AFNI package: https://afni.nimh.nih.gov/node/5     AFNI Tutorial

Multivariate Pattern Analysis in Python: http://www.pymvpa.org/    MVPA Example

Presentation program, Neurobehavioral System : https://www.neurobs.com/

EEG Lab: https://sccn.ucsd.edu/eeglab/index.php

FSL package: https://fsl.fmrib.ox.ac.uk/fslcourse/

Drift Diffusion Model (a python toolbox)  :http://ski.clps.brown.edu/hddm_docs/

Multivariate EQS program, http://www.mvsoft.com/      

SPM package (very slow, not preferred): http://www.fil.ion.ucl.ac.uk/spm/

Brain Connectivity Toolbox

Brain predictability toolbox

Network science

R package: R help for beginner    R help_CN  

Online_Python     Interesting blog