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
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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
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
On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto: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 <http://cnec-projects.com> _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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aurelie ponz -
Douglas Greve