ENH: Add sphere registration to fit workflow, check for precomputed

[effigies]

Not much to say. Moved some of the surface conversion into first-order fit, even though they are easy to calculate post hoc because they are needed if msmsulc is used. Initially tried to make some of it conditional, but it made it annoying to construct the complement after the fact. A few extra surfaces in the anatomical derivatives are not our biggest problems, space-wise.

[pep8speaks]

Hello @effigies! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file smriprep/utils/bids.py:

Line 30:80: E501 line too long (91 > 79 characters)

• In the file smriprep/workflows/anatomical.py:

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• In the file smriprep/workflows/base.py:

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• In the file smriprep/workflows/outputs.py:

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Comment last updated at 2023-10-02 18:08:57 UTC

[codecov]

Codecov Report

Attention: 84 lines in your changes are missing coverage. Please review.

Comparison is base (f6b842f) 59.13% compared to head (3b5b230) 58.44%.

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #370      +/-   ##
==========================================
- Coverage   59.13%   58.44%   -0.70%     
==========================================
  Files          26       26              
  Lines        1845     1860      +15     
  Branches      235      238       +3     
==========================================
- Hits         1091     1087       -4     
- Misses        698      716      +18     
- Partials       56       57       +1     

Flag	Coverage Δ
ds005	∅ <ø> (∅)
ds054	46.49% <16.00%> (-0.34%)	⬇️
pytest	36.50% <2.00%> (-0.68%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
smriprep/workflows/base.py	75.00% <0.00%> (ø)
smriprep/workflows/surfaces.py	22.62% <0.00%> (+0.30%)	⬆️
smriprep/utils/bids.py	46.87% <12.50%> (+8.87%)	⬆️
smriprep/workflows/outputs.py	53.01% <30.76%> (-0.97%)	⬇️
smriprep/workflows/anatomical.py	38.85% <14.47%> (-5.89%)	⬇️

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[effigies]

@mgxd I believe this is ready for review if you've got time.

[effigies]

The current failure relates to passing BIDS filenames to Path2BIDS. We expect rh.thickness_converted.shape.gii and instead get sub-01_hemi-R_thickness.shape.gii because it's being found in the output directory. Need to think about how whether to bypass the extraction or make Path2BIDS more flexible.

[effigies]

This is passing. Codecov is complaining about coverage because coverage is bad.

[mgxd]

seems like a good time for sets

Suggested change

	needed_anat_surfs = ["white", "pial", "midthickness"]
	needed_metrics = ["thickness", "sulc"]
	needed_spheres = ["sphere_reg", "sphere"]
	needed_anat_surfs = {"white", "pial", "midthickness"}
	needed_metrics = {"thickness", "sulc"}
	needed_spheres = {"sphere_reg", "sphere"}

[effigies]

Sets can vary in order with each interpreter's initial hash seed, so I'd worry about this causing some node to consider its inputs changed. The n is so small here that I think efficiency is not a significant concern.

[mgxd]

then we should just be able to do

Suggested change

	surfs = [surf for surf in needed_anat_surfs if surf not in found_surfs]
	spheres = [sphere for sphere in needed_spheres if sphere not in found_surfs]
	surfs = list(needed_anat_surfs - found_surfs.keys())
	spheres = list(needed_spheres - found_surfs.keys())

[mgxd]

Suggested change

	metrics = [metric for metric in needed_metrics if metric not in found_surfs]
	metrics = list(needed_metrics - found_surfs.keys())

[effigies]

@mgxd It would be nice to depend on this. Is your previous suggestion blocking?

[mgxd]

No, it is not blocking