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Use confounds file with non-steady-state columns to identify dummy volumes #1330

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merged 1 commit into from
Nov 21, 2024

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@tsalo tsalo commented Nov 21, 2024

When --dummy-scans is set to auto (the default), XCP-D attempts to infer the right number of dummy volumes from the fMRIPrep confounds file. However, starting in #1255, I connected the output of a node that removes the dummy volume columns from the confounds file to the node that looks for those columns, which resulted in dummy volumes not being flagged and removed by the post-processing workflow. This was identified by a user, Bianca Serio, in https://neurostars.org/t/filenotfounderror-no-bold-data-found-in-allowed-spaces-fslr/30968.

THIS BUG AFFECTS VERSIONS 0.10.0rc1 - 0.10.0

Changes proposed in this pull request

  • Use unfiltered confounds file to identify non-steady-state (i.e., dummy) volumes to remove from the BOLD data, rather than the filtered version that only include motion columns.

@tsalo tsalo added the bug Issues noting problems and PRs fixing those problems. label Nov 21, 2024
@tsalo tsalo added this to the HBCD milestone Nov 21, 2024
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codecov bot commented Nov 21, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 78.96%. Comparing base (0e07ef1) to head (86a27e3).
Report is 1 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1330   +/-   ##
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  Coverage   78.96%   78.96%           
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  Files          59       59           
  Lines        7406     7406           
  Branches      962      962           
=======================================
  Hits         5848     5848           
  Misses       1268     1268           
  Partials      290      290           

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@tsalo tsalo merged commit d57988c into PennLINC:main Nov 21, 2024
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@tsalo tsalo deleted the fix-dummy branch November 21, 2024 20:23
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