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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