fMRIPrep confounds extracted before or after ICA-AROMA?

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Hi, another lab that I’m helping set up fMRIprep is wondering whether confounds in the TSV file are generated before or after ICA-AROMA? I found the notebook here (https://nbviewer.jupyter.org/github/poldracklab/fmriprep-notebooks/blob/master/05%20-%20Discussion%20AROMA%20confounds%20-%20issue-817%20[J.%20Kent].ipynb), but wanted to confirm.

Thanks!
-Saren

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Hi Saren,

Currently the other confounds are generated “before” ICA-AROMA.

Best,
James

Here’s a post on some potential ways to include other regressors with the ICA-AROMA denoised outputs

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