Dear Douglas,

Thank you very much for your reply. 

I edited aseg.presurf.mgz and reran below command:

recon-all -autorecon2-noaseg -autorecon3 -subjid <Subj_ID>

However, the aseg.stats did not show the expacted changes. Hence, I checked the aseg.mgz of that subject, the filled area of the brain in aseg.presurf.mgz did not show in aseg.mgz. Did I misunderstand the whole process? Should I edit aseg.mgz directly to generate the statistics?

Thank you again for your attention.

Best regards,

Krystal

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: 24 September 2023 05:22:56
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

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Ideally, you should have edited the aseg.presurf.mgz, then rerun recon-all starting just after the aseg. That said, if you edited the aseg.mgz and then re-ran that mri_segstats command, the stats should have changed.

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Dear FreeSurfer experts,

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).

Thanks a lot!

Yours faithfully,

Krystal

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Krystal Xiwing Yau <krystaly@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

 

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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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