the freeview qc script load the original T1 and FLAIR scans but the surfaces and predictions in the freesurfer space. This is not an issue for the T1w scans, but if the FLAIR scan is not aligned to T1w then it will not be aligned with the predition
use the T1 and FLAIR instead:
T1: <meld_data>/fs_outputs/<subject_folder>/mri/orig.mgz
FLAIR : <meld_data>/fs_outputs/<subject_folder>/mri/FLAIR.prenorm.mgz
the freeview qc script load the original T1 and FLAIR scans but the surfaces and predictions in the freesurfer space. This is not an issue for the T1w scans, but if the FLAIR scan is not aligned to T1w then it will not be aligned with the predition
use the T1 and FLAIR instead:
T1: <meld_data>/fs_outputs/<subject_folder>/mri/orig.mgz
FLAIR : <meld_data>/fs_outputs/<subject_folder>/mri/FLAIR.prenorm.mgz