Inter-subject differences in local cerebral blood flow (CBF) and cerebral blood volume (CBV) contribute to differences in BOLD signal reactivity and, therefore, unmodelled variance in group level fMRI analyses. A simple way of elevating blood CO(2) concentrations to characterise subject differences in vascular reactivity is through breath-holds but two aspects of this measure are often neglected: (1) breath-holds are usually modelled as blocks even though CO(2) accumulates over time and (2) increases in CO(2) differ between subjects. This study demonstrates that the BOLD breath-hold response is best modelled by convolving the end-tidal CO(2) trace with a standard haemodynamic response function and including its temporal derivative. Inclusion of the BOLD breath-hold response as a voxel-dependent covariate in a group level analysis increases the spatial extent of activation in stimulus evoked and resting state datasets. By expressing the BOLD breath-hold response as a percentage signal increase with respect to an absolute change in the partial pressure of CO(2) (expressed in mmHg), the spatial extent of stimulus-evoked activation is further improved. This demonstrates that individual end-tidal CO(2) increases to breath-hold should be accounted for to provide an accurate measure of vascular reactivity resulting in more statistically active voxels in group level analyses.
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