External Email - Use Caution Thank you so much for your quick response. I saw this link and mentioned this to my server administrator, but he seemed to disagree that that was the source of the issue. There were definitely permissions issues when he first downloaded Matlab R2014b onto the server, but I think they've been resolved (I no longer have trouble accessing files and subdirectories within the MCRv84 folder). That being said, I haven't been able to find "checkRequiredMCRProducts," " deployrc," or "matlabrc," and I don't know where to begin to look. Please let me know if you have any suggestions! ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> Sent: Thursday, October 10, 2019 3:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command
Dear Ola, This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem. https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22&o=newest&f=1 Can you please double check this is not your case? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Olamide Abiose <oabi...@stanford.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 10 October 2019 at 14:29 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Issues with segmentHA_T1.sh command External Email - Use Caution Hello, I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated! Thank you very much. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: 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) Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
