You have to run recon-all through to the end. You can then extract a GM mask from that. You will need to register your PET image to the anatomical (mri_coreg), map the PET into the anatomical space, then use mri_segstats to compute the mean PET in the GM mask. Alternatively, you may want to use PETsurfer (search for it on the wiki).

Hello FS team, 

I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. 

I have T1 MRI images from multiple subjects and I need to extract the brain gray matter mask (just cortical regions, without cerebellum). I will then use this mask as an ROI to extract PET activity. 

Would you happen to know a way for this? 

Thank you greatly, 

Anna

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