Dear FS experts,

Could you explained me how to interpret results from the QA tools. Please find attached the recon_checker summary log.

1) How to know there is a problem according to results below:

checking subcortical label: Left-Cerebral-Exterior, 0 +/-

checking subcortical label: Left-Cerebral-White-Matter, 0 +/-

checking subcortical label: Left-Cerebral-Cortex, 0 +/-

checking subcortical label: Left-Lateral-Ventricle, 1.77932 +/-

checking subcortical label: Left-Inf-Lat-Vent, 0.115084 +/-

checking subcortical label: Left-Cerebellum-Exterior, 0 +/-

checking subcortical label: Left-Cerebellum-White-Matter, 0.768042 +/-

checking subcortical label: Left-Cerebellum-Cortex, 2.50118 +/-

checking subcortical label: Left-Thalamus, 0 +/-

checking subcortical label: Left-Thalamus-Proper, 0.324235 +/-

checking subcortical label: Left-Caudate, 0.190688 +/-

checking subcortical label: Left-Putamen, 0.24631 +/-

checking subcortical label: Left-Pallidum, 0.0782828 +/-

checking subcortical label: 3rd-Ventricle, 0.127606 +/-

checking subcortical label: 4th-Ventricle, 0.0697322 +/-

checking subcortical label: Brain-Stem, 1.2108 +/-

checking subcortical label: Left-Hippocampus, 0.191568 +/-

checking subcortical label: Left-Amygdala, 0.0665945 +/-

checking subcortical label: Left-Insula, 0 +/-

checking subcortical label: Left-Operculum, 0 +/-

checking subcortical label: Line-1, 0 +/-

checking subcortical label: Line-2, 0 +/-

checking subcortical label: Line-3, 0 +/-

checking subcortical label: CSF, 0.0903738 +/-

checking subcortical label: Left-Lesion, 0 +/-

checking subcortical label: Left-Accumbens-area, 0.0259807 +/-

checking subcortical label: Left-Substancia-Nigra, 0 +/-

checking subcortical label: Left-VentralDC, 0.196737 +/-

checking subcortical label: Left-undetermined, 0 +/-

checking subcortical label: Left-vessel, 0.0043689 +/-

checking subcortical label: Left-choroid-plexus, 0.0806885 +/-

2) When looking at the white matter QA, three colors are used: red (pial surface ?), yellow (white surface ?) and green (?). Does it make sense to verify all colored surfaces or only the white matter surface in this WM QA ?

How to decide when rejecting bad preprocessed subject ?

Best regards,

Matthieu