Dear Tiril, 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 ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tiril Pedersen Gurholt t.p.gurholt@medisin.uio.no Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 22 September 2017 at 20:47 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in segmentHA_T1
Dear Experts,
I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6).
When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib».
See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed.
Any ideas as to how to fix these problems?
Best regards,
Tiril
Error message:
#-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017 ------------------------------------------ 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/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] 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/jdk1.8.0_144.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.
#-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017 ------------------------------------------ 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/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] 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/jdk1.8.0_144.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.