Re: [Freesurfer] recon-all: too many levels of symbolic links

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/BugReportinghttp://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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