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.
