Abstract
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.
Highlights
Most functional magnetic resonance image scans are acquired using echo planar imaging (EPI), which rapidly acquires single or multiple 2D slices and stacks them to create a 3D volume
All t-tests were calculated with respect to the slice timing correction (STC) “Before motion correction (MC)” case within each method/motion/interleave block, which is highlighted in gray, and the pipeline with the highest average z-score value is bolded within each STC/Interleave/Motion category
In an effort to critically examine the effects of STC in the context of a standard preprocessing pipeline, we have performed a series of experiments in which we manipulate the preprocessing pipeline on data with various levels of motion and with various slice acquisition orders
Summary
Most functional magnetic resonance image (fMRI) scans are acquired using echo planar imaging (EPI), which rapidly acquires single or multiple 2D slices and stacks them to create a 3D volume. This process typically takes between 0.5 and 4 s (known as the repetition time, or TR), depending on the fMRI pulse sequence, field of view (FOV), and number of acquired slices (Stehling et al, 1991). In order for an accurate time series analysis to be carried out on the fMRI data, these temporal offsets between slices must be corrected for.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
