Hi Alex,
Do you happen to have jenv installed on your system? Another user on the help list had this same issue a couple years ago, and it seemed like uninstalling jenv was their solution.
best
Andrew
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Date: Tuesday, March 31, 2020 at 6:16 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error
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)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental
Neuroscience" <ladn@email.gwu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 31, 2020 at 17:59
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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. <JIGLESIASGONZALEZ@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)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn@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. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Alex,
Can you please try this?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn@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
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