Hi Alex,
Unfortunately, I can’t think of any other way to resolve or troubleshoot this.
It might be helpful to post this issue to a java forum or matlab central.
Andrew
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: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 8, 2020 at 11:26 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error
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.
<jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@mgh.harvard.edu>>
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:
<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: Tuesday, March 31, 2020 at 17:59
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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.
<jiglesiasgonza...@mgh.harvard.edu<mailto: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<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 28, 2020 at 02:07
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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
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_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
