The computation of physiological factors and factor images by factor analysis in dynamic structures using the constraints of positive factors and spatial distribution of these factors (FADS), currently used by a number of research workers, is investigated. While the positivity constraints used may be quite acceptable physically, they cannot be strictly said to have direct correlations with the underlying physiological mechanisms in a dynamic study. In principle, FADS estimates the underlying model in the absence of a priori physiological information, and therefore, it is possible that in some situations an incorrect model is extracted. A procedure called IBFADS (information-based factor analysis in dynamic structures) is described which incorporates the IM (intersection method) technique previously developed into FADS, in order to reduce the error in the estimation of the correct model. IM uses a constraint based on physiology of one of the dynamic structures in the model. A computer simulated dynamic phantom study is used to demonstrate IBFADS.