External Email - Use Caution
Hello Alex,
Thanks for the additional command output. If a machine does not have
certain locale files installed, then I’m not sure what can be done apart from
our having a (Debian) linux installer that might update them. Basically
I think this is similar to a system library issue where we cannot guarantee
that when using the freesurfer tar archive, all the system dependencies are
going to be satisfied. If you have root privileges, then with the dpkg
utility you can install the tools to generate locale files (and there should be
no need to manually edit/add locale files). I do see postings from Debian
linux users indicating they’ve had to update the system locales in order to run
some software. I will look further into it.
- R.
On Oct 13, 2020, at 05:27, Alex Craven <alex.cra...@uib.no>
wrote: External Email - Use
Caution Hi,Thanks for your
response. Yes: the errors appear for the individual commands specified, for
example:alex@fmri-proc1:~$ mri_ca_label --help error: No such file or
directoryerror: Could not set localesysname Linuxhostname
fmri-proc1machine x86_64setenv SUBJECTS_DIR
/data/working/freesurfer7/subjectscd /home/alexmri_ca_label --help error:
No such file or directoryerror: Could not set localeerror: No such file or
directoryerror: Could not set
locale
Help[... normal help output follows]alex@fmri-proc1:~$ mri_ca_normalize
--helperror: No such file or directoryerror: Could not set localeerror: No such
file or directoryerror: Could not set localeerror: No such file or
directoryerror: Could not set
locale
Help[... normal help output follows]Our standard set of locales (note, no
en_US variant):alex@fmri-proc1:~$ locale
-aCC.UTF-8de_DE.utf8en_AU.utf8nb_NO.utf8nn_NO.utf8pl_PL.utf8POSIXAdding
en_US.UTF-8, the errors go away:alex@fmri-proc1:~$ sudo /bin/bash -c 'echo
"en_US.UTF-8 UTF-8" >> /etc/locale.gen; locale-gen'alex@fmri-proc1:~$
mri_ca_normalize
--help
Help[...normal help output...]I'll re-iterate that the commands run to
completion either way, so the problem is likely more aesthetic than anything
else.recon-all loops over a set of allinfocmds towards the start of the
process; adding a line of debug info to the loop around line 703 yields the
following (which is where my previous list of affected commands was derived);
ARC prefix in the output denotes my additions. Note that some individual
commands present the error multiple times; there's no obvious difference in
library dependencies (reported by ldd) between these cases, so I believe this
fault probably arises internally and not from any external
dependency.alex@fmri-proc1:~$ env SUBJECTS_DIR=/working/alex/fs_test
/opt/freesurfer7/bin/recon-ac -i /data/current/xxxx/002_struct_T1.nii -subjid
xxxx -allSubject Stamp:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551Current Stamp:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551INFO: SUBJECTS_DIR is
/working/alex/fs_testActual FREESURFER_HOME /opt/freesurfer7Linux fmri-proc1
4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/LinuxARC:
'lta_convert'ARC: 'mri_and'ARC: 'mri_annotation2label'ARC: 'mri_aparc2aseg'ARC:
'mri_surf2volseg'ARC: 'mri_binarize'ARC: 'mri_ca_label'error: No such file or
directoryerror: Could not set localeARC: 'mri_ca_normalize'error: No such file
or directoryerror: Could not set localeARC: 'mri_ca_register'error: No such
file or directoryerror: Could not set localeerror: No such file or
directoryerror: Could not set localeerror: No such file or directoryerror:
Could not set localeARC: 'mri_cc'ARC: 'mri_compute_overlap'ARC:
'mri_compute_seg_overlap'ARC: 'mri_concat'ARC: 'mri_concatenate_lta'ARC:
'mri_convert'error: No such file or directoryerror: Could not set localeerror:
No such file or directoryerror: Could not set localeerror: No such file or
directoryerror: Could not set localeARC: 'mri_diff'ARC:
'mri_edit_wm_with_aseg'ARC: 'mri_em_register'error: No such file or
directoryerror: Could not set localeARC: 'mri_fill'ARC:
'mri_fuse_segmentations'ARC: 'mri_fwhm'ARC: 'mri_gcut'ARC: 'mri_info'ARC:
'mri_label2label'ARC: 'mri_label2vol'ARC: 'mri_log_likelihood'ARC:
'mri_mask'ARC: 'mri_matrix_multiply'ARC: 'mri_normalize'ARC:
'mri_normalize_tp2'ARC: 'mri_or'ARC: 'mri_relabel_hypointensities'ARC:
'mri_relabel_nonwm_hypos'ARC: 'mri_remove_neck'error: No such file or
directoryerror: Could not set localeerror: No such file or directoryerror:
Could not set localeARC: 'mri_robust_register'ARC: 'mri_robust_template'ARC:
'mris_anatomical_stats'ARC: 'mris_ca_label'ARC: 'mris_calc'error: No such file
or directoryerror: Could not set localeerror: No such file or directoryerror:
Could not set localeARC: 'mris_convert'ARC: 'mris_curvature'ARC:
'mris_curvature_stats'ARC: 'mris_diff'ARC: 'mris_divide_parcellation'ARC:
'mri_segment'ARC: 'mri_segstats'ARC: 'mris_euler_number'ARC:
'mris_fix_topology'ARC: 'mris_topo_fixer'ARC: 'mris_jacobian'ARC:
'mris_label2annot'ARC: 'mris_left_right_register'ARC: 'mris_place_surface'ARC:
'mrisp_paint'ARC: 'mris_register'ARC: 'mris_smooth'ARC: 'mris_sphere'ARC:
'mris_surface_stats'ARC: 'mri_stats2seg'ARC: 'mris_thickness'ARC:
'mris_thickness_diff'ARC: 'mris_topo_fixer'ARC: 'mri_surf2surf'ARC:
'mri_surf2vol'ARC: 'mri_surfcluster'ARC: 'mris_volmask'ARC:
'mri_tessellate'ARC: 'mri_vol2surf'ARC: 'mri_vol2vol'ARC: 'mri_voldiff'ARC:
'mri_watershed'ARC: 'tkregister2_cmdl'Best regards,Alex.On 12/10/20 22:59,
fsbuild wrote: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
-aCC.utf8en_AUen_AU.utf8en_BWen_BW.utf8en_CAen_CA.utf8en_DKen_DK.utf8en_GBen_GB.iso885915en_GB.utf8…
many other countries …POSIX- R.On Oct 12, 2020, at 06:58, Alex
Craven <alex.cra...@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
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