Interesting. Ive never encountered that issue before but Ive also never conducted an install test on subject bert on Mavericks or Yosemite. Ill take a look. Thanks for the update.
-Zeke On 10/23/2014 12:03 PM, Matthew Riddle wrote: > Hi Zeke, > > So I may have solved the issue. Since /applications is write protected by > default, I had to run the recon-all with sudo. But it seems like the > subroutines of recon-all don't inherit the permissions, so I moved my > Subjects directory to Documents, and then I can run recon-all without the > initial crash, since permissions are no longer an issue. Hopefully it will > run all the way through. > > Best > > -Matt > > Sent from my iPhone > >> On Oct 23, 2014, at 10:34 AM, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote: >> >> Matt, >> >> Can you send me the actual recon-all.log file? It might be helpful for >> me to diagnose the issue. Thanks. >> >> -Zeke >> >>> On 10/23/2014 07:48 AM, Matthew Riddle wrote: >>> 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 >> _______________________________________________ >> 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
