Thanks Alan for your response! I've tried typing sudo yum update into the terminal window, however it does not work. It says yum:command not found. I've tried googling how to do this, but I can't find anything. This is what I type into the terminal window:
sudo yum command Am I doing it wrong? Thanks! Krista On Thu, Nov 14, 2013 at 10:48 AM, Alan Francis <alandarkene...@gmail.com>wrote: > Hi Krista: > > You may want to update tcsh. You can do this by using SUDO and 'yum > update'. > > best, > > Alan > > > On Thu, Nov 14, 2013 at 10:42 AM, krista kelly > <krista.kell...@gmail.com>wrote: > >> Hello, >> >> I'm running freesurfer's recon-all using Linux and the past few subjects >> I've run, recon-all has exited with errors. I've ran a few subjects so far >> with no problems, and now all of a sudden there's an issue and I can't >> figure out why. I have been able to run these "problem' subjects using >> Linux on other computers with no issues, so it can't be a raw data issue. I >> have pasted the terminal window text below. If anyone has any idea why this >> is occurring, I'd love to know! >> >> Thanks! >> >> -------- freesurfer-Linux-centos4-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /usr/local/freesurfer >> FSFAST_HOME /usr/local/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /usr/local/freesurfer/subjects >> MNI_DIR /usr/local/freesurfer/mni >> >> Freesurfer Virtual Machine >> sudo password: freesurfer >> >> fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache -notal-check -cw256 >> -subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz >> >> 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 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 >> 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux >> -cw256 option is now persistent (remove with -clean-cw256) >> /usr/local/freesurfer/subjects/BV33 >> >> mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz >> /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz >> >> mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz >> /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz... >> TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (0.999683, 0.0209404, 0.0139622) >> j_ras = (-0.0209424, 0.999781, 0) >> k_ras = (-0.0139591, -0.000292399, 0.999903) >> writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz... >> #-------------------------------------------- >> #@# MotionCor Thu Nov 14 10:28:28 EST 2013 >> Found 1 runs >> /usr/local/freesurfer/subjects/BV33/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 /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz >> /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz >> >> /usr/local/freesurfer/subjects/BV33 >> >> mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz >> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 >> >> mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz >> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz... >> TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (0.999683, 0.0209404, 0.0139622) >> j_ras = (-0.0209424, 0.999781, 0) >> k_ras = (-0.0139591, -0.000292399, 0.999903) >> Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels. >> Data is conformed to 1 mm size and 256 voxels for all directions >> changing data type from float to uchar (noscale = 0)... >> MRIchangeType: Building histogram >> Reslicing using trilinear interpolation >> writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz... >> >> mri_add_xform_to_header -c >> /usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm >> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz >> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz >> >> INFO: extension is mgz >> #-------------------------------------------- >> #@# Talairach Thu Nov 14 10:28:40 EST 2013 >> /usr/local/freesurfer/subjects/BV33/mri >> >> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale >> --i orig.mgz --o orig_nu.mgz >> >> Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 >> 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux >> >> recon-all -s BV33 exited with ERRORS at Thu Nov 14 10:29:51 EST 2013 >> >> For more details, see the log file >> /usr/local/freesurfer/subjects/BV33/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> fsuser@xubuntu-VirtualBox:~$ open >> /usr/local/freesurfer/subjects/BV33/scripts/recon-all >> Couldn't get a file descriptor referring to the console >> fsuser@xubuntu-VirtualBox:~$ >> >> >> _______________________________________________ >> 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. >> >> >
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