Extract WM and CSF signal from fmriprep output

Hi all,

I would like to use WM and CSF average signal as nuisance regressors for my task-based fmri data. As I have used ICA-AROMA, I cannot use the WM and CSF averages in the confounds files. I want to extract the average WM and CSF signal from my unsmoothened ICA-AROMA data with the WM and CSF masks provided by fmriprep in the anat folder. I assume these masks are already eroded, but I am not sure about this. Could anyone tell me if the masks in the anat folder are already eroded?

Also, I was wondering how fmriprep extracts the WM/CSF averages. I have tried different methods (fslmeants/Marsbar/rex) to replicate the output in the confounds file, but always got slightly different output. Is there a prefered way for extracting WM/CSF signals?

Kind regards,
Bauke

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