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The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort of subjects. The MRI data acquired by the HCP differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by thedoi:10.1016/j.neuroimage.2013.04.127 pmid:23668970 pmcid:PMC3720813 fatcat:odadekdvwzakxlxc4u24smozp4