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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthieu Vanhoutte <matthieuvanhou...@gmail.com> Sent: Tuesday, June 14, 2016 6:13:14 AM To: Freesurfer support list; vi...@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
