The Configurable Pipeline for the Analysis of Connectomes (C-PAC) is an open-source software pipeline for automated preprocessing and analysis of resting-state fMRI data. C-PAC builds upon a robust set of existing software packages including AFNI, FSL, and ANTS, and makes it easy for both novice users and experts to explore their data using a wide array of analytic tools. Users define analysis pipelines by specifying a combination of preprocessing options and analyses to be run on an arbitrary number of subjects. Results can then be compared across groups using the integrated group statistics feature.