title: An Automated, Adaptive Framework for Optimizing Preprocessing Pipelines in Task-Based Functional MRI.
abstract: BOLD fMRI is sensitive to blood-oxygenation changes correlated with brain function; however, it is limited by relatively weak signal and significant noise confounds. Many preprocessing algorithms have been developed to control noise and improve signal detection in fMRI. Although the chosen set of preprocessing and analysis steps (the "pipeline") significantly affects signal detection, pipelines are rarely quantitatively validated in the neuroimaging literature, due to complex preprocessing interactions. This paper outlines and validates an adaptive resampling framework for evaluating and optimizing preprocessing choices by optimizing data-driven metrics of task prediction and spatial reproducibility. Compared to standard "fixed" preprocessing pipelines, this optimization approach significantly improves independent validation measures of within-subject test-retest, and between-subject activation overlap, and behavioural prediction accuracy. We demonstrate that preprocessing choices function as implicit model regularizers, and that improvements due to pipeline optimization generalize across a range of simple to complex experimental tasks and analysis models. Results are shown for brief scanning sessions (<3 minutes each), demonstrating that with pipeline optimization, it is possible to obtain reliable results and brain-behaviour correlations in relatively small datasets.
authors.affiliation: Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Nathan W
authors.initials: NW
authors.lastname: Churchill
authors.affiliation: Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Robyn
authors.initials: R
authors.lastname: Spring
authors.affiliation: Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada.
authors.forename: Babak
authors.initials: B
authors.lastname: Afshin-Pour
authors.affiliation: Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada.
authors.forename: Fan
authors.initials: F
authors.lastname: Dong
authors.affiliation: Rotman Research Institute, Baycrest Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Strother
mesh_terms: D000328:Adult; D001921:Brain / Q000502:physiology*; D003071:Cognition / Q000502:physiology; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D009038:Motion; D015999:Multivariate Analysis; D011597:Psychomotor Performance / Q000502:physiology*; D021641:Recognition, Psychology / Q000502:physiology; D015203:Reproducibility of Results; D055815:Young Adult