On the first one, you have to add -all, otherwise it won't do anything
On 11/8/17 11:51 AM, aurelie ponz wrote:
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
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
THANK YOU very much in advance
Aurelie
<http://cnec-projects.com>
On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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
<http://cnec-projects.com>
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