Dear all,

I am new to FS QA tool and would like to understand interpretation of results from QA tool as indicated by Matthieu below. Any guidance or directions will be of great help as I need to QC ~400 subjects and think this tool can come in handy.

1) Which problems to identify by looking at recon_checker.log file. Is SNR value helpful to decide if that subject needs to be corrected for error and if so what minimum value of SNR should we use for reference?

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 ?

Thanks,

Sneha

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Tuesday, June 14, 2016 6:13:14 AM To: Freesurfer support list; vinke@nmr.mgh.harvard.edu Subject: [Freesurfer] Interpretation of QA tools results

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