Yes indeed I have been importing aseg+aparc.mgz I didn't know they were volume parcellation files. Now that I know I will try to run as volume atlas. That I guess will allow me to work with cerebellum. Which is essential to what I am doing. Please let me know if this is feasible. I cannot work just with cortex. If it is harder to work with mixed models. I will have to learn that. It is not an option to work just with cortex in my case. About FreeSurfer I am using fsaverage. Although I do know how to work with FreeSurfer, FSL, and SPM as well.
If you feel it is possible to work on a tutorial to achieve what I need(all regions of the brain to compute source reconstruction, connectivity, test, difference in 2 runs). Please let me know how can I help. You would just need to guide me and review the tutorial in case of errors. I am willing to learn and help this project for all those in the same situation I am be able to work with this.