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.
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_q...
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
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.
External Email - Use Caution
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.
On 9/15/2023 4:05 AM, Krystal Xiwing Yau wrote:
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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ocK8sSVVbbEgrMAAgJbtpZ8tWAcU6QOsiCDHAZBy_iG172... https://secure-web.cisco.com/1evNHkNaSNuSXdC2wFFw-2ABMa_g4EmNLnf6JTUpVKnrAXTPwEkpWybFSCDGn5a_sJXl8Je5G-RcLh3sKmvlWQvmb__KihFN1QpWKfrfY-fMngyZdcGtHxVd4KnCj3UFv9e3q26WBu93h7PSqmoCKtsG0vfpttod9gzaX7o8mzb7jetnawA8MGvoCyN4IvlGjmYmXfBr64jjJq5mhOwJcKVGgTJGgpwGWBT3AGaQ07-Z80pcPaSGS3sPYMzpi73uoOa8sRBUG28bP-K-EitYL0mBP7hakxWsgpQypAsogUHuj7SZbhfk8LzD2NYQKxDcWVyGiYJ8YsF8AS55wnAJwUA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FTkMeditSegmentations:
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1p6pdrFeokNy_B9rkxD3S5UELxoJkUSlMJuOQ_hOtbZ64o9...
External Email - Use Caution
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
External Email - Use Caution
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.
On 9/15/2023 4:05 AM, Krystal Xiwing Yau wrote:
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1eqU51_RpTglbpzRatECj3WH_XqEy_Ka7MTk9ikTO8KAjhS...https://secure-web.cisco.com/1evNHkNaSNuSXdC2wFFw-2ABMa_g4EmNLnf6JTUpVKnrAXTPwEkpWybFSCDGn5a_sJXl8Je5G-RcLh3sKmvlWQvmb__KihFN1QpWKfrfY-fMngyZdcGtHxVd4KnCj3UFv9e3q26WBu93h7PSqmoCKtsG0vfpttod9gzaX7o8mzb7jetnawA8MGvoCyN4IvlGjmYmXfBr64jjJq5mhOwJcKVGgTJGgpwGWBT3AGaQ07-Z80pcPaSGS3sPYMzpi73uoOa8sRBUG28bP-K-EitYL0mBP7hakxWsgpQypAsogUHuj7SZbhfk8LzD2NYQKxDcWVyGiYJ8YsF8AS55wnAJwUA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FTkMeditSegmentations:
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Krystal Xiwing Yau krystaly@hku.hkmailto:krystaly@hku.hk Sent: 14 September 2023 17:14:12 To: freesurfer@nmr.mgh.harvard.edumailto: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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZPzX4uAZ-Ug986U8Ik9KO3_O4dxlNlbWWmnctYwa08zsfp...https://secure-web.cisco.com/1p6pdrFeokNy_B9rkxD3S5UELxoJkUSlMJuOQ_hOtbZ64o9neDjsLPlIPkhy48PxHzzZp5bLoPzEWVtxvDl4_kgFm6tgaAl-a3WECDmLBoD0XyM_TC6b6iIIJMJBCvYftqaA25F-U1MKmiWftGXv7hramrqUc4OwPcwJRT5Puspg6Q46HKb8ae7ni90nlmK90i2u6WFCScJbyVbrRyOt7PqXcb1CSfdsu4BXzdXPooC7y4UYEQgFLGZl5gMZBfIAlloMFlqbytT2-USdtOF30tg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
oh, that is not due to an error in the aseg itself. That's due to the surface being cut off, probably due to a topological defect. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 10/4/2023 5:07 AM, Krystal Xiwing Yau wrote:
External Email - Use Caution
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
External Email - Use Caution
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.
On 9/15/2023 4:05 AM, Krystal Xiwing Yau wrote:
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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithDat... https://secure-web.cisco.com/1evNHkNaSNuSXdC2wFFw-2ABMa_g4EmNLnf6JTUpVKnrAXTPwEkpWybFSCDGn5a_sJXl8Je5G-RcLh3sKmvlWQvmb__KihFN1QpWKfrfY-fMngyZdcGtHxVd4KnCj3UFv9e3q26WBu93h7PSqmoCKtsG0vfpttod9gzaX7o8mzb7jetnawA8MGvoCyN4IvlGjmYmXfBr64jjJq5mhOwJcKVGgTJGgpwGWBT3AGaQ07-Z80pcPaSGS3sPYMzpi73uoOa8sRBUG28bP-K-EitYL0mBP7hakxWsgpQypAsogUHuj7SZbhfk8LzD2NYQKxDcWVyGiYJ8YsF8AS55wnAJwUA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FTkMeditSegmentations:
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Krystal Xiwing Yau