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
