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 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 Mailtrack<https://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 <dgr...@mgh.harvard.edu<mailto:dgr...@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<mailto:Freesurfer@nmr.mgh.harvard.edu> > 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 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
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