Hello Anthony, The problem isnt with the location of the bert folder but rather with the permissions of the bert folder itself (and the permissions within).
To run the bert case please 'cd' into the directory containing the bert folder and type the following: sudo chmod -R a+wr bert -Zeke On 11/05/2014 02:42 PM, Anthony Dick wrote: > Hello Martin, > > I did this (ran it from both the Desktop and Documents). Also tried > re-installing Freesurfer. The subjects folder also has permissions: > > drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop > drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents > > I also set permissions for freesurfer/bin using the chmod command: chmod > -R a+x freesufer/bin/* > > Not really sure what the issue is, but it seems to be related to the > upgrade to Yosemite. > > Anthony > > On 11/5/14, 1:39 PM, Martin Reuter wrote: >> Hi Anthony, >> >> wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a >> place where you have write permissions (as User). >> >> Best, Martin >> >> On 11/05/2014 12:56 PM, Anthony Dick wrote: >>> >>> Hello, >>> >>> >>> I am encountering the exact same problem on Yosemite (10.10). The log >>> file is attached. Any ideas? I am pretty stumped. >>> >>> >>> Anthony >>> >>> >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Riddle >>> <mrid...@nyspi.columbia.edu> >>> *Sent:* Thursday, October 23, 2014 7:48 AM >>> *To:* freesurfer@nmr.mgh.harvard.edu >>> *Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks >>> and Yosemite) >>> Dear Freesurfer Team, >>> >>> I recently installed Freesurfer on a new Macbook pro, which was >>> upgraded to Yosemite, and I re-installed X11 after the upgrade, but >>> I’m still experiencing an issue with freesurfer that I’m hoping you >>> might have some idea about. >>> >>> Just to test the install and see what my total time was to run a >>> recon-all on this machine, I ran the normal recon-all on bert with >>> the command from an X11 terminal: >>> >>> sudo –E recon-all –s bert –all >>> >>> The processes crashes in a minute or two at the same place each time, >>> and this is the last bit of output. >>> >>> MRIchangeType: Building histogram >>> writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... >>> \n mri_add_xform_to_header -c >>> /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm >>> /Applications/freesurfer/subjects/bert/mri/orig.mgz >>> /Applications/freesurfer/subjects/bert/mri/orig.mgz \n >>> INFO: extension is mgz >>> #-------------------------------------------- >>> #@# Talairach Thu Oct 23 07:32:53 EDT 2014 >>> /Applications/freesurfer/subjects/bert/mri >>> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 >>> --no-rescale --i orig.mgz --o orig_nu.mgz \n >>> Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version >>> 14.0.0: Fri Sep 19 00:26:44 PDT 2014; >>> root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 >>> >>> recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 >>> >>> >>> I tried this on an almost identical machine running Mavericks, and >>> got the exact same problem. >>> >>> From my bugr output: >>> >>> FREESURFER_HOME: /Applications/freesurfer >>> >>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >>> >>> Kernel info: Darwin 14.0.0 x86_64 >>> >>> >>> >>> The recon-all.log file doesn’t provide any additional information, it >>> just mirrors the output from the terminal. >>> >>> Thanks, >>> >>> -Matt >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Martin Reuter >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreu...@nmr.mgh.harvard.edu >> reu...@mit.edu >> Web :http://reuter.mit.edu >> >> >> _______________________________________________ >> 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
