Increasingly, clinical trials based on brain imaging are adopting multiple sites/centers to increase their subject pool and to expedite the studies, and more longitudinal studies are using multiple imaging methods to assess structural and functional changes. Careful investigation of the test-retest reliability and image quality of inter- or intra- scanner neuroimaging measurements are critical in the design, statistical analysis and interpretation of results. We propose a framework and specific metrics to quantify the reproducibility and image quality for neuroimaging studies (structural, BOLD and Diffusion Tensor Imaging) collected across identical scanners and following a major hardware repair (gradient coil replacement). We achieved consistent measures for the proposed metrics: structural (mean volume in specific regions and stretch factor), functional (temporal Signal-to-Noise ratio), diffusion (mean Fractional Anisotropy and Mean Diffusivity in multiple regions). The proposed frame work of imaging metrics should be used to perform daily quality assurance testing and incorporated into multi-center studies.