It is changing with each subject because each subject's brain is different, and you can't get a subject-specific mask from fsaverage5. Can you load all your data into matlab and then compute a mask based on non-zero voxels?

Hi freesurfers,

I am doing a connectivity analysis on cortical areas. I load the 2d fmri surface file in fsaverage5 space into matlab and I get 20484 vertices for both hemispheres. Some of which are zero because I previously specified to get only the cortex vertices. However, the number of non-cortex vertices changes across subjects. 

Is it possible to get from fsaverage5 any overlay mask that specifies if it is cortical or not, so when I load it into matlab i can get a logical vector of 20484 elements? 

Thanks

Dorothy

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