Hi Zeke,
Here¹s the recon-all.log file. I didn¹t erase the old one before I started the run, so all the original bert information is there, my stuff starts near the bottom.
Thanks again for taking a look.
-Matt
On 10/23/14, 10:33 AM, "Z K" zkaufman@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 I¹m still experiencing an issue with freesurfer that I¹m 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 doesn¹t 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.