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Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.
Supporting Files of paper titled "Dynamic Simulation of Parkinson's Disease and ALS Propagation in the Brain: A Reaction-Diffusion on Brain Networks Approach"
micapipe from the Multimodal imaging and connectome analysis lab (http:https://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below