External Email - Use Caution
Hello Alex, After you have set FREESURFER_HOME and source’d the shell setup script, please try running the binaries you suspect directly from the command line, e.g., with —help option, and see if you get the same error, e.g. $ mri_ca_label —help<help output deleted> $ mri_ca_normalize —help<help output deleted> It would also be interesting to know what locales have been setup/installed on your machine from the output of the locale command, which might display something like, $ locale -aC C.utf8 en_AU en_AU.utf8en_BW en_BW.utf8 en_CA en_CA.utf8 en_DK en_DK.utf8 en_GB en_GB.iso885915 en_GB.utf8… many other countries …POSIX - R. On Oct 12, 2020, at 06:58, Alex Craven <alex.craven@uib.no> wrote: External Email - Use Caution Greetings,Several binaries in the Freesurfer 7.1.1 release appear to ignore (or misinterpret) system-wide locale settings. This causes a large number of errors to be reported throughout the recon process, particularly on startup. The commands appear to complete successfully despite the reported errors.The errors are displayed as:error: No such file or directoryerror: Could not set locale...repeated dozens of times.A probably not exhaustive list of affected components:mri_ca_labelmri_ca_normalizemri_ca_registermri_convertmri_em_registermri_remove_neckmris_calcstrace output for one such command suggests that it's attempting to load the en_US locale, on a system where that is locale is not configured, and where system-wide settings indicate the something else should be used (eg: LANG=en_AU.UTF-8)openat(AT_FDCWD, "/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3fstat(3, {st_mode=S_IFREG|0644, st_size=8896640, ...}) = 0mmap(NULL, 8896640, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f727c65d000close(3) = 0openat(AT_FDCWD, "/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3fstat(3, {st_mode=S_IFREG|0644, st_size=2995, ...}) = 0read(3, "# Locale name alias data base.\n#"..., 4096) = 2995read(3, "", 4096) = 0close(3) = 0openat(AT_FDCWD, "/usr/lib/locale/en_US/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en_US.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)openat(AT_FDCWD, "/usr/lib/locale/en.utf8/LC_NUMERIC", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)write(2, "error: ", 7error: ) = 7write(2, "No such file or directory", 25No such file or directory) = 25write(2, "\n", 1) = 1write(2, "error: ", 7error: ) = 7write(2, "Could not set locale\0", 21Could not set locale^@) = 21write(2, "\n", 1) = 1System info:Debian 9.1.0 base system, using freesurfer-linux-centos7_x86_64-7.1.1Linux fmri-proc1 4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/LinuxWorkaround:Generating the en_US.UTF-8 locale, by adding/uncommenting the line "en_US.UTF-8 UTF-8" in /etc/locale..gen and re-running locale-gen effectively hides this problem.Best regards,Alex._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B