External Email - Use Caution
Dear all
as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W...)
'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.'
as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option.
The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127).
I am using freesurfer 7.1. Has there been any development to solve this?
Thank you in advance
Fabio Bernardoni
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQ...; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ3... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Sorry, the developer of this program has moved on in her career so we have no one to support it anymore. We maybe looking at it again in the next year or so.
On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
External Email - Use CautionDear all
as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W...)
'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.'
as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option.
The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127).
I am using freesurfer 7.1. Has there been any development to solve this?
Thank you in advance
Fabio Bernardoni
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQ...; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ3... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
dear douglas
thanks for your answer. I understand the developer is not maintaining the program computing lGI. however, my question refers ultimately to the recon-all preprocessing. I am trying to make it run again using different random seed, but apparently it uses the same random seed. or am I wrong? whether this rerun with a new random seed solves the lGI problem is yet to be proven.
thanks
fabio
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM9...; http://secure-web.cisco.com/1N4i9jIw8bJ2yyEYm19KEnx7NejoYUvpMYJhTzabx3pM9WaR... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnO...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnO... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU Gesendet: Mittwoch, 26. Januar 2022 23:02:04 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] lGI value aberrantly high, again
Sorry, the developer of this program has moved on in her career so we have no one to support it anymore. We maybe looking at it again in the next year or so.
On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
External Email - Use CautionDear all
as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W...)
'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.'
as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option.
The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127).
I am using freesurfer 7.1. Has there been any development to solve this?
Thank you in advance
Fabio Bernardoni
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQ...; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ3... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14i9E-YGvrEzXve81BOIRzFbOTHdft8ramMVk-tUFe1lWvl...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14i9E-YGvrEzXve81BOIRzFbOTHdft8ramMVk-tUFe1lWvl... 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 http://secure-web.cisco.com/1I6IQnjl-n1nOAn4Hwo9RYkhcrnl1-Vyahui6RSlDRo1wGrT... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
The lGI is run from recon-all so it is still the lGI that is the problem
On 2/1/2022 3:41 AM, Bernardoni, Fabio wrote:
External Email - Use Cautiondear douglas
thanks for your answer. I understand the developer is not maintaining the program computing lGI. however, my question refers ultimately to the recon-all preprocessing. I am trying to make it run again using different random seed, but apparently it uses the same random seed. or am I wrong? whether this rerun with a new random seed solves the lGI problem is yet to be proven.
thanks
fabio
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM9...; http://secure-web.cisco.com/1N4i9jIw8bJ2yyEYm19KEnx7NejoYUvpMYJhTzabx3pM9WaR... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnO...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnO... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU Gesendet: Mittwoch, 26. Januar 2022 23:02:04 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] lGI value aberrantly high, again
Sorry, the developer of this program has moved on in her career so we have no one to support it anymore. We maybe looking at it again in the next year or so.
On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
External Email - Use CautionDear all
as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W..., https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9W...)
'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.'
as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option.
The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127).
I am using freesurfer 7.1. Has there been any development to solve this?
Thank you in advance
Fabio Bernardoni
Dr. Fabio Bernardoni wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQ...; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ3... +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN...
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPN... Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14i9E-YGvrEzXve81BOIRzFbOTHdft8ramMVk-tUFe1lWvl...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14i9E-YGvrEzXve81BOIRzFbOTHdft8ramMVk-tUFe1lWvl... 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 http://secure-web.cisco.com/1I6IQnjl-n1nOAn4Hwo9RYkhcrnl1-Vyahui6RSlDRo1wGrT... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bernardoni, Fabio -
Douglas N. Greve