Retain orthogonalized confounds #975

tsalo · 2023-10-17T13:14:43Z

Closes #974.

Changes proposed in this pull request

Extract column-specific metadata from the fMRIPrep confounds file.
Move confound orthogonalization from the denoising workflow to the confounds preparation workflow.
Retain the orthogonalized confounds (with _orth appended to the column names) in the output confounds file.

codecov · 2023-10-17T18:07:28Z

Attention: 3 lines in your changes are missing coverage. Please review.

Files	Coverage Δ
xcp_d/utils/confounds.py	`84.65% <100.00%> (+0.46%)`	⬆️
xcp_d/utils/utils.py	`100.00% <ø> (ø)`
xcp_d/workflows/bold.py	`94.36% <ø> (ø)`
xcp_d/workflows/cifti.py	`93.65% <ø> (ø)`
xcp_d/workflows/outputs.py	`87.23% <100.00%> (ø)`
xcp_d/workflows/postprocessing.py	`96.61% <ø> (ø)`
xcp_d/interfaces/censoring.py	`93.71% <90.00%> (-0.67%)`	⬇️

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tsalo added 3 commits October 16, 2023 14:16

Reorganize orthogonalization.

937a804

Update utils.py

acca7eb

Patch everything together.

7169998

tsalo added the enhancement New feature or request label Oct 17, 2023

tsalo self-assigned this Oct 17, 2023

tsalo added 7 commits October 17, 2023 09:29

Update confounds.py

7c5e751

Fix up tests.

15f932e

Update censoring.py

2490ca0

Update censoring.py

d988fb2

Update censoring.py

de2a34c

Whoops!

3fd9e0c

Update expected outputs.

5555325

tsalo added 2 commits October 17, 2023 14:44

Test the orthogonalization.

6ec5a69

Update test_interfaces_censoring.py

6a5af44

tsalo added this to the post-manuscript milestone Oct 18, 2023

tsalo merged commit 8ffb4b8 into PennLINC:main Oct 20, 2023
4 checks passed

tsalo deleted the confounds_metadata branch October 20, 2023 13:22