Complex and magnitude‐only preprocessing of 2D and 3D BOLD fMRI data at 7 T

A challenge to ultra high field functional magnetic resonance imaging is the predominance of noise associated with physiological processes unrelated to tasks of interest. This degradation in data quality may be partially reversed using a series of preprocessing algorithms designed to retrospectively estimate and remove the effects of these noise sources. However, such algorithms are routinely validated only in isolation, and thus consideration of their efficacies within realistic preprocessing pipelines and on different data sets is often overlooked. We investigate the application of eight possible combinations of three pseudo‐complementary preprocessing algorithms – phase regression, Stockwell transform filtering, and retrospective image correction – to suppress physiological noise in 2D and 3D functional data at 7 T. The performance of each preprocessing pipeline was evaluated using data‐driven metrics of reproducibility and prediction. The optimal preprocessing pipeline for both 2D and 3D functional data included phase regression, Stockwell transform filtering, and retrospective image correction. This result supports the hypothesis that a complex preprocessing pipeline is preferable to a magnitude‐only pipeline, and suggests that functional magnetic resonance imaging studies should retain complex images and externally monitor subjects' respiratory and cardiac cycles so that these supplementary data may be used to retrospectively reduce noise and enhance overall data quality. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.