Hi Alan,
Including this into Braph is definitely interesting, but would require some serious amount of coding, which go beyond some simple scripting.
One possible alternative approach would be to correct the input data for the relevant nuissance variables before introducing them into Braph (best suited for the MRI and PET workflows), or to correct the per-subject results calculated by Braph (best suited for the global measures in the fMRI and EEG workflows).
Cheers
Joana