CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).

CONN includes a rich set of connectivity analyses (seed-based correlations, ROI-to-ROI graph analyses, group ICA, masked ICA, generalized PPI, ALFF, ICC, GCOR, LCOR, etc.) in a simple-to-use and powerful software package

CONN is available for resting state data (rsfMRI) as well as task-related designs. It covers the entire pipeline from raw fMRI data to hypothesis testing.

Highlights:
Comprehensive quality assurance methods/measures/displays (scrubbing/ART, CompCor/ICA/GSR denoising, GCOR/FD QC covariates)
Connectome-wide analyses (ICA, MVPA)
Dynamic connectivity analyses (dyn-ICA)
FWE-control of connectivity matrices (NBS)
Non-parametric cluster-level statistics (permutation tests)
ANOVA, regression, longitudinal, and mixed designs

Parallelization options (SGE/Grid Engine, PBS/Torque, LSF, Slurm)
Mac/Windows/Linux/HPC
SPM8/SPM12

http://www.conn-toolbox.org