Hi!
I am new to resting state fmri and I want to check I am preprocessing my data correctly. I have initially preprocessed my data in fmriprep with --use-aroma. I am wanting to analyse fALFF values and seed-based connectivity (ROI’s in insula and dACC). After fmriprep, I want to linear detrend and do grand mean scaling, and then I want to regress out nuisance variables.
I was hoping for advice in the following aspects
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After fmriprep, how can I do linear detrend and grand mean scaling. Can I use FEAT in FSL (without registration)? Do these also need to be applied to the confound time-series .tsv file outputted from fmriprep? (and if so, how?)
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To regress out aroma confounds and mean CSF + WM, I was thinking to use fsl_regfilt. But to do so, which of the output files do I use? Is there an easy way to combine them?
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If I didn’t want to regress out mean CSF+WM, just AROMA confounds, can I apply linear de-trending/grandmean scaling on the nonagressive aroma output from fmriprep? Is this considered an acceptable approach.
Thank you in advance for your insight 