Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running another process alongside it.  I'll stop the other one and try again.

On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time?
On Wed, 14 Nov 2012, Linda Zhang wrote:

Dear all,
After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3).  The
last few lines are as follows:

0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
Killed
ERROR: mri_ca_register with non-zero status 137
but continuing despite the error
#--------------------------------------
#@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
/home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z 

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux

recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012


Another set is exiting simply with:

#@# EM Registration Mon Nov 12 17:43:05 HKT 2012
/home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta 

Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux

recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



What's the problem I should be addressing?

Thanks!

Cheers,
Linda



On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      Hi Linda

      it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our
      average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else

      cheers
      Bruce


      On Fri, 2 Nov 2012, Linda Zhang wrote:

            Dear all,
            I've been running recon-all on my dataset, but all of them are exiting with
            the same error.  

            The command line is:
            recon-all -subjid ncpoCCW -autorecon2 -autorecon3

            The error reads:
            #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012
            INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
            INFO: Creating symlink to lh.EC_average subject...

             cd /home/virtualuser/freesurfer/subjects; ln -s
            /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - 


             mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label
            lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

            painting output onto subject ncpoCCW.
            processing subject lh.EC_average...
            MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere
            .reg): could not open file
            eroding label 1 times before writing
            thresholding label stat at 0.400 before writing
            Too many levels of symbolic links
            mris_spherical_average: could not read surface file
            /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg
            Too many levels of symbolic links
            Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC
            2011 i686 GNU/Linux

            recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012

            What should I do?  Thanks!

            Cheers,
            Linda




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