It is very critical for image processing of IIR (Imaging Infrared) seekers to achieve improved guidance performance for missile systems to determine appropriate thresholds in various environments. In this paper, we propose automatic threshold determination methods for proper thresholds to extract definite target signals in an EOCM (Electro-Optical Countermeasures) environment with low SNR (Signal-to-Noise Ratios). In particular, thresholds are found to be too low to extract target signals if one uses the Otsu method so that we suggest a Shifted Otsu method to solve this problem. Also we improve extracting target signal by changing Shifted Otsu thresholds according to the TBR (Target to Background Ratio). The suggested method is tested for real IIR images and the results are compared with the Otsu method. The HPDAF (Highest Probabilistic Data Association Filter) which selects the target originated measurements by taking into account of both signal intensity and statistical distance information is applied in this study.