Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn

Abstract

Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity analyses. Many viable strategies for denoising fMRI are used in the literature, and practitioners rely on denoising benchmarks for guidance in the selection of an appropriate choice for their study. However, fMRI denoising software is an ever-evolving field, and the benchmarks can quickly become obsolete as the techniques or implementations change. In this work, we present a denoising benchmark featuring a range of denoising strategies, datasets and evaluation metrics for connectivity analyses, based on the popular fMRIprep software. The benchmark prototypes an implementation of a reproducible framework, where the provided Jupyter Book enables readers to reproduce or modify the figures on the Neurolibre reproducible preprint server ( https://neurolibre.org/). We demonstrate how such a reproducible benchmark can be used for continuous evaluation of research software, by comparing two versions of the fMRIprep. Most of the benchmark results were consistent with prior literature. Scrubbing, a technique which excludes time points with excessive motion, combined with global signal regression, is generally effective at noise removal. Scrubbing was generally effective, but is incompatible with statistical analyses requiring the continuous sampling of brain signal, for which a simpler strategy, using motion parameters, average activity in select brain compartments, and global signal regression, is preferred. Importantly, we found that certain denoising strategies behave inconsistently across datasets and/or versions of fMRIPrep, or had a different behavior than in previously published benchmarks. This work will hopefully provide useful guidelines for the fMRIprep users community, and highlight the importance of continuous evaluation of research methods.

Author summary

Many strategies exist to denoise fMRI signal. However, denoising software is ever-evolving, and benchmarks quickly become obsolete. Here, we present a denoising benchmark featuring several strategies and datasets to evaluate functional connectivity analysis, based on fMRIprep. The benchmark is implemented in a fully reproducible framework. The provided Jupyter Book enables readers to reproduce core computations and figures from the Neurolibre reproducible preprint server ( https://neurolibre.org/). Most results were consistent with prior literature. Scrubbing was generally effective, but is incompatible with statistical analyses requiring the continuous sampling of brain signals, for which a simpler strategy is preferred. Importantly, we found that certain denoising strategies behaved inconsistently across datasets and/or fMRIPrep versions, or differently from the literature. Our benchmark can enable the continuous evaluation of research software and provide up-to-date denoising guidelines to fMRIprep users. This generic reproducible infrastructure can facilitate the continuous evaluation of research tools across various fields.