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
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 directory error: Could not set locale sysname Linux hostname fmri-proc1 machine x86_64
setenv SUBJECTS_DIR /data/working/freesurfer7/subjects cd /home/alex mri_ca_label --help
error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale Help
[... normal help output follows]
alex@fmri-proc1:~$ mri_ca_normalize --help
error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale Help [... normal help output follows]
Our standard set of locales (note, no en_US variant):
alex@fmri-proc1:~$ locale -a
C C.UTF-8 de_DE.utf8 en_AU.utf8 nb_NO.utf8 nn_NO.utf8 pl_PL.utf8 POSIX
Adding 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 -all
Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /working/alex/fs_test Actual FREESURFER_HOME /opt/freesurfer7 Linux fmri-proc1 4.9.110-arc #1 SMP Tue Aug 14 17:45:49 CEST 2018 x86_64 GNU/Linux ARC: '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 directory* *error: Could not set locale* *ARC: 'mri_ca_normalize'* *error: No such file or directory* *error: Could not set locale* *ARC: 'mri_ca_register'* *error: No such file or directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* ARC: '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 directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* ARC: 'mri_diff' ARC: 'mri_edit_wm_with_aseg' *ARC: 'mri_em_register'* *error: No such file or directory* *error: Could not set locale* ARC: '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 directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* ARC: 'mri_robust_register' ARC: 'mri_robust_template' ARC: 'mris_anatomical_stats' ARC: 'mris_ca_label' *ARC: 'mris_calc'* *error: No such file or directory* *error: Could not set locale* *error: No such file or directory* *error: Could not set locale* ARC: '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 -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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alex Craven -
fsbuild