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.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.kelly16@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:~$


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