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/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM90KVg1F580Ru3Y546PmS-h-yp2hhRc5_K7k433uq2EJ9eaN9s8N9_CsTS54vv8mPbTTC2nPXc9xuueUufUXY3wMTbe-X_hCg0_ZeY_3dPgUiI9Z8XB_Gj9VNMxWl_xWy1cJLx0YYY58z5B_NtHWLg0JcHnV3Bii40hBJXokL86POx5de5HjDYxX4xjuGmgmKVcOu7L97BLr6q4WUSuF41E4SlFTBFZ6U2Tm1xn9izIPo9PZQTv9aJG7uBQpIMI0PKO3sNOOljdWZHt7nV5/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1N4i9jIw8bJ2yyEYm19KEnx7NejoYUvpMYJhTzabx3pM9WaR339FXo0cTYTnMG39Foa8qvhVU2_8sNrquKhF4qAsTbKSG9Z0oc8FpUcbGEy7i36ukcG61fyttQYv8XXhwwxXvV3hBnHapvelFfE8Pn5pDQ0WAfV4wZFJBGhZA626M5UmsO0459TbVf4ixVsEZYfxGNenU8juB_rCXF3DaBEPluT9pyjsQE-iaDbPS2NSUkf5WLaqMg5LGErAya774gsfdaTWVSLHUYor57w1MmZSDyTiP8oZOjJpFtyyto7rDK7yUW-8sU54kPtcWm2wjmaIqnNeBo56a9qayzutOJA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +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/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnOQM7fTSV13LSRRhFWKc7YOcgyF0u1v7WIS8StfxEqbSN1QZUB9W2l4c7t1Qjas9CpbS75zCrZj0nqO9wQo1_jIv8sdZpBYG5Y1bbDLqV993EdxHEWToOzJwKgqdHpSke8vqy6Xb93g_c4PgqGddOT6YXhMcGMWHr4f9WiF1Ur3FSvlMm4ALJZ4-uD5xvcTpf1A4-M_hhU9Jgj6nZWlkthGy2DPSFOcnC9sf_c205y0GHfslg0VbOZS240aXVnYwiTgl0QUCS7nqox8rL4XWbMGuswgO1Se9lRBxjP-Xg/http%3A%2F%2Fwww.uniklinikum-dresden.de 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/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnOQM7fTSV13LSRRhFWKc7YOcgyF0u1v7WIS8StfxEqbSN1QZUB9W2l4c7t1Qjas9CpbS75zCrZj0nqO9wQo1_jIv8sdZpBYG5Y1bbDLqV993EdxHEWToOzJwKgqdHpSke8vqy6Xb93g_c4PgqGddOT6YXhMcGMWHr4f9WiF1Ur3FSvlMm4ALJZ4-uD5xvcTpf1A4-M_hhU9Jgj6nZWlkthGy2DPSFOcnC9sf_c205y0GHfslg0VbOZS240aXVnYwiTgl0QUCS7nqox8rL4XWbMGuswgO1Se9lRBxjP-Xg/http%3A%2F%2Fwww.uniklinikum-dresden.de 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve <dgr...@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 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_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html, > > https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html, > > https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html) > > '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-pgRDlfQq65obryki5fZ9inqQJGhUQCH12N3Pt0ACl5Sz6LbLbSEiQUG8WQO9t88xjEbBwfnJl5zMPv5YGf2um_2huADEEKMstPPgZ-2NbXimHQPHK5qCSvFMpSsGruW0svSkAaRlYlbli_Lh272QlD4J26lfLiQzwTVCqVKRna8BCUGR8yVWddr_LDg_XEqia5dNbzYZDkwnUBTG2F9ISpoIXh3TOciVMBbhbfFjq4oyGcs3f8IYSIi2hIbnpM9C-K7UBqfq6JgC8MOXudQm7m45/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ38YRbvIQam95p0_9OaNAtoH0qHBY20t69GRnCZNTRBEMY7L0dD_0kA9XSvn1emw5Cg068ZJTAc2rajYXBSywtHWwSBJv5Bk3AMNCwDT208lNW5A1KBEHxU6ClKWG0biFGmUlIMeH8DzBxdhTFSc46EnzdD9atOQtFO8_qTgvGgNFOhfvwKS67YeTzV4Q22C-y953EVIfJo84NUaLXgIRwlO-_erSBNdJlV-6iBgXbIA2PkyekWYcjKAGknDwCZ9FeDCXXrfPaTjhOLpleBfcBwLPTaoDD3w_UZqZxxZw/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +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-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de > > 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-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. G. 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