I am trying to run fmriprep in an own built docker container. The docker container starts a python script which runs fmriprep. When running fmriprep it tells me: fmriprep: error: The selected working directory is a subdirectory of the input BIDS folder. Please modify the output path.
This is not the case when I run fmriprep just with a terminal command. So is it really necessary to have two different folders? the docker-wrapper fmriprep-docker never threw up this error.