I’ve done a bunch of reading through the archives both here and on the CONN listserv about denoising, but I’m still unclear about how to best use fmriprep-processed ICA-AROMA (non-aggressive) files in CONN (18b).
At the denoising step, I would normally include WM, CSF, effect of rest, and ART regressors. I have gathered that I probably should not include motion regressors here if I am using non-aggressive AROMA data. But should I still include WM, CSF, and effect of rest as confounds at the denoising step? Or have those effects already been removed?
Also at the denoising step: include detrending, or no?
Finally, on the fact that CONN and fmriprep are using different versions of MNI space: transform the images, transform the CONN atlas, ignore the issue because the effect is likely tiny, or some other solution?
Thanks in advance for any advice.