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

[tsalo]

Closes #3337.

Changes proposed in this pull request

• Use output_dir function argument for BIDSURI objects instead of the config.execution.fmriprep_dir field. This will let other preps (e.g., ASLPrep) use these workflow functions without having to mock up fmriprep_dir fields in their config objects.

[effigies]

Are there any of these in smriprep?

[tsalo]

Not yet. I think I was planning to add BIDSURIs to smriprep and sdcflows at some point, but I haven't gotten around to it yet.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.03%. Comparing base (ea65196) to head (f8121f0).
Report is 79 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3338   +/-   ##
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  Coverage   71.03%   71.03%           
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  Files          56       56           
  Lines        4233     4233           
  Branches      638      638           
=======================================
  Hits         3007     3007           
  Misses       1114     1114           
  Partials      112      112           

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