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📝 Clarify Regressors syntax #257

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shnizzedy opened this issue Sep 14, 2021 · 1 comment
Open
2 tasks

📝 Clarify Regressors syntax #257

shnizzedy opened this issue Sep 14, 2021 · 1 comment

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@shnizzedy
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Related problem

The example regressor config in the docs is

nuisance_corrections:

  2-nuisance_regression:

    # this is a fork point
    #   run: [On, Off] - this will run both and fork the pipeline
    run: [On]

    # Select which nuisance signal corrections to apply
    Regressors:

      -  Name: 'default'

         Motion:
           include_delayed: true
           include_squared: true
           include_delayed_squared: true

         aCompCor:
           summary:
             method: DetrendPC
             components: 5
           tissues:
             - WhiteMatter
             - CerebrospinalFluid
           extraction_resolution: 2

         CerebrospinalFluid:
           summary: Mean
           extraction_resolution: 2
           erode_mask: true

         GlobalSignal:
           summary: Mean

         PolyOrt:
          degree: 2

         Bandpass:
           bottom_frequency: 0.01
           top_frequency: 0.1
           method: default

      -  Name: 'defaultNoGSR'

         Motion:
           include_delayed: true
           include_squared: true
           include_delayed_squared: true

         aCompCor:
           summary:
             method: DetrendPC
             components: 5
           tissues:
             - WhiteMatter
             - CerebrospinalFluid
           extraction_resolution: 2

         CerebrospinalFluid:
           summary: Mean
           extraction_resolution: 2
           erode_mask: true

         PolyOrt:
          degree: 2

         Bandpass:
           bottom_frequency: 0.01
           top_frequency: 0.1
           method: default

which doesn't include or explain all of the possible options

Proposed feature

Update the documentation and/or the comments in the YAML to describe each possible key and value in a Regressor (and update the validation schema to match any newly described constraints)

Acceptance criteria

  • comments in default pipeline and/or description in docs
  • updated validation schema (if applicable)

Alternatives

No response

Additional context

No response

@shnizzedy
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Related: FCP-INDI/C-PAC_GUI#114

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