The effect of echo time and post-processing procedure on blood oxygenation level-dependent (BOLD) functional connectivity analysis

While spontaneous BOLD fMRI signal is a common tool to map functional connectivity, unexplained inter- and intra-subject variability frequently complicates interpretation. Similar to evoked BOLD fMRI responses, spontaneous BOLD signal is expected to vary with echo time (TE) and corresponding intra/extravascular sensitivity. This may contribute to discrepant conclusions even following identical post-processing pipelines. Here we applied commonly-utilized independent component analysis (ICA) as well as seed-based correlation analysis and investigated default mode network (DMN) and visual network (VN) detection from BOLD data acquired at three TEs (3 T; TR = 2500 ms; TE = 15 ms, 35 ms, and 55 ms) and from quantitative R2* maps. Explained variance in ICA analysis was significantly higher (P < 0.05) when R2*-derived maps were considered relative to single-TE data with no post-processing. While explained variance in the BOLD data increased with motion correction, R2* derived DMN and VN were minimally affected by motion correction. Explained variance increased in all data when physiological noise confounds were removed using CompCor. Notably, the R2*-derived connectivity patterns were least affected by motion and physiological noise confounds in a seed-based correlation analysis. Intermediate (35 ms) and long (55 ms) TE data provided similar spatial and temporal characteristics only after reducing motion and physiological noise contamination. Results provide an exemplar for how 3 T spontaneous BOLD network detection varies with TE and post-processing procedure over the range of commonly acquired TE values.