Abstract
Multi-echo fMRI data acquisition has been widely investigated and suggested to optimize sensitivity for detecting the BOLD signal. Several methods have also been proposed for the combination of data with different echo times. The aim of the present study was to investigate whether these advanced echo combination methods provide advantages over the simple averaging of echoes when state-of-the-art group-level random-effect analyses are performed. Both resting-state and task-based dual-echo fMRI data were collected from 27 healthy adult individuals (14 male, mean age = 25.75 years) using standard echo-planar acquisition methods at 3T. Both resting-state and task-based data were subjected to a standard image pre-processing pipeline. Subsequently the two echoes were combined as a weighted average, using four different strategies for calculating the weights: (1) simple arithmetic averaging, (2) BOLD sensitivity weighting, (3) temporal-signal-to-noise ratio weighting and (4) temporal BOLD sensitivity weighting. Our results clearly show that the simple averaging of data with the different echoes is sufficient. Advanced echo combination methods may provide advantages on a single-subject level but when considering random-effects group level statistics they provide no benefit regarding sensitivity (i.e., group-level t-values) compared to the simple echo-averaging approach. One possible reason for the lack of clear advantages may be that apart from increasing the average BOLD sensitivity at the single-subject level, the advanced weighted averaging methods also inflate the inter-subject variance. As the echo combination methods provide very similar results, the recommendation is to choose between them depending on the availability of time for collecting additional resting-state data or whether subject-level or group-level analyses are planned.
Highlights
Increases in blood oxygenation level dependent (BOLD) signal in functional magnetic resonance imaging are only transient and it is advantageous to acquire fMRI data with high temporal resolution
Out of the four examined echoweighting strategies the BOLD sensitivity (BS) weighting of Echo combination #2 produces the time-series with the highest sensitivity when averaged across the entire group
We have investigated whether there is an optimal way of combining dual-echo fMRI data for random-effects group-level analysis
Summary
Increases in blood oxygenation level dependent (BOLD) signal in functional magnetic resonance imaging (fMRI) are only transient and it is advantageous to acquire fMRI data with high temporal resolution. Prescribing oblique slices (Deichmann et al, 2003), employing z-shimming (Ordidge et al, 1994; Weiskopf et al, 2006) or acquiring images at higher resolution (Weiskopf et al, 2007) avoid the signal drop-out depending on whether TE is shifted in the phase or frequency encoding direction by the local susceptibility gradient. These methods are not necessarily advantageous in all voxels containing brain tissue and may even be disadvantageous for voxels that are not in the vicinity of susceptibility induced magnetic field gradients
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