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.
multishell option is replaced by HARDI_singleTissue or HARDI_multitissue
HARDI_multitissue applies mrtrix msmt reconstruction