress in the analysis of fMRI data and generation of independent components among subjects. IABC integrates GIG-ICA ,NeuroMark and SMARTICA to estimate the brain functional network of individual subjects from fMRI data. IABC can also automatically determine an optimal number of spatial maps, visualize brain functions network and generate report of parameters information, pictures of independent components, function network connection and time courses.