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Parallelize parcellation and replace atlases #254

Merged
merged 37 commits into from
Apr 6, 2023
Merged

Parallelize parcellation and replace atlases #254

merged 37 commits into from
Apr 6, 2023

Commits on Apr 5, 2023

  1. Work on parallelizing the parcellation.

    @tsalo
    tsalo committed Apr 5, 2023
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  2. Keep parallelizing.

    @tsalo
    tsalo committed Apr 5, 2023
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  3. Replace atlas files.

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    tsalo committed Apr 5, 2023
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  4. Swap out ParcellateCBF interface.

    @tsalo
    tsalo committed Apr 5, 2023
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  5. Replace ApplyTransforms throughout.

    @tsalo
    tsalo committed Apr 5, 2023
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  6. Forgot to change the package name.

    @tsalo
    tsalo committed Apr 5, 2023
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  7. Modify refine_ref_mask.

    @tsalo
    tsalo committed Apr 5, 2023
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  8. Update API docs.

    @tsalo
    tsalo committed Apr 5, 2023
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  9. Fix interface.

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    tsalo committed Apr 5, 2023
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  10. Fix up the tests. Hopefully CircleCI works.

    @tsalo
    tsalo committed Apr 5, 2023
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  11. Fix test and update gitignore.

    @tsalo
    tsalo committed Apr 5, 2023
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  12. Update expected outputs.

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    tsalo committed Apr 5, 2023
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  13. Try out another output space.

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    tsalo committed Apr 5, 2023
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  14. Try that.

    @tsalo
    tsalo committed Apr 5, 2023
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  15. Use NLin6Asym --> NLin2009cAsym transform.

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    tsalo committed Apr 5, 2023
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  16. I forgot to fix up the GE workflow.

    @tsalo
    tsalo committed Apr 5, 2023
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  17. Add output space for GE test.

    @tsalo
    tsalo committed Apr 5, 2023
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  18. Update test_cli.py

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    tsalo committed Apr 5, 2023
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  19. Update expected outputs.

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    tsalo committed Apr 5, 2023
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  20. Update test_001 parameters.

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    tsalo committed Apr 5, 2023
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Commits on Apr 6, 2023

  1. Move _adjust_indices back into _gather_confounds.

    @tsalo
    tsalo committed Apr 6, 2023
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  2. Keep working on outputs.

    @tsalo
    tsalo committed Apr 6, 2023
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  3. Update .gitignore

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    tsalo committed Apr 6, 2023
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  4. Update .gitignore

    @tsalo
    tsalo committed Apr 6, 2023
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  5. Simplify outputs.

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    tsalo committed Apr 6, 2023
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  6. Fix typo in node names and fix connections.

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    tsalo committed Apr 6, 2023
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  7. Is it all due to den vs. density in the config?

    @tsalo
    tsalo committed Apr 6, 2023
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  8. Fix up the outputs.

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    tsalo committed Apr 6, 2023
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  9. Fix standard-space output connections.

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    tsalo committed Apr 6, 2023
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  10. Whoops!

    @tsalo
    tsalo committed Apr 6, 2023
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  11. So annoying.

    @tsalo
    tsalo committed Apr 6, 2023
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  12. Update confounds.py

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    tsalo committed Apr 6, 2023
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  13. Try fixing the re-indexing function.

    @tsalo
    tsalo committed Apr 6, 2023
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  14. I missed CBF!

    @tsalo
    tsalo committed Apr 6, 2023
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  15. I forgot to return the modified dfs.

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    tsalo committed Apr 6, 2023
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  16. Fix _adjust_indices. 

    I just rewrote it from scratch.
    @tsalo
    tsalo committed Apr 6, 2023
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  17. test_002 expected things it shouldn't expect.

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    tsalo committed Apr 6, 2023
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