Looking at Neurostars’ backlog of issues tagged with fmriprep, many people seem to have issues with the gridding and spatial reference of outputs from fMRIPrep and the usage of templates.
We are starting discussions about how to make that bit of the command line interface more usable and user-friendly. Your feedback will be very much appreciated at https://github.com/poldracklab/fmriprep/issues/1588.
Thanks very much