Thank you Douglas for your quick response !

I used the recon-all -i '<image.nii> -subjid <subjname>

Since it wasnt working I tried recon-all -autorecon1 -i '<image.nii> -subjid <subjname> and it worked for SOME files (including the T1) but I don't get the hl/rl.pial files.
Then I tried the autorecon2 on the sa;e data and it does'nt work.

Here is the bug I got.

fsuser@xubuntu-VirtualBox:/media/sf_T1_Groove/Groove_010$ recon-all -autorecon2 -i leo2014_19_anat01.nii -subjid Groove_010_2

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_010_2

mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii...
TR=945000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, -0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz...
#-------------------------------------
#@# EM Registration Wed Nov 8 11:42:54 EST 2017
/usr/local/freesurfer/subjects/Groove_010_2/mri

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta

aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9 using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/usr/local/freesurfer/subjects/Groove_010_2/mri/nu.mgz, -1): could not open file
mri_em_register: could not open input volume nu.mgz.

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

recon-all -s Groove_010_2 exited with ERRORS at Wed Nov 8 11:42:56 EST 2017

For more details, see the log file /usr/local/freesurfer/subjects/Groove_010_2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

THANK YOU very much in advance

Aurelie

On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

what is your command line? Please send the recon-all.log file

On 11/8/17 5:24 AM, aurelie ponz wrote:
Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer VirtualBox.

I dont get any error but no files are created except the 0001.mgz.

Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_009

mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any solutions but I didnt found a solution,

Many thanks in advance,

Aurelie
_______________________________________________
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.