Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz
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_freeview 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 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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *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/TkMeditWorkingWithData/TkMeditSegmentations <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 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 on behalf of Krystal Xiwing Yau *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 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that t
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/1ocK8sSVVbbEgrMAAgJbtpZ8tWAcU6QOsiCDHAZBy_iG172i-T-V_tgAjByMCQ-eeNa3lUdO9GtPoI4ZPx_tkz_fYvT1vlH8TpMEPqrQpcWEML7qNYZ-Nzy5e036c9zEXXlTE29V3EvtLRLbQUV_evEv5o1o9ceOeOeQpLBf0GT3EFcPmVRht4DMmDd5kNbcuTlU2pEKFi7K9KRNVs9VpWpxQwIfprBBmHFL0wGBU4OKbQa6sT0bOsHWQCwJ95uEODDYfk6lInvXoLsY-PRtlGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkMeditGuide%2FTkMeditWorkingWithData%2FTkMeditSegmentations <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 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 on behalf of Krystal Xiwing Yau *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_hOtbZ64o9neDjsLPlIPkhy48PxHzzZp5bLoPzEWVtxvDl4_kgFm6tgaAl-a3WECDmLBoD0XyM_TC6b6iIIJMJBCvYftqaA25F-U1MKmiWftGXv7hramrqUc4OwPcwJRT5Puspg6Q46HKb8ae7ni90nlmK90i2u6WFCScJbyVbrRyOt7PqXcb1CSfdsu4BXzdXPooC7y4UYEQgFLGZl5gMZBfIAlloMFlqbytT2-USdtOF30tg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz
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 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 on behalf of Krystal Xiwing Yau 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
