Micapipe: A pipeline for multimodal neuroimaging and connectome analysis

•Micapipe is a comprehensive pipeline to process multimodal MRI data.•Micapipe generates matrices describing cortico-cortical microstructural similarity, functional connectivity, structural connectivity, and spatial proximity.•The pipeline provides easy-to-verify outputs and visualizations for quality control.•Outputs are hierarchically organized with BIDS-conform naming.•Our evaluations show reproducible processing across several 3T and 7T datasets.