External Email - Use Caution Hi all, Not sure if this was resolved off-list or not, but I just ran into it myself and it turned out to be a permissions-related error in that the user didn't have read access to some of the required files in the Matlab runtime. Setting them appropriately resolved the issue.
Best, Niels On Thu, Jul 5, 2018 at 9:37 PM Sean Ma <tehsh...@umich.edu> wrote: > 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, > > Sean > University of Michigan > > > > On Tue, Jul 3, 2018 at 5:59 AM, Iglesias Gonzalez, Eugenio < > e.igles...@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 >> >> http://www.jeiglesias.com >> >> http://cmictig.cs.ucl.ac.uk/ >> >> >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sean Ma < >> tehsh...@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.igles...@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-boun...@nmr.mgh.harvard.edu> on behalf of Sean Ma < >> tehsh...@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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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