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 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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