Hi pt,
Thank you again! I used the example 11 resting-state analysis of proc py which has the FreeSurfer option. Anat_final file (MNI warped) should be used for each errts files mask so the two runs don't share the exact same mask. Do you think I need to rerun the proc.py?
I also googled about the approach using the Power atlas and it seems reasonable to exclude some ROIs (especially subcortical ROIs) for which at least one subject had 10% or more null data. Could you please let me know if this makes sense?
Best,
JW
