Replace niworkflows calls with dependency calls (second attempt)

[tsalo]

Closes None, but works toward #199.

Changes proposed in this pull request

• Create new aslprep.interfaces.niworkflows module.
  • Move aslprep.niworkflows.interfaces.registration.EstimateReferenceImage to this module.
• Move aslprep.niworkflows.interfaces.registration._get_vols_to_discard() to aslprep.utils.misc.
• Create new aslprep.utils.spaces module. This contains the bundled niworkflows version's spaces module.
• Add to aslprep.workflows.asl.util module.
  • init_validate_asl_wf and init_asl_reference_wf are already present.
  • init_enhance_and_skullstrip_asl_wf:
    • There was an image dilation step applied to the input image, then a header-check to make sure the dilation step didn't mess up the header.
    • There was a pre_mask bool parameter for when the mask was vs. was not already calculated. The "mask was not pre-generated" logic has been removed, even though the parameter remains.
    • However, in the current version of sdcflows, init_enhance_and_skullstrip_bold_wf is only used for the PEPOLAR workflow, which shouldn't apply to ASL data. I think this means that we can switch to the newer version of sdcflows and not need the modified version of init_enhance_and_skullstrip_bold_wf we currently have.

Documentation that should be reviewed

[codecov-commenter]

Codecov Report

Patch coverage: 64.48% and project coverage change: +15.37 🎉

Comparison is base (12112e9) 50.67% compared to head (9367df3) 66.05%.

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #299       +/-   ##
===========================================
+ Coverage   50.67%   66.05%   +15.37%     
===========================================
  Files         139       74       -65     
  Lines       12657     6071     -6586     
===========================================
- Hits         6414     4010     -2404     
+ Misses       6243     2061     -4182     

Impacted Files	Coverage Δ
aslprep/cli/run.py	0.00% <0.00%> (ø)
aslprep/sdcflows/interfaces/reportlets.py	0.00% <0.00%> (ø)
aslprep/sdcflows/viz/utils.py	0.00% <0.00%> (ø)
aslprep/sdcflows/workflows/fmap.py	0.00% <0.00%> (ø)
aslprep/sdcflows/workflows/gre.py	0.00% <0.00%> (-18.75%)	⬇️
aslprep/sdcflows/workflows/pepolar.py	0.00% <0.00%> (-18.69%)	⬇️
aslprep/sdcflows/workflows/phdiff.py	0.00% <0.00%> (-36.37%)	⬇️
aslprep/sdcflows/workflows/unwarp.py	0.00% <0.00%> (ø)
aslprep/utils/plotting.py	76.80% <ø> (-4.30%)	⬇️
aslprep/utils/sentry.py	0.00% <ø> (ø)
... and 23 more

... and 2 files with indirect coverage changes

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