Hi Kylie, Hi Alfonso, 

I am running into the same problem. I have inserted all the structural and cunctional images, covariates, and the conditions. When clicking done everything gets set up all right. However, I am then told the same error: "not ready to start denoising step. Please complete the setup step first...". 
At this point I have only run done for a few participants to test how things run. 
Do I need to press done for all participants before I can move on to denoising?
Jonas