I am having a similar issue. I installed docker, followed the tutorial on how to run fmriprep and everything seems fine until I try to run:
$fmriprep-docker /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/Nifti /Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/derivatives participant --participant-label 2475376 --fs-license-file /Users/franklinfeingold/freesurfer.txt --ignore slicetiming
I get “command not found”. I dug around the previous posts here and I suspect I have to set up my “environment” but not sure what that entails.