In quantitative PET and SPECT imaging signal activity is typically estimated from calculations in a 3D region of interest (ROI) of the reconstructed slices. In these calculations, unpredictable bias arising from the null functions of the imaging system (e.g. signal size and location) affects ROI estimates. An alternative to the ROI method is the scanning linear estimator (SLE), which operates on the raw projection data. In this work, we compared the ROI and SLE methods through analytic simulations of a realistic NCAT human phantom modeling 111In-Octreotide studies. The task was to estimate the signal activity of a spherical lesion in the liver, and its size and location are known. The performance of SLE and ROI methods were compared for two assumptions about the activity in the liver: 1) a uniform distribution of known value and 2) a non-uniform and random distribution. For all imaging scenarios in this simulation study the SLE estimated the uptake values better than the ROI estimation when compared using the ensemble-mean-squared error (EMSE).