Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried
re-installing Freesurfer. The subjects folder also has permissions:
drwx------+ 1632 adick staff 54K Nov 5 13:01 Desktop
drwx------+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions for freesurfer/bin using the chmod command: chmod
-R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the
upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Riddle
<mrid...@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
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web :http://reuter.mit.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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