Software developed and maintained by the CNR lab: 

CONN is an open-source SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). It has been used in over 5,000 neuroimaging studies to date, and it is ranked at NITRC as one of the top 10 most visited and downloaded tools and resources in neuroimaging. 

Features include import of DICOM, ANALYZE, and NIfTI files, automatic import tools for BIDS datasets and fMRIPrep outputs, flexible preprocessing pipelines of functional and anatomical volumes, control of residual physiological and motion artifacts, integrated quality control procedures and measures, Seed-Based Correlations (SBC), ROI-to-ROI analyses, complex-network analyses, generalized Psycho-Physiological Interaction models (gPPI), Independent Component Analyses, masked ICA, Amplitude of Low-Frequency Fluctuations, Intrinsic Connectivity (ICC), Local Homogeneity (LCOR), Global Correlations (GCOR), Inter-hemispheric correlations (IHC), functional connectivity Multivoxel Pattern Analyses (fc-MVPA), dynamic connectivity analyses, group- and population-level inferences and models, univariate and multivariate statistics, and control for multiple comparisons using parametric and non-parametric permutation/randomization techniques.

Visit for more details or CONN NITRC site to download this software.

SPM_SS is an open-source SPM toolbox for performing analyses of functional MRI data using subject-specific functional localizers to identify voxels/regions of interest separately for each subject. 

The toolbox implements ROI-level and voxel-level analyses, using an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics).

Visit SPM_SS NITRC site for more details or to download this software.

spm_crossvalidation is an open-source tool for leave-one-out cross-validation of SPM and CONN group-level analysis results

Matlab SPM-based tools for extracting cross-validated data from functional ROIs. Works in conjunction with the standard SPM second-level results window. Re-evaluates second-level analyses and contrast leaving one subject out at a time (leave-one-out cross-validation), and extracts subject-specific effect size estimates from the conjunction of supra-threshold voxels and one or multiple a-priori defined ROIs.

 Visit spm_crossvalidation github site to download this software.

design_efficiency is an open-source tool for the analysis of subject-level experimental design efficiency in task fMRI studies

This tool computes design efficiency of arbitrary block- or event- related designs. It supports continuous and sparse acquisition sequences with nonuniform sampling, and arbitrary first-level designs and contrasts. It includes a simple GUI for inspection of the effect of some of the most common design parameters, including scanning duration, number of conditions, block lengths, etc.

Visit design_efficiency github site  to download this software.