Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
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]segmentationfaultwhilerunning -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 faultwhile 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 faultwhile 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
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
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] segmentationfault 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 faultwhile 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 faultwhile 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
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 faultwhile 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
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 faultwhile 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 faultwhile 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
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 faultwhile 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 faultwhile 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
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
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
