Fmriprep intermediate results

A number of people in our lab are now using fmriprep and my question is about the intermediate results folder defined by the --work-dir switch.

Those files tend to take large storage space which is usually many times the size of the actual output data. Is it the case that these intermediate results files can be deleted when fmriprep has completed? Are there any instances where these work files should be kept?

Hello, and welcome to NeuroStars! In general, you can delete the intermediate files after fmriprep runs successfully.

If execution is interrupted for any reason, the intermediate files allow fmriprep to resume execution from the interrupt point. It can also be useful to retain the intermediate files if there is an error during execution, since they can be used to facilitate error diagnosis.