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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