Motion-induced artifact detection has become a fixture in the assessment of functional magnetic resonance imaging (fMRI) quality control. However, the effects of other MR image quality (IQ) metrics on intrinsic connectivity brain networks are largely unexplored. Accordingly, we report herein the initial assessment of the effects of a comprehensive list of IQ metrics on resting state networks using a multivariate analysis of covariance (MANCOVA) approach based on high-order spatial independent component analysis (ICA). Three categories of MR IQ metrics were considered: (1) metrics for artifacts including the AFNI outlier ratio and quality index, framewise displacement, and ghost to signal ratio, (2) metrics for the temporal quality of MRI data including the temporal framewise change in global BOLD signals (DVARS), global correlation of time-series, and temporal signal to noise ratio, (3) metrics for the structural quality of MRI data including the entropy focus criterion, foreground-background energy ratio, full-width half maximum smoothness, and static signal to noise ratio. After FDR-correction for multiple comparisons, results showed significant effects of the static and temporal signal to noise ratios on the spatial map intensities of the basal ganglia, default-mode and cerebellar networks. AFNI outlier ratio, framewise displacement and DVARS exhibited significant effects on the BOLD power spectra of sensorimotor networks. The global correlation of time-series displayed wide-spread modulation of the spectral power in most networks. Further investigations of the effect of IQ metrics on the characteristics of intrinsic connectivity brain networks allow more accurate interpretation of the fMRI results.