ENH: Allow multiple {non,}standard spaces (--output-spaces)

[oesteban]

This is a large refactor using two major inter-related features:

• Uses ENH: Create a spatial normalization workflow smriprep#72 and its continuation within
  ENH: Support for multiple --output-spaces smriprep#75 to permit the specification of several
  spatial normalization targets (close Support templates other than MNI152NLin2009cAsym #1558).
• Uses the refactor of Reports generation of
  ENH: Refactor of the Report generation tools niworkflows#344, which enables rendering reports with
  several normalization spaces. Correspondingly, report generation
  code and config files have been removed.

Correspondingly, the new interface for --output-spaces is also
incorporated (close #1588).

[oesteban]

This is working seemingly fine with ds005 locally, including --use-aroma and --use-syn-sdc along with --output-spaces anat MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2 fsaverage:den-10k MNI152Lin:res-2.

I expect many issues building docs and running ds054 though.

[effigies]

If you want a review before the CI is fixed, let me know.

[oesteban]

Let's wait for Circle to be all green 👍

[oesteban]

Okay, this is looking much better. Last commit is a good candidate for getting all green lights.

Documentation is not failing anymore and it looks fine: https://3557-53608443-gh.circle-artifacts.com/0/home/circleci/out/docs/usage.html#defining-standard-and-nonstandard-spaces-where-data-will-be-resampled
Also interesting to check the description of the --output-spaces argument expanded by the sphinx argparse extension.

EDIT: ds054 is passing
EDIT: ds210 is passing although it says there are 3 runs in the report (only run-1 is shown). I've dug back for over a year and yet reports show only one run (while listing 3). @emdupre any thoughts of when this could've happened?

[oesteban]

Ref. ds210, it seems the reports generator has been confused with the echos since forever. In principle, there's only one run in our test version of ds210. (opened #1598)

[emdupre]

I can check and see if things have been updated, but it should be showing only one "echo" because that image is actually the optimal combination. We implemented that as the default in the last big ME PR !

[oesteban]

I think that big PR is working alright, my suspicion is that this is a little bug of the reports generator.

[oesteban]

@effigies this is finally ready for you