Hi all,

If I want to use ICA-AROMA to denoise my data, and use tcompcor and acompcor as additional nuisance regressors, does the order in which I apply them matter? Or do I need to find a way to apply them at the same time? To ask another way, am I in danger of reintroducing noise with another regressor after applying ICA-AROMA, since I’m applying those regressors (tcompcor, acompcor) to already partially cleaned data (ICA-AROMA denoised), while the regressors (tcompcor, acompcor) were derived from the pre-denoised data.

I see in this paper it matters if the nuisance regressors are highpass filtered or not, which fmriprep covers with adding the cosine basis set as regressors. So would I have to apply fsl’s regfilt to the confound.tsv (at least the columns of interest) that is output by FMRIPREP too?

Sorry if it wasn’t clear and thanks for the help!

James