It appears that Phase2_output_afid_postQC_for_PHASE3 uses more stringent QC measurements leading to NAN values for some values. This is not optimal and it also propagates into PHASE3 as well.
We have decided to go ahead with Phase2_output_afid_postQC and this folder should be used for all Phase2 data using single subjects.
Perhaps a name change is in order for Phase2_output_afid_postQC_for_PHASE3 ?