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Replace restricted confound sets with config files #1255

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@tsalo tsalo commented Sep 11, 2024

Closes #1252 and closes #1231.

Changes proposed in this pull request

  • Design YAML-based configuration files that define confound sets for nuisance regression.
  • Add new --derivatives argument that accepts paths to derivatives datasets.
    • The primary derivatives dataset (i.e., the one provided through a positional argument instead of the --derivatives keyword argument) is internally referred to as "preprocessing".
    • Derivatives are linked to the confound configuration files via keywords. E.g., --derivatives aroma=/path/to/fmripost-aroma.
  • Remove --custom-confounds argument. This is a breaking change.
  • Keep filtered motion parameters and original motion parameters in the motion file.
  • Separate handling of the motion parameters used for outlier detection from motion parameters that are used in the nuisance regression.

@tsalo tsalo changed the title Custom playground Replace restricted confound sets with config files Sep 17, 2024
@tsalo tsalo added enhancement New feature or request breaking-change PRs that change results or interfaces. labels Sep 17, 2024
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