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Identify the last good echo in adaptive mask instead of sum of good echoes #1061

Merged
merged 47 commits into from
Apr 18, 2024
Merged

Identify the last good echo in adaptive mask instead of sum of good echoes #1061

merged 47 commits into from
Apr 18, 2024

Commits on Mar 15, 2024

  1. Limit adaptive mask calculation to brain mask. 

    Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <[email protected]>
    @tsalo @handwerkerd
    tsalo and handwerkerd committed Mar 15, 2024
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  2. Use compute_epi_mask in t2smap workflow.

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    tsalo committed Mar 15, 2024
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  3. Try fixing the tests.

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    tsalo committed Mar 15, 2024
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  4. Fix make_adaptive_mask.

    @tsalo
    tsalo committed Mar 15, 2024
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  5. Update test_utils.py

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  6. Update test_utils.py

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    tsalo committed Mar 15, 2024
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  7. Improve docstring.

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Commits on Mar 16, 2024

  1. Identify the last good echo instead of sum. 

    Improve docstring.

Update test_utils.py

Update test_utils.py

Fix make_adaptive_mask.

Try fixing the tests.

Use `compute_epi_mask` in t2smap workflow.

Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <[email protected]>
    @tsalo @handwerkerd
    tsalo and handwerkerd committed Mar 16, 2024
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  2. Fix.

    @tsalo
    tsalo committed Mar 16, 2024
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  3. Update utils.py

    @tsalo
    tsalo committed Mar 16, 2024
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  4. Update utils.py

    @tsalo
    tsalo committed Mar 16, 2024
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  5. Try fixing.

    @tsalo
    tsalo committed Mar 16, 2024
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  6. Update utils.py

    @tsalo
    tsalo committed Mar 16, 2024
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  7. Update utils.py

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    tsalo committed Mar 16, 2024
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  8. add checks

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    tsalo committed Mar 16, 2024
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  9. Just loop over voxels.

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  10. Update utils.py

    @tsalo
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  11. Update utils.py

    @tsalo
    tsalo committed Mar 16, 2024
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  12. Update test_utils.py

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  13. Revert "Update test_utils.py" 

    This reverts commit 259b002.
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  14. Update test_utils.py

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  15. Update test_utils.py

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    tsalo committed Mar 16, 2024
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  16. Remove checks.

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    tsalo committed Mar 16, 2024
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Commits on Mar 18, 2024

  1. Don't take absolute value of echo means.

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  2. Log echo-wise thresholds in adaptive mask.

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    tsalo committed Mar 18, 2024
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  3. Add comment about non-zero voxels.

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Commits on Mar 30, 2024

  1. Update utils.py

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    tsalo committed Mar 30, 2024
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  2. Update utils.py

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Commits on Apr 8, 2024

  1. Merge remote-tracking branch 'upstream/main' into fix-old-adaptive-mask

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    tsalo committed Apr 8, 2024
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  2. Update test_utils.py

    @tsalo
    tsalo committed Apr 8, 2024
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  3. Update test_utils.py

    @tsalo
    tsalo committed Apr 8, 2024
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  4. Update test_utils.py

    @tsalo
    tsalo committed Apr 8, 2024
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  5. Log the thresholds again.

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    tsalo committed Apr 8, 2024
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Commits on Apr 11, 2024

  1. Merge branch 'fix-old-adaptive-mask' into fix-old-adaptive-mask-2

    @tsalo
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  2. Update test_utils.py

    @tsalo
    tsalo committed Apr 11, 2024
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  3. Update test_utils.py

    @tsalo
    tsalo committed Apr 11, 2024
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  4. Update test_utils.py

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    tsalo committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. Merge remote-tracking branch 'upstream/main' into fix-old-adaptive-ma… 

    …sk-2
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Commits on Apr 16, 2024

  1. Merge remote-tracking branch 'upstream/main' into fix-old-adaptive-ma… 

    …sk-2
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  2. Merge remote-tracking branch 'upstream/main' into fix-old-adaptive-ma… 

    …sk-2
    @tsalo
    tsalo committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. Add simulated data to adaptive mask test.

    @tsalo
    tsalo committed Apr 17, 2024
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  2. Clean up the tests.

    @tsalo
    tsalo committed Apr 17, 2024
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  3. Merge remote-tracking branch 'upstream/main' into fix-old-adaptive-ma… 

    …sk-2
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    tsalo committed Apr 17, 2024
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  4. Add value that tests the base mask.

    @tsalo
    tsalo committed Apr 17, 2024
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  5. Remove print in test.

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    tsalo committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. Update tedana/utils.py 

    Co-authored-by: Dan Handwerker <[email protected]>
    @tsalo @handwerkerd
    tsalo and handwerkerd authored Apr 18, 2024
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  2. Update tedana/utils.py 

    Co-authored-by: Dan Handwerker <[email protected]>
    @tsalo @handwerkerd
    tsalo and handwerkerd authored Apr 18, 2024
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