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docs/outputs.rst

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@@ -297,7 +297,8 @@ ICA-AROMA can be enabled with the flag ``--use-aroma``.
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do not include ICA-AROMA confounds during your design specification or denoising procedure.
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**CompCor confounds**.
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:abbr:`CompCor (Component Based Noise Correction)` is a component-based noise correlation method.
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:abbr:`CompCor (Component Based Noise Correction)` is a :abbr:`PCA (principal component analysis)`,
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hence component-based, noise pattern recognition method.
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In the method, principal components are calculated within an :abbr:`ROI (Region of Interest)`
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that is unlikely to include signal related to neuronal activity, such as :abbr:`CSF (cerebro-spinal fluid)`
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and :abbr:`WM (white matter)` masks.
@@ -321,6 +322,10 @@ from the union of these.
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[Muschelli2014]_ can be applied using
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the :abbr:`WM (white matter)` and :abbr:`CSF (cerebro-spinal fluid)` masks. To determine the provenance
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of each component, consult the metadata file (see below).
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Make sure you check on `this didactic discussion on NeuroStars.org
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<https://neurostars.org/t/fmrirep-outputs-very-high-number-of-acompcors-up-to-1000/5451>`__
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where Patrick Sadil gets into details about PCA and how that base technique applies
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to CompCor in general and *fMRIPrep*'s implementation in particular.
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Each confounds data file will also have a corresponding metadata file
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(``~desc-confounds_regressors.json``).

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