I would like to further follow up with this issue - I tried to run the following command as instructed on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations:

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).

Krystal

 

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!