Three dimensional echo-planar imaging at 7 Tesla

Abstract

Functional MRI (fMRI) most commonly employs 2D echo-planar imaging (EPI). The advantages for fMRI brought about by the increasingly popular ultra-high field strengths are best exploited in high-resolution acquisitions, but here 2D EPI becomes impractical for several reasons, including the very long volume acquisitions times. In this study at 7 T, a 3D EPI sequence with full parallel and partial Fourier imaging capability along both phase encoding axes was implemented and used to evaluate the sensitivity of 3D and corresponding 2D EPI acquisitions at four different spatial resolutions ranging from small to typical voxel sizes (1.5-3.0 mm isotropic). Whole-brain resting state measurements (N=4) revealed a better, or at least comparable sensitivity of the 3D method for gray and white matter. The larger vulnerability of 3D to physiological effects was outweighed by the much shorter volume TR, which moreover allows whole-brain coverage at high resolution within fully acceptable limits for event-related fMRI: TR was only 3.07 s for 1.5 mm, 1.88 s for 2.0 mm, 1.38 s for 2.5 mm and 1.07 s for 3.0 mm isotropic resolution. In order to investigate the ability to detect and spatially resolve BOLD activation in the visual cortex, functional 3D EPI experiments (N=8) were performed at 1 mm isotropic resolution with parallel imaging acceleration of 3x3, resulting in a TR of only 3.2 s for whole-brain coverage. From our results, and several other practical advantages of 3D over 2D EPI found in the present study, we conclude that 3D EPI provides a useful alternative for whole-brain fMRI at 7 T, not only when high-resolution data are required.

Fig 1

Theoretical sensitivity of 2D and 3D EPI as a function of the number of acquired slices (top) the relative performance of 3D vs. 2D EPI (bottom) in the absence of physiological noise as derived from the signal equations (Eqs1 and 2) for the case without parallel undersampling. Since the resulting volume TR are identical for both methods, their relative sensitivities scale with the MR signal. The dashed lines indicate the approximate number of slices needed for whole-brain coverage (≥ 100mm axial slab) at the different spatial resolutions.

Fig 2

Plots of sensitivity against voxel volume for the 2D (dashed lines) versus 3D EPI protocols (straight lines), shown separately for GM (top), WM (middle) and CSF (bottom). The errors bars indicate standard error over subjects (N= 4).

Fig 3

Whole brain mean intensity images with 1mm³ resolution, obtained with 3D EPI at 7 T using the 32 channel coil and factor 3×3 acceleration, resulting in a TR of only 3.2 s. The top panel (a) shows all 104 slices in mosaic view as well as a zoomed view of slice49. Panel (b) - (d) give a zoomed view of ten slices covering the occipital cortex, overlaid with the visual activation obtained with a smoothing kernel of 3mm (b), 0.75 mm (c) and no smoothing (d).