Graph Theory GLM (GTG) MATLAB Toolbox. This MATLAB toolbox calculates & runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous & categorical between-participant predictors & categorical within-participant predictors. Significance is determined via non-parametric permutation tests, including correction for multiple comparisons. Both fully connected & thresholded networks are tested. The toolbox also provides a data processing path for resting state & task fMRI data. Options for partialing nuisance signals include: local & total white matter signal (Jo et al., 2013), PCA of white matter/ventricular signal (Muschelli et al., 2014), Saad et al. (2013)’s GCOR, & Chen et al. (2012)’s GNI. In addition, Power et al. (2014)’s motion scrubbing method & Patel et al. (2014)’s WaveletDespike are available.