External Email - Use Caution Hello!
So I have installed the latest Java, reinstalled the Runtime following the instructions on the Freesurfer website, and have attempted to remove Java.opts files, to then run the analysis. Still nothing has changed. Any other suggestions? Thank you, Alex On Tue, Mar 31, 2020 at 6:17 PM Iglesias Gonzalez, Juan E. < [email protected]> wrote: > Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java? > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: *<[email protected]> on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" <[email protected]> > *Reply-To: *Freesurfer support list <[email protected]> > *Date: *Tuesday, March 31, 2020 at 17:59 > *To: *Freesurfer support list <[email protected]> > *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error > > > > * 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. < > [email protected]> 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: *<[email protected]> on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" <[email protected]> > *Reply-To: *Freesurfer support list <[email protected]> > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list <[email protected]> > *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. < > [email protected]> 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: *<[email protected]> on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" <[email protected]> > *Reply-To: *Freesurfer support list <[email protected]> > *Date: *Saturday, March 21, 2020 at 23:33 > *To: *Freesurfer support list <[email protected]> > *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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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