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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bernardo Regal <regalbernardo@gmail.com>
Sent: Wednesday, July 4, 2018 12:56:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -s 1 exited with ERRORS
 

        External Email - Use Caution        

Hi, 

Now appears this message:

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /opt/freesurfer-v5
FSFAST_HOME       /opt/freesurfer-v5/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /opt/freesurfer-v5/subjects
MNI_DIR           /opt/freesurfer-v5/mni
bash: /usr/share/virtualenvwrapper/virtualenvwrapper.sh: No such file or directory
11:50:16 regal@genedys2: ~ $ export SUBJECTS_DIR=/home/regal/Data/Subjects/test_old_version
11:50:20 regal@genedys2: ~ $ recon-all -s mysubject2 -i /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/regal/Data/Subjects/test_old_version
Actual FREESURFER_HOME /opt/freesurfer-v5
Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux
/home/regal/Data/Subjects/test_old_version/mysubject2

 mri_convert /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig/001.mgz 

mri_convert /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed Jul  4 11:50:37 CEST 2018
Found 1 runs
/home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig/001.mgz /home/regal/Data/Subjects/test_old_version/mysubject2/mri/rawavg.mgz 

/home/regal/Data/Subjects/test_old_version/mysubject2

 mri_convert /home/regal/Data/Subjects/test_old_version/mysubject2/mri/rawavg.mgz /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig.mgz --conform 

mri_convert /home/regal/Data/Subjects/test_old_version/mysubject2/mri/rawavg.mgz /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/regal/Data/Subjects/test_old_version/mysubject2/mri/rawavg.mgz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
writing to /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig.mgz...

 mri_add_xform_to_header -c /home/regal/Data/Subjects/test_old_version/mysubject2/mri/transforms/talairach.xfm /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig.mgz /home/regal/Data/Subjects/test_old_version/mysubject2/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Wed Jul  4 11:50:44 CEST 2018
/home/regal/Data/Subjects/test_old_version/mysubject2/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 

Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux

recon-all -s mysubject2 exited with ERRORS at Wed Jul  4 11:50:46 CEST 2018

For more details, see the log file /home/regal/Data/Subjects/test_old_version/mysubject2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

11:50:46 regal@genedys2: ~ $ 



Do you think it is better to upgrade to the latest version?
Does anyone know how to fix this ?

Thank you for your help, 

Best regards, 

Bernardo

Mailtrack Sender notified by
Mailtrack 07/04/18, 11:55:12 AM

2018-07-03 19:35 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:
Your recon-all command line is not correct, try something like

recon-all -s mysubject -i
/home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -all



On 07/03/2018 01:29 PM, Bernardo Regal wrote:
>
>         External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I have a problem to convert the files using the recon-all.
> It appears, recon-all -s 1 exited with ERRORS.
>
> Before I had the last version (stable v6.0.0). As I did not find a
> solution of how to fix this problem, so I decided to make a downgrade
> to the previous version (5.3.0 stable).  I thought that maybe the
> oldest version of this program was solved. But no, I still have the
> same problem.  How I can fix this problem permanently?
>
> My code is:
> $ export SUBJECTS_DIR=/home/regal/Data/Subjects/test_old_version
> $ recon-all -s 1
> /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii
> -autorecon-all
> than:
>
> " ERROR: Flag
> /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii
> unrecognized.
> -s 1 /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii
> -autorecon-all
> Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20)
> x86_64 GNU/Linux
>
> recon-all -s 1 exited with ERRORS at Tue Jul  3 18:47:19 CEST 2018
>
> For more details, see the log file
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting "
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 2) Platform: Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1
> (2018-03-20) x86_64 GNU/Linux
>
>
> Thank you for your help,
>
> Best regards
>
> --
> Bernardo Regal
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
>       Sender notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
> 07/03/18, 7:27:54 PM 
>
>
>
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--
Bernardo Regal