External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run recon-all, whether the full recon or a part of the process (e.g. recon-all -autorecon3 -s $SUBJECT -localGI) and am finding there would be what seems to be a glibc error (e.g. https://secure-web.cisco.com/1aJXVSDwcefv7rhlrTYwyBgTiVEvYt2dSphBaETv3j1Zlek90zQLJo4qGKhCrJ90bKTAukepr5uODNpp_8v82fLDrJHfSqFIIRuQFgPEgjtSVFpixU211A5XLYYsUJ__8GD077d2k1kx65umEx3F65IbGkXs6GDT1LSYvtqP00s7MnsX6StBvAyVmq-K6YwJjjFu7520aOBQykTWjpg6rQtZGOdVobAYlHZPBcbSPvSTqbBDarlrETWasgKl6xOIKv64CuvrHLjuEZpEESCu53g/https%3A%2F%2Fgithub.com%2Fpuppeteer%2Fpuppeteer%2Fissues%2F2207) that occurs during any one of the MATLAB steps of the recon-all process. Certain versions of MATLAB appear to be missing the correct installations for glibc so I did follow the steps to install it (e.g. https://secure-web.cisco.com/1Zt0UN3L2lns-RzoRlpw4wwob_uSJBgC8w5Pk-IdqY6Mvbq09yxYOEfBaneWtQsEFGvaUESY2fGFqiUykgNj9HAweOYpbaFP_UnPEj32QgCat6nu3VDQcUagTMaTecTfVA9tODl0nOUMSsK1ALxhL_3IVf-p0gZKGRhmklQDfoGGbTum_fQEQ7u9aH2UMP5yvGv1Pd1XsE-W7Y61O8xjqIFHV5StEwnmBoZ4ZZVO8ZnKJtatMPl--ArahB8gXhE5juOWmB9ZRq_qSB2plstMOsQ/https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fanswers%2F1454674-why-does-matlab-crash-on-linux-with-inconsistency-detected-by-ld-so-elf-dl-tls-c-597-_dl_allo ), but this error has been wildly inconsistent. For instance, the challenging issue is that this Freesurfer installation appears to work perfectly fine for some cases but would error out (one example set of errors below) causing me to think it is the glibc issue. Further, it is not consistent which MATLAB-based step causes the error (it could error out in one of the many MATLAB steps for one brain scan but it would be a different MATLAB step for another brain scan). Therefore, I have multiple error-ed out recon-all files across 15 scans (different participants) which all appear to stop at different stages of the process. Error example: MATLAB is selecting SOFTWARE OPENGL rendering. Inconsistency detected by ld.so: ../elf/dl-tls.c: 481: _dl_allocate_tls_init: Assertion `listp->slotinfo[cnt].gen <= GL(dl_tls_generation)' failed! ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2023:09:04:18:17:29 mris_compute_lgi N 2 e 17.45 S 4.32 U 44.58 P 280% M 2246188 F 0 R 1909235 W 0 c 909 w 36844 I 0 O 39440 L 1.01 1.06 1.07 @#@FSLOADPOST 2023:09:04:18:17:47 mris_compute_lgi N 2 1.74 1.22 1.13 Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s XXXXXX_SurferOutput exited with ERRORS at Mon Sep 4 18:17:47 EDT 2023 I've searched the list and no similar errors have been reported for recent MATLAB installations. Does anyone have any thoughts on how to trouble-shoot this one? I can send the recon-all log as well if need be though there are a number of them. 1) FreeSurfer version: freesurfer-linux-ubuntu18_amd64-7.4.1 2) Platform: Ubuntu 18 3) uname -a: Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: Can send following deidentification if need be but there are multiple examples of recon-all.log errors 5) MATLAB 2020a
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