External Email - Use Caution Dear FreeSurfer experts,
I would like to further follow up with this issue - I tried to run the following command as instructed on https://secure-web.cisco.com/1DoD2qpUJoxGcDNOZSB1YhPJsD5GKpgHYq9R-yPlq1zTC_qaqWxFji3HTjaKE6hz8E9Az-p_XziNeB7-nmb2je3J9g8bX3lgh8DQid8Exh3eLYkjw9brHl53Un3D3KNbDvNhVjuqq0a1lESE7u-_ga3SvrN4JSBf8mEKcrVetqOWsC2GV2EkVl6BNc7UgPv1JFASm-URu5Bt-shx_KA1zW7adpIvMt31aQnp83JDX1II9haLguP6Sxvdp9DmPKezQKp0P_Z-0HzJz3DztkNRNN5Q7stiYIi6zSOHJthkdCKmt9zsCasHBngsfuYuJducy6IgFOut50iJ04XbF6-kRQA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FTkMeditSegmentations%3A recon-all -autorecon2-noaseg -subjid <Subj_ID> However, I still got no increased numbers in the volumes that I edited on aseg.presurf.mgz via Freeview. However, I observed an increase under "Surface Hole" item. Should I care about it? I'm using FreeSurfer 7.3.2 on Linux (OS Name: Ubuntu 23.04). Thanks a lot! Yours faithfully, Krystal ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Krystal Xiwing Yau <kryst...@hku.hk> Sent: 14 September 2023 17:14:12 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz External Email - Use Caution Dear FreeSurfer experts, I edited some images that under-segmented the brain by coloring the missing brain regions. When I used the edited aseg.mgz to regenerate aseg.stats, the new statistics did not show the increase of the volumes that I edited. Please see the following command lines that I have run on Linux: mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject Sub-180 May I know what step(s) I have missed before generating the aseg.stats? Please kindly advise. Thank you very much! Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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