Dear all, I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows: #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 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/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - ln: creating symbolic link `./lh.EC_average': File exists 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/lindadata/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 No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory 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 Fri Dec 14 19:07:07 HKT 2012 For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Cheers, Linda On 14 November 2012 22:29, Linda Zhang <lzhan...@gmail.com> wrote: > 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" <fis...@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<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 <fis...@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 >>> >>> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>>
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