Hello Bruce,
I reattached the whole recon-all. log.
I've solved
the following error:
--------------------------------------------------------------------------
GNU libc version: 2.19
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html
--------------------------------------------------------------------------
However, I still get the error message: "Could not set locale" whenever
I run the recon-all.
Could you tell me how I can solve the problem?
Thank you in advance for your help.
Regards,
Kayeong Tak
From: °¡¿µ Ź <kytak1123@hotmail.com>
Sent: Thursday, July 5, 2018 12:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all error: could not set locale
Hi Bruce,
Thank you for your prompt response.
Attached is the whole recon-all.log from a failed run.
The complete screen output:
kt@kt-B85M-DS3H-A:~/Downloads/Thalamus$ ./reconall
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20180703-82d87f8
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20180703-82d87f8
INFO: SUBJECTS_DIR is /home/kt/Downloads/Thalamus/Outputs
Actual FREESURFER_HOME /home/kt/Downloads/freesurferDev
Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
'/home/kt/Downloads/freesurferDev/bin/recon-all' -> '/home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts/recon-all.local-copy'
/home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG
mri_convert /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz
Could not set locale
No such file or directory
Could not set locale
No such file or directory
Could not set locale
mri_convert.bin /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz
error parsing license file, expected 4 values
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii...
--------------------------------------------------------------------------
GNU libc version: 2.19
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html
--------------------------------------------------------------------------
Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 161019_x3DT1_SAG exited with ERRORS at 2018. 07. 05. (¸ñ) 10:45:52 KST
For more details, see the log file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you again for your help.
Regards,
Kayeong Tak
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Thursday, July 5, 2018 5:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all error: could not set locale
Hi Kayeong
can you send us the whole recon-all.log from a failed run and the complete
screen output? The locale is needed to specify the format of numbers I
believe (e.g. 1,00 vs. 1.00)
cheers
Bruce
On Wed, 4 Jul
2018, ?? ? wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer Team,
>
>
> I am aware that segmentation of thalamic nuclei is only available in developmental versions
> of Freesurfer.
>
> After I have downloaded the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev), I
> get the following error whenever I use the recon-all command:
>
>
> Could not set locale
> No such file or directory
>
>
> Recon-all works fine when I use the stable 6.0 version.
>
> Could anyone tell me how I can fix this problem?
>
>
> Also, I was wondering it is ok to use recon-all from 6.0 version and thalamic nuclei
> analysis from dev version.
>
>
> Thanks in advance,
>
> Kayeong Tak
>
>
>