External Email - Use Caution Hi Olamide,
How to check your line errors without the bash script you are using? Could you at least send the .sh script? Best regards, Rosalia On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose <oabi...@stanford.edu> wrote: > 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
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