The Benefit of Slice Timing Correction in Common fMRI Preprocessing Pipelines

Due to the nature of fMRI acquisition protocols, slices cannot be acquired simultaneously, and as a result, are temporally misaligned from each other. To correct from this misalignment, preprocessing pipelines often incorporate slice timing correction (STC). However, evaluating the benefits of STC is challenging because it (1) is dependent on slice acquisition parameters, (2) interacts with head movement in a non-linear fashion, and (3) significantly changes with other preprocessing steps, fMRI experimental design, and fMRI acquisition parameters. Presently, the interaction of STC with various scan conditions has not been extensively examined. Here, we examine the effect of STC when it is applied with various other preprocessing steps such as motion correction (MC), motion parameter residualization (MPR), and spatial smoothing. Using 180 simulated and 30 real fMRI data, we quantitatively demonstrate that the optimal order in which STC should be applied depends on interleave parameters and motion level. We also demonstrate the benefit STC on sub-second-TR scans and for functional connectivity analysis. We conclude that STC is a critical part of the preprocessing pipeline that can be extremely beneficial for fMRI processing. However, its effectiveness interacts with other preprocessing steps and with other scan parameters and conditions which may obscure its significant importance in the fMRI processing pipeline.