New to BIDS? Check out resources on the Brain Imaging Data Structure https://bids.neuroimaging.io/

A list of useful software containers that work on BIDS-formatted data (BIDS apps):

Freesurfer: https://github.com/bids-apps/freesurfer
fMRIPrep: https://fmriprep.org/en/stable/
QSIPrep: https://qsiprep.readthedocs.io/en/latest/index.html
SPM: https://github.com/bids-apps/SPM and https://github.com/cpp-lln-lab/bidspm
MRTrix3: https://github.com/bids-apps/MRtrix3_connectome
ASLPrep: https://github.com/PennLINC/aslprep
xcp_d: https://github.com/PennLINC/xcp_d