Hi Bruce, This is what I get:
FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average On 19 December 2012 21:43, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > ls -1 $FREESURFER_HOME/subjects > cvs_avg35/ > cvs_avg35_inMNI152/ > fsaverage/ > fsaverage3/ > fsaverage4/ > fsaverage5/ > fsaverage6/ > fsaverage_sym/ > lh.EC_average/ > README > rh.EC_average/ > sample-001.mgz > sample-002.mgz > surfer.log > V1_average/ > > not sure why it thinks it doesn't exist. What are the permissions on > > /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average > > can you do an ls on > > /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf > > and post the results? Also do: > > ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average > > > On Wed, 19 Dec 2012, Linda Zhang wrote: > > 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<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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