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 alandarkenergy@gmail.comwrote:
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.kelly16@gmail.comwrote:
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:~$
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