But after the process I don't have the option to display the data on the cortex anymore. Why is that?
Because you got rid of the spatial dimension, you don't have cortical maps anymore, but isolated values.
For visualization purposes, you can project these values on the cortex, to get 3D maps that you can review like your initial files, with the process " Simulate > Full source maps from scouts".
https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations#Generate_full_source_maps_from_scouts
Do not use this for further processing, prefer working at the ROI level.