C-arms are well suited for obtaining cone-beam projections intra-operatively. Due to the compact size of the detector used, the data are usually truncated within the field of view. As a result, direct application of a standard cone-beam reconstruction algorithm gives rise to undesirable artifacts and incorrect values in the reconstructed image volume. When prior information such as a pre-operative CT scan is available, fully truncated cone-beam projections can be used to recover the change within a small region of interest without such artifacts. A method for integrating prior CT is developed using the concept of pi-lines and tested on real flat-panel and simulated cone-beam data.