The premise of image guided radiotherapy is the use of imaging to target the delivery of radiotherapy with high precision. Despite the high resolution of amorphous silicon flat panel imagers the detection of small implanted radiographic gold markers (length: 5mm, diameter: 0.8mm), visualised on portal images with low SNR and the inherent low contrast of mega-voltage photons, remains a significant, safety critical challenge. Convolution/correlation and sum of the squares of the difference (SSD) detection algorithms make use of marker templates to detect radiographic markers. However, direct convolution is not specific enough and SSD techniques fail in low SNR conditions. This report defines a robust SSD measure operating on a model template-to-clinical convolution image and a semi-empirical template self-convolution image, which is used to assign an objective measure of confidence to individual markers and unambiguously determine the separation of true and false detection distributions. The algorithm was tested on 9 clinical pelvic images produced by placing a template with 14 randomly arranged gold markers on patients during portal imaging. Using 95% confidence limits in a localised regional search for each of the 14 seeds, the number of correct detections averaged at 13, while the average number of false detections was less than 1.