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 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 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 . 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
