This is a good point you raise, @JoffJones, regarding the discrepancy between the WM/CSF obtained from T1 / native space, and the AROMA components obtained from MNI space. FWIW, I have since decided to proceed with Scenario 1 explained by @jdkent on Jan 7. Perhaps others on this thread could speak to using AROMA component time-series (MNI space) to preprocessing data in native space.