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The fMRI community has made great strides in decoupling neuronal activity from other physiologically induced T2* changes, using sensors that provide a ground-truth with respect to cardiac, respiratory, and head movement dynamics. However, blood oxygenation level-dependent (BOLD) time-series dynamics are confounded by scanner artifacts, in complex ways that can vary not only between scanners but even, for the same scanner, between sessions. The lack of equivalent ground truth has thus far stymied the development of reliable methods for identification and removal of scanner-induced noise. To address this problem, we first designed and built a phantom capable of providing dynamic signals equivalent to that of the resting-state brain. Using the dynamic phantom, we quantified voxel-wise noise by comparing the ground-truth time-series with its measured fMRI data. We derived the following data-quality metrics: Standardized Signal-to-Noise Ratio (ST-SNR) and Dynamic Fidelity that can be directly compared across scanners. Dynamic phantom data acquired from four scanners showed scanner-instability multiplicative noise contributions of about 6-18% of the total noise. We further measured strong non-linearity in the fMRI response for all scanners, ranging between 8-19% of total voxels. To correct scanner distortion of fMRI time-series dynamics at a single-subject level, we trained a convolutional neural network (CNN) on paired sets of measured vs. ground-truth data. Tests on dynamic phantom time-series showed a 4- to 7-fold increase in ST-SNR and about 40-70% increase in Dynamic Fidelity after denoising. Critically, we observed that the CNN temporal denoising pushes ST-SNR > 1. Denoising human-data with ground-truth-trained CNN showed markedly increased detection sensitivity of resting-state networks.