Dear FSL experts,
I am in the process of transitioning to using FSL from another software package, and I have what is probably a very simple question. I apologize if this has been answered elsewhere on this listserv; I searched but could not find anything. I am working through analysis for an fMRI neurofeedback study. Participants received neurofeedback training (or a control intervention) across three runs. I expect there to be training effects across runs, so I would like to set things up so that I do not average across runs for higher level analyses. What I'd like to end up with are separate parameter estimates for each run in MNI space, which will allow me to pull estimates (ideally expressed as percent signal change) for each run from subject-level ROIs (registered to MNI space) for offline analyses and to conduct whole-brain analyses comparing, for example, responses during the third vs. the first run within and across groups. Could you please tell me how I would need to set up my second level models in this case?  Would it just be a separate EV for each run? Thank you very much for any guidance.