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!