Sorry, I actually meant: unset JAVA_TOOL_OPTIONS
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Eugenio Iglesias" <e.igles...@bcbl.eu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, August 14, 2015 11:51:54 AM Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says "export XAPPLRESDIR;", please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Prabesh Kanel" <pk...@my.fsu.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Prabesh Kanel" <pk...@my.fsu.edu> To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
