External Email - Use Caution Hello Eugenio, No I wasn't! When I first tried to run the subfields I wasn't pointed to downloading a version of Java. I do have Java on the MAC I'm using, but the error "unable to start JVM because of a bad java option" still appears. Any other ideas on how to fix this? Thanks, Alex
On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > HI Alex, > > Were you pointed to downloading a version of Java when you first tried to > run > > the subfields? If so, did you follow the instructions? > > Cheers, > > /Eugenio > > > > > > 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 "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" <l...@email.gwu.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error > > > > * External Email - Use Caution * > > Dear Freesurfer experts, > > > > Hope everyone is well! I'm unfortunately continuing to have errors running > the hippocampal subfield segmentation. Apparently it's being caused by > issues with the java.opts files. I tried removing it (as recommended by a > link someone set me from the Matlab help website), but it made no > difference. Please find my code and error message below: > > > > > > > > CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42 > -hippocampal-subfields-T1 > > Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 ajobsaid wheel 859204 Mar 24 12:59 > /Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log > > Darwin CCASPH-A1900447.cloud.ccas.gwu.edu 18.7.0 Darwin Kernel Version > 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 > x86_64 > > #-------------------------------------------- > > #@# Hippocampal Subfields processing (T1 only) left Tue Mar 24 15:09:44 > EDT 2020 > > \n /Applications/freesurfer/bin/segmentSF_T1.sh > /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42 > /Applications/freesurfer/BAP/3003 left \n > > See log file: > /Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log > > ------------------------------------------ > > Setting up environment variables > > --- > > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: > > Warning: application is running on a locale different from the original > platform locale. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > 2020-03-24 15:09:45.262 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.263 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.263 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.265 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.265 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.265 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > Fatal Error on startup: Unable to start the JVM because of a bad Java > option or unknown error. > > > > #-------------------------------------------- > > #@# Hippocampal Subfields processing (T1 only) right Tue Mar 24 15:09:45 > EDT 2020 > > \n /Applications/freesurfer/bin/segmentSF_T1.sh > /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42 > /Applications/freesurfer/BAP/3003 right \n > > See log file: > /Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log > > ------------------------------------------ > > Setting up environment variables > > --- > > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: > > Warning: application is running on a locale different from the original > platform locale. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > 2020-03-24 15:09:46.333 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.334 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.334 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.334 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.335 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.335 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.336 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.336 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:46.336 > segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > Fatal Error on startup: Unable to start the JVM because of a bad Java > option or unknown error. > > > > > > Started at Tue Mar 24 15:09:43 EDT 2020 > > Ended at Tue Mar 24 15:09:46 EDT 2020 > > #@#%# recon-all-run-time-hours 0.001 > > recon-all -s Sub_42 finished without error at Tue Mar 24 15:09:46 EDT 2020 > > > > Hopefully someone has an idea of what could be done next. Thanks! > > > > All the best, > > Alex > > > > On Sun, Mar 22, 2020 at 10:57 AM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear Alex, > > Can you please try this? > > > https://uk.mathworks.com/matlabcentral/answers/196961-why-do-i-receive-fatal-error-on-startup-unable-to-start-the-jvm-because-of-a-bad-java-option-or-un > > 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 "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" <l...@email.gwu.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Saturday, March 21, 2020 at 23:33 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] Hippocampal Subfield Segmentation Error > > > > * External Email - Use Caution * > > Dear Freesurfer experts, > > > > I am having a problem with hippocampal subfield segmentation. The issue > appears to be related to JavaVM - after I run the code: recon-all -s > (subject ID) -hippocampal-subfields-T1 > > This is the error: > > > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > Fatal Error on startup: Unable to start the JVM because of a bad Java > option or unknown error. > > Please check your java.opts file. > > Any suggestions? > > > > Thank you, > > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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