ENH+RF: Allow precomputed derivatives in T1w or T2w space

[mgxd]

Closes #293

This PR alters how precomputed derivatives are handled by nibabies, and will make previously valid inputs invalid.

This allows the ingress of an anatomical mask and/or aseg in either T1w or T2w space. Derivatives are expected to use the space entity to signal which modality it was derived from, and more specifically, include a JSON sidecar with SpatialReference key pointing to the specific anatomical used to derive the file.

derivatives/precomputed/
├── README
├── dataset_description.json
└── sub-981854
    └── ses-1mo
        └── anat
            ├── sub-981854_ses-1mo_space-T1w_desc-aseg_dseg.json
            ├── sub-981854_ses-1mo_space-T1w_desc-aseg_dseg.nii.gz
            ├── sub-981854_ses-1mo_space-T1w_desc-brain_mask.json
            └── sub-981854_ses-1mo_space-T1w_desc-brain_mask.nii.gz

The sidecars are composed of:

{"SpatialReference": "sub-981854/ses-1mo/anat/sub-981854_ses-1mo_T1w.nii.gz"}

TODO:

• Test the various combinations
• Update the documentation (docstrings, RTD)
• Add testing for the new Derivatives class
• Update the testing data to reflect changes

[codecov]

Codecov Report

Patch coverage: 50.40% and project coverage change: +1.03% 🎉

Comparison is base (86ab4ec) 32.25% compared to head (b6838ef) 33.28%.
Report is 2 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #305      +/-   ##
==========================================
+ Coverage   32.25%   33.28%   +1.03%     
==========================================
  Files          55       55              
  Lines        5048     5195     +147     
==========================================
+ Hits         1628     1729     +101     
- Misses       3420     3466      +46     

Files Changed	Coverage Δ
nibabies/workflows/anatomical/preproc.py	23.52% <0.00%> (+5.67%)	⬆️
nibabies/workflows/anatomical/base.py	8.26% <5.45%> (-1.02%)	⬇️
nibabies/workflows/anatomical/template.py	10.76% <11.53%> (+0.76%)	⬆️
nibabies/workflows/anatomical/registration.py	12.72% <13.04%> (-4.42%)	⬇️
nibabies/workflows/base.py	26.21% <33.33%> (+0.43%)	⬆️
nibabies/utils/bids.py	42.85% <73.13%> (+14.49%)	⬆️
nibabies/utils/tests/test_bids.py	100.00% <100.00%> (ø)

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[mgxd]

@madisoth The latest patch should fix #309 - would you mind testing with the latest commit?

EDIT: Passed without error.