External Email - Use Caution
External Email - Use Caution
Hi Eugenio,_______________________________________________Thanks for the tip.I've deleted the /MCR* folder in /tmp and made sure I had enough space in /tmp - 9GB.Unfortunately, the same error message still exists.Let me know if I could further send any debugging logs to help isolate this issue.Thanks for your help!Best,SeanUniversity of MichiganOn Tue, Jul 3, 2018 at 5:59 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:External Email - Use Caution
I was thinking it could be a corrupt MCR cache. Could you please:
a) Delete /tmp/MCR* directories
b) Make sure you've got enough space in /tmp/
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sean Ma <tehsheng@umich.edu>
Sent: Tuesday, July 3, 2018 1:43:18 AM
To: Freesurfer support list
Cc: Hoopes, Andrew
Subject: Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java errorExternal Email - Use Caution
Hi Eugenio,
I’ve followed the wiki and installed it based on the instructions. My server runs on RHEL7.
Best,
Sean
On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:
External Email - Use Caution
That’s rather ugly.
Sean: did you install the runtime from the Mathworks website, or did you download / uncompress following the instrucitons in the wiki?
Andrew: any ideas?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sean Ma <tehsheng@umich.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 2 July 2018 at 20:33
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error
External Email - Use Caution
Hi Eugenio,
I'd like to report a Matlab runtime Java error when running the Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful completion of `recon-all`. Matlab 2014b runtime has been successfully expanded at /MCRv84.
The error I've encountered follows. Any suggestions on how I can overcome this error?
Thanks for your pointers!
Best,
Sean Ma
University of Michigan
==================================
[tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Mon Jul 2 15:16:41 EDT 2018
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64:
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
Error in deployrc (line 9)
Error in matlabrc (line 238)
@#@FSTIME 2018:07:02:15:16:41 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89
@#@FSLOADPOST 2018:07:02:15:17:13 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87
Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Mon Jul 2 15:17:13 EDT 2018
For more details, see the log file /mnt/blab/Sean_Working/FS6results/b30002_02712/scripts/hippocampal-subfields-T1.log
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