Dear Freesurfer experts, I am attempting to use QAtools to retrieve QA measures for my subjects. I can obtain WM SNR/avg/sd, but it appears the structural segmentation table is from a previous version of freesurfer (as the file order is different) and doesn't appear to work with my subjects processed recently in v5.3. To fix this I would imagine one would need to create a new template off of a subject with the -gen-asegLUT flag or use the -asegLUT flag.
Attempting to use -asegLUT flag with the ASegStatsLUT.txt results in: Processing each subcortical label ... mysubject has 35 outliers ... (With all structures as outliers, and without reporting the SNR/avg/sd for each segmentation) When attempting to write out a new segmentation table with the -gen-asegLUT flag the error I receive is: gawk: /usr/local/freesurfer/QAtools/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1) fatal: division by zero attempted (standard_in) 1: syntax error (standard_in) 1: syntax error The command is here: $QA_tools/recon_checker -s mysubject -asegLUT $FREESURFER_HOME/ASegStatsLUT.txt Am I going about this correctly? Best, KZ _______________________________________________ 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.
