I tried to run a recon-all on a brand new subject and ran into the same issue, so I just moved the subjects directory on a hunch. I'm used to running Freesurfer on a CentOS system, so I'd never really considered OSX being as picky as it seems to be about write permissions. Bert's recon has been running for a couple of hours now without an issue, so let's hope it keeps going. I'll get back to you after it (hopefully) completes and let you know if it solves the issue.
-Matt
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 23, 2014 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
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" 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 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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