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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

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

---

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 error

 

        External 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

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

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

 

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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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