This study aims to improve the method used to produce cerebrovascular reactivity (CVR) maps by MRI. Previous methods have used a standard boxcar presentation of carbon dioxide (CO 2 ). Here this is replaced with a sinusoidally modulated CO 2 stimulus. This allowed the use of Fourier analysis techniques to measure both the amplitude and phase delay of the BOLD CVR response, and hence characterize the arrival sequence of blood to different regions of the brain. This characterization revealed statistically significant relative delays between regions of the brain (ANOVA < 0.0001). In addition, post hoc comparison showed that the frontal (P < 0.001) and parietal (P 5 0.004) lobes reacted earlier than the occipital lobe. Cerebrovascular reactivity (CVR) mapping using MRI is increasingly used to assess the effects of cerebrovascular conditions such as atherosclerotic steno-occlusive disease (1,2) and Moyamoya (3). CVR is conventionally mapped by administering CO 2 mixed with air through an open oxygen face mask. In early measurements, this stimulus was applied in an interleaved fashion with blocks of air, while BOLD-weighted images and measurements of end-tidal PCO 2 (PETCO 2 ) are acquired (4,5). This PETCO 2 time-course is then regressed against the BOLD data on a pixel-by-pixel basis to create CVR maps showing the strength of the correlation (2,6). The underlying assumption in generating maps in this way is that the CVR response occurs in all parts of the brain simultaneously. However, if the change in PCO 2 carried by the blood arrived in various areas of the brain at different times, or if there were a delayed vascular response to this change in PCO 2 in some brain regions, then the correlation between the BOLD signal and the PETCO 2 , and thus CVR, could be underestimated. Furthermore, variations in the arrival time of blood or response time of the vasculature, in different areas of the brain may provide useful diagnostic information.The aim of this study is to improve upon the existing BOLD CVR methodology by acquiring potentially useful information about the regional delays in the BOLD CVR response while minimizing errors due to any regional delays. This is achieved by combining a sinusoidally varying carbon dioxide stimulus with Fourier analysis techniques. To apply an accurate sinusoidal stimulus, a computerized gas blender was used along with a modelbased algorithm for prospective targeting and control of end-tidal PO 2 (PETO 2 ) and PCO 2 (7). This algorithm allows more accurate and independent control of PETO 2 and PETCO 2 than that achieved by simply presenting CO 2 mixed with air. This enables arbitrarily shaped changes in PETCO 2 to be administered, such as the sinusoid used here. This stimulus delivery can then be coupled with Fourier analysis techniques, as used in retinotopic mapping (8). This analysis method was chosen as synchronization of the MRI, and PETCO 2 data is not required, as it is the frequency of the signal that is detected, reducing confounding effects of inaccurate synchronization. In ...