Replace config.execution.fmriprep_dir uses in BIDSURI calls with output_dir parameter

[tsalo]

What would you like to see added in fMRIPrep?

All of the workflows in fMRIPrep that currently use BIDSURI to track sources currently rely on config.execution.fmriprep_dir for the output directory, and yet all of those functions have an output_dir parameter.

It would be easier for other preps that use fMRIPrep as a dependency (i.e., ASLPrep) if we used output_dir instead of the config object's package-specific fmriprep_dir field.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

I think I completely overlooked the output_dir parameter when I started implementing BIDSURI-based source tracking (#3255, #3262, #3263, #3297) because I originally wanted to reference the config object directly within the BIDSURI interface, which ended up not working.

[effigies]

Sounds good to me.