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<http://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<mailto: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<mailto: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<mailto:l...@email.gwu.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Saturday, March 21, 2020 at 23:33 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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