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 -a
C
C.utf8
en_AU
en_AU.utf8
en_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 directory
error: Could not set locale

...repeated dozens of times.


A probably not exhaustive list of affected components:

  • mri_ca_label
  • mri_ca_normalize
  • mri_ca_register
  • mri_convert
  • mri_em_register
  • mri_remove_neck
  • mris_calc


strace 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) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=8896640, ...}) = 0
mmap(NULL, 8896640, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f727c65d000
close(3)                                = 0
openat(AT_FDCWD, "/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=2995, ...}) = 0
read(3, "# Locale name alias data base.\n#"...., 4096) = 2995
read(3, "", 4096)                       = 0
close(3)                                = 0
openat(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: )                  = 7
write(2, "No such file or directory", 25No such file or directory) = 25
write(2, "\n", 1
)                       = 1
write(2, "error: ", 7error: )                  = 7
write(2, "Could not set locale\0", 21Could not set locale^@)  = 21
write(2, "\n", 1
)                       = 1


System info:

Debian 9.1.0 base system, using freesurfer-linux-centos7_x86_64-7.1.1

Linux fmri-proc1 4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/Linux


Workaround:

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.

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