In this paper, a computerised system for measuring muscle thicknesses of the transverse abdominus (TrA), internal oblique and external oblique muscles based on ultrasonography is presented. The system is designed to allow for quantitative analysis of changes in muscle recruitment and activity, which facilitates the study of such changes and its relationship with low back pain. The abdominal muscle area was localised and imaged under different standing conditions using B-mode ultrasonography. To account for issues such as misalignments due to probe and subject motion as well as speckle noise inherent to ultrasonography, automatic ensemble registration is performed on the acquired images using a sequential quadratic programming approach based on a novel log-Rayleigh likelihood function. Regions of interest are then automatically identified based on the medial border of the TrA for the purpose of quantitative muscle thickness measurements. Experimental results show that the proposed system achieves registration errors of under 0.4 mm when compared with ground-truth measurements, as well as allow for the measurement of muscle thickness changes in the millimetre range. The proposed system is currently in operational use as an analysis tool for studying the relationship between abdominal muscle thickness changes and postural changes.