Re: [Freesurfer] recon-all -s 1 exited with ERRORS
External Email - Use Caution Hi, I have 24 gb total of ram. I have 9gb of free memory ram. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 07/05/18, 2:17:58 PM 2018-07-04 11:59 GMT+02:00 Mr. Tass : > External Email - Use Caution > > make sure u have 8gb if ram at least > > Get Outlook for Android <https://aka.ms/ghei36> > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bernardo Regal < > regalberna...@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 &g
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 [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 07/04/18, 11:55:12 AM 2018-07-03 19:35 GMT+02:00 Douglas N. Greve : > 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
[Freesurfer] recon-all -s 1 exited with ERRORS
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 [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_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 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.
