Using FSL post fmriprep


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

  1. 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?)

  2. 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?

  3. 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 :slight_smile:

Hi @bmol239, and welcome to neurostars!

Not a direct answer to your question, but you might find XCP_D to be helpful for this.