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
[Freesurfer] mri_convert mnc to nii
Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation software. I have used mri_convert binary, but the orientation on the nii images is completely wonky. Any advice in terms of how to use the --in_orientation argument --out_orientation argument flags? Reading the documentation on the FS wiki emphasizes how important is to get this right. Any pointers will be much appreciate it. Thanks, Fidel ___ 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] mri_convert mnc to nii
Hi Fidel How do you know it is wrong? Have you looked at the minc and the nifti in freeview? Cheers Bruce On Aug 15, 2015, at 10:19 PM, Schumman Resonance schumm...@gmail.com wrote: Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation software. I have used mri_convert binary, but the orientation on the nii images is completely wonky. Any advice in terms of how to use the --in_orientation argument --out_orientation argument flags? Reading the documentation on the FS wiki emphasizes how important is to get this right. Any pointers will be much appreciate it. Thanks, Fidel ___ 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 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] configure overlay display in tksurfer by keyboard inputs
Hi all, I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am unable to set threshold values in the edit boxes in the configure overlay display in tksurfer. Does anybody know how to fix this (without specifying the threshold on the command line each time)? Thank you! yours, Lars M. Rimol, PhD Department of Medicine John A. Burns School of Medicine University of Hawai'i 1356 Lusitana Street, University Tower Honolulu, HI 96813 ___ 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 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] configure overlay display in tksurfer by keyboard inputs
Hi Lars can you give more details? What prevents you from entering values? Do you get any errors when tksurfer loads? cheers Bruce On Sat, 15 Aug 2015, Lars M. Rimol wrote: Hi all, I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am unable to set threshold values in the edit boxes in the configure overlay display in tksurfer. Does anybody know how to fix this (without specifying the threshold on the command line each time)? Thank you! yours, Lars M. Rimol, PhD Department of Medicine John A. Burns School of Medicine University of Hawai'i 1356 Lusitana Street, University Tower Honolulu, HI 96813 ___ 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.
