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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Riddle <mriddle@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 




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-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
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  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

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