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Bring up to date with fMRIPrep 24.1.1 #455

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Merged
tsalo merged 30 commits into from
Nov 4, 2024
Merged

Bring up to date with fMRIPrep 24.1.1 #455

tsalo merged 30 commits into from
Nov 4, 2024

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@tsalo tsalo commented Oct 31, 2024 •
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Closes #386.

Changes proposed in this pull request

  • Change --asl2t1w-init to --asl2anat-init. THIS IS A BREAKING CHANGE.
  • Change --asl2t1w-dof to --asl2anat-dof. THIS IS A BREAKING CHANGE.
  • Switch from black to ruff.
  • Copy over current (as of 24.1.1) fMRIPrep code and modify cases where there's a conflict.

tsalo added 27 commits October 31, 2024 16:19
@tsalo
Update fMRIPrep version.
832703b
@tsalo
Merge remote-tracking branch 'upstream/main' into fmriprep-24
75393ad
@tsalo
Update linting rules.
436dd19
@tsalo
Run ruff --fix.
1d4eaaf
@tsalo
Fix some style issues.
ecc4901
@tsalo
Fix remaining ruff issues.
42c8602
@tsalo
Update more stuff.
b43b72f
@tsalo
Update test_cli.py
6fdd6ad
@tsalo
Run ruff format.
dba9ff7
@tsalo
Fix stuff.
ca1aa05
@tsalo
Merge remote-tracking branch 'upstream/main' into fmriprep-24
6527acb
@tsalo
Keep bringing it up to date.
aa2e888
@tsalo
Fix things up some more.
8cb0a66
@tsalo
Keep working.
704e4e0
@tsalo
Update config.py
71b96fc
@tsalo
Fix.
2fcaabf
@tsalo
Update base.py
1004366
@tsalo
Update bids.py
84109c4
@tsalo
Update.
67db5a3
@tsalo
Update run.py
42a6671
@tsalo
Use init_bold_fsLR_resampling_wf from fMRIPrep.
3fd084f
@tsalo
Fix generate_reports calls.
c444764
@tsalo
Don't try to invert.
2fa774a
@tsalo
Use internal copy of generate_reports.
10bc7ab
@tsalo
Add --aggregate-session-reports.
4f604ba
@tsalo
Update report specs.
1046735
@tsalo
Update asl.py
c2d489c
@tsalo tsalo marked this pull request as ready for review November 1, 2024 20:12
@tsalo tsalo added the enhancement New feature or request label Nov 4, 2024
@tsalo tsalo added maintenance Issues/PRs related to maintenance. Dependency versions, dependencies, etc. nipreps Maintains consistency with the rest of the nipreps ecosystem (especially fMRIPrep). breaking-change PRs that change results or interfaces. labels Nov 4, 2024
@tsalo tsalo merged commit 4db9196 into PennLINC:main Nov 4, 2024
3 checks passed
@tsalo tsalo deleted the fmriprep-24 branch November 4, 2024 19:10
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breaking-change PRs that change results or interfaces. enhancement New feature or request maintenance Issues/PRs related to maintenance. Dependency versions, dependencies, etc. nipreps Maintains consistency with the rest of the nipreps ecosystem (especially fMRIPrep).

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Use T2w for anat coregistration

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