The effect of slice order and thickness on fMRI activation data using multislice echo-planar imaging

Abstract Multislice echo-planar imaging (EPI) is a commonly used technique for fMRI studies. Brain activation images acquired using fMRI are sensitive to T 2 * changes, reflecting the level of blood oxygenation (BOLD contrast), and may also contain an element of T 1 contrast which detects blood flow changes in large vessels. If slice inflow (T 1 ) effects are significant in multislice EPI, then as the order in which the slices are acquired is changed, differences in the activation maps are predicted. However, in experiments presented here using visual stimulation, the data demonstrate that highly consistent results can be achieved for repetition times (TR) of 6.0, 3.0, and 1.5 s. This suggests that, for whole-brain multislice EPI, fMRI activation is dominated by T 2 *, BOLD contrast. The thickness of the imaging slice is also an important parameter in these studies, having implications for spatial resolution, sensitivity, and acquisition time. In separate visual cortex experiments the effect on the values of the fMRI Z scores and the number of activated voxels is investigated as a function of slice thickness (from 1 to 8 mm). The maximum Z scores in the data are similar for all slice thicknesses and, after resampling to allow a direct comparison to be made, the volume of visual cortex detected as significantly activated increases with slice thickness.