I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please. 

So I have 2 questions regarding that. 

1. Is there any chance that you could direct me step by step how to do this with Freesurfer. 

2. While I am running extraction with Freesurfer, should I be using ROI nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?

I would really appreciate if you could help me with this please. 

Thank you very much in advance

Kind regards

Mina