Characterizing contrast origins and noise contribution in spin-echo EPI BOLD at 3 T

In this work, we characterize contrast origins and noise contributions of spin echo (SE) EPI BOLD signal at 3 T. SE BOLD is a fMRI method of choice for imaging brain regions affected by susceptibility artifacts at lower fields, but its sensitivity remains a limiting factor for whole-brain imaging. To resolve this, the signal and noise contributions as well as TE dependence of SE EPI are characterized in this study. By integrating a two-compartment BOLD model with a physiological-thermal noise model, a new SE-BOLD signal model was introduced. The new SE-BOLD model was fit into SE-EPI fMRI data acquired during hypercapnic manipulations at various TEs, using typical fMRI voxel dimensions (3.4 × 3.4 × 5 mm³). Our model predicts intra- and extravascular signal and noise contributions consistent with our understanding of the SE-EPI contrast mechanism. The intravascular BOLD contribution is shown to dominate at TEs lower than tissue T₂, but the physiological noise contributions in SE-EPI signal is also shown to be lower than that of gradient-echo (GE). Furthermore, SE-EPI contrast-to-noise ratio (CNR) is not maximized at tissue T₂ as is typically assumed. To summarize, a new SE-BOLD model was proposed to characterize SE-BOLD contrast and physiological noise contribution at 3 T. Results suggests that SE-BOLD sensitivity can be improved by using shorter TEs, making it a more attractive choice for fMRI, especially in regions with susceptibility artifacts. Such optimizations could also help extend the application of SE BOLD to WM fMRI studies.