MAINT: Update to the new API of sMRIPrep

[oesteban]

Replaces #1827 because I need extra flexibility to solve issues (and I believe @adelavega will appreciate that I take care of this).

[auto-comment]

Thank your for raising your pull request.

Some of the fMRIPRep maintainers will review your changes as soon as time permits.
I'm attaching below a Review Checklist for the reviewers, to copy and paste
it in their review comment.

## PR Review

*Please check off boxes as applicable, and elaborate in comments below.  Your review is not limited to these topics, as described in the reviewer guide*

- [ ] As the reviewer I confirm that there are no conflicts of interest for me to review this work.

Please check what applies in the following aspects of the PR:

#### Code documentation

- [ ] New functions and modules are documented following the guidelines.
- [ ] Existing code required amendments in documentation and has been updated.
- [ ] Sufficient inline comments ensure readability by other contributors in the long term.

#### Documentation site

- [ ] The modifications to *fMRIPrep* in this PR **do not require extra documentation**. This is a common situation when a bug fix that does not change the code base substantially is submitted.
- [ ] This PR requires documentation. The corresponding documentation will be submitted as an additional PR in the future.
- [ ] This PR requires extra documentation, and will be included within this PR. Please check the boxes that apply best:
  - [ ] An existing feature is substantially modified, changing the interface and/or logic of a module.
  - [ ] A new feature is being added, therefore full documentation of it will be included
  - [ ] This PR addresses an error in existing documentation.
- [ ] Yes, all expected sections of documentation were generated by the CI build, and look as expected

#### Tests

- [ ] The new functionalities in this PR are covered by the existing tests
- [ ] New test batteries have been included with this PR

#### Data

- [ ] This PR does not require any additional data to be uploaded to OSF.
- [ ] This PR requires additional data for tests.

#### Dependencies: smriprep

- [ ] This PR does not require any update on `smriprep`; or
- [ ] `smriprep` has correctly been pinned.

#### Dependencies: niworkflows

- [ ] This PR does not require any update on `niworkflows`; or
- [ ] `niworkflows` has correctly been pinned.

#### Dependencies: sdcflows

- [ ] This PR does not require any update on `sdcflows`; or
- [ ] `sdcflows` has correctly been pinned.

#### Dependencies: Nipype

- [ ] This PR does not require any update on `nipype`; or
- [ ] `nipype` has correctly been pinned.

#### Dependencies: other

- [ ] This PR does not require any update on other dependencies; or
- [ ] other dependencies have correctly been pinned.

#### Reports generated within CI tests

- [ ] Yes, I have checked the reports of ds005 and they are not modified or the changes are as expected
- [ ] Yes, I have checked the reports of ds054 and they are not modified or the changes are as expected
- [ ] Yes, I have checked the reports of ds010 and they are not modified or the changes are as expected

### Review Comments (other than those left inline with the code)

[oesteban]

@adelavega you'd be very welcome to add your name to the contributors' list (which is ordered alphabetically by lastname):

https://github.com/poldracklab/fmriprep/blob/7bc943ef0739eba1e1cde4ff390d505d7c2256ef/.maint/contributors.json

[effigies]

Looks good. Tiny aesthetic thing that you can ignore or [skip ci] on.

[mgxd]

looking good, just missing a little documentation