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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] https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& Sender notified by Mailtrackhttps://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& 07/04/18, 11:55:12 AM

2018-07-03 19:35 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edumailto: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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Bernardo Regal

Hi Bernardo

can you send us the recon-all.log file?

cheers Bruce On Wed, 4 Jul 2018, Bernardo Regal wrote:

External Email - Use Caution

[3f59805705f4d8ccafe6527c8dff34e531a203d9.png?u=2457469] 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 
  >
  >
  >
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  The information in this e-mail is intended only for the person to whom it is
  addressed. If you believe this e-mail was sent to you in error and the e-mail
  contains patient information, please contact the Partners Compliance HelpLine at
  http://www.partners.org/complianceline . If the e-mail was sent to you in error
  but does not contain patient information, please contact the sender and properly
  dispose of the e-mail.

-- Bernardo Regal

can you send the /home/regal/Data/Subjects/test_old_version/mysubject1/mri/mri_nu_correct.mni.log file?

On 07/05/2018 08:30 AM, Bernardo Regal wrote:

External Email - Use Caution

Hi Bruce,

I attach the file recon-all.log.

Thanks

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& 07/05/18, 2:28:44 PM

2018-07-04 16:32 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:

Hi Bernardo

can you send us the recon-all.log file?

cheers
Bruce
On Wed, 4 Jul 2018, Bernardo Regal wrote:


            External Email - Use Caution

    [3f59805705f4d8ccafe6527c8dff34e531a203d9.png?u=2457469]
    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
    <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 <mailto: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
    <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&
    <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&
    <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
          >
          > 07/03/18, 7:27:54 PM
          >
          >
          >
          > _______________________________________________
          > Freesurfer mailing list
          > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
          >
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

          _______________________________________________
          Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


          The information in this e-mail is intended only for the
    person to whom it is
          addressed. If you believe this e-mail was sent to you in
    error and the e-mail
          contains patient information, please contact the
    Partners Compliance HelpLine at
    http://www.partners.org/complianceline
    <http://www.partners.org/complianceline> . If the e-mail was
    sent to you in error
          but does not contain patient information, please contact
    the sender and properly
          dispose of the e-mail.




    --
    Bernardo Regal


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

-- Bernardo Regal

---

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