Hi Eugenio, It worked when I added unset.
Thank you, Prabesh Sent from my iPhone > On Aug 15, 2015, at 11:43 AM, Eugenio Iglesias <e.igles...@bcbl.eu> wrote: > > Hi Prabesh (et al), > I installed Ubuntu 15.04 at home and unsetting JAVA_TOOL_OPTIONS solved the > problem (in the end it worked for you, too, right?). > 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 support list" <freesurfer@nmr.mgh.harvard.edu> > Sent: Friday, August 14, 2015 9:05:38 AM > Subject: Re: [Freesurfer] segmentation fault while running > -hippocampal-subfields-T1 flag > > Hi Eugenio, > > Thank you for your help. I saw your first email and tried running with > JAVA_TOOL_OPTIONS and it worked. It is still running without segmentation > fault. After I finish that one I will run with unset JAVA_TOOL_OPTIONS. I > will let you know the result of second run. > > 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: Friday, August 14, 2015 11:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] segmentation fault while running > -hippocampal-subfields-T1 flag > > 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 > _______________________________________________ > 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
