We have developed a flexible x-ray micro-CT system, named FaCT, capable of changing its geometric configuration and acquisition protocol in order to best suit an object being imaged for a particular diagnostic task. High-performance computing technologies have been a major enabling factor for this adaptive CT system in terms of system control, fast reconstruction, and data analysis. In this work, we demonstrate an adaptive procedure in which a quick, sparse-projection pre-scan is performed, the data are reconstructed, and a region of interest is identified. Next, a diagnostic-quality scan is performed where, given the region of interest, the control computer calculates an illumination window for on-line control of an x-ray source masking aperture to transmit radiation only through the region of interest throughout the scan trajectory. Finally, the diagnostic scan data are reconstructed, with the region of interest being clearly resolved. We use a combination of a multi-core CPU and a pair of NVIDIA Tesla GPUs to perform these tasks.