Re: [Freesurfer] Cannot allocate memory error
Hi Aziz freeview is the tool for visualizing the data, so use it to examine the outputs of recon-all and figure out what is causing the big defect cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, So, I should run the freeview after got those error messages. I will try. Thank you, Aziz. On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl wrote: Hi Aziz it will be in the subject's surf dir. You can visualize it via: freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz without other files. Best Regards, Aziz. On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl wrote: Hi Aziz yes, you ran out of RAM. That said, a defect with 66K vertices is pretty big - more than 1/3 of a typical surface. You should check to make sure nothing big is wrong (hemis attached, skull left around, etc). Look at the inflated.nofix surface and it should be obvious what the defect is cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages CORRECTING DEFECT 46 (vertices=66623, convex hull=8931) Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation Cannot allocate memory Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux I am not sure if this problem came from the insufficient memory on my computer. Otherwise, please let me suggestions for solving this problem. Thank you, Aziz. ___ 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz ___ 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz ___ 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:
Re: [Freesurfer] Cannot allocate memory error
Hi Bruce, So, I should run the freeview after got those error messages. I will try. Thank you, Aziz. On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl wrote: > Hi Aziz > > it will be in the subject's surf dir. You can visualize it via: > > freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix > > > > cheers > Bruce > > > On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: > > Hi Bruce, >> How can I look at inflated.nofix as you mentioned? I think I ran recon-all >> for the 001.mgz without other files. >> >> Best Regards, >> Aziz. >> >> On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl > > >> wrote: >> Hi Aziz >> >> yes, you ran out of RAM. That said, a defect with 66K vertices >> is pretty big - more than 1/3 of a typical surface. You should >> check to make sure nothing big is wrong (hemis attached, skull >> left around, etc). Look at the inflated.nofix surface and it >> should be obvious what the defect is >> >> cheers >> Bruce >> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: >> >> Hi experts, >> >> I ran the command >> >> $recon-all -all -subjid 0696 >> >> I have got these error messages >> >> CORRECTING DEFECT 46 (vertices=66623, convex >> hull=8931) >> Excessive topologic defect encountered: could not >> allocate 322592700 edges >> for retessellation >> Cannot allocate memory >> >> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu >> SMP Tue Apr 10 20:41:14 >> UTC 2012 i686 i686 i386 GNU/Linux >> >> I am not sure if this problem came from the >> insufficient memory on my >> computer. Otherwise, please let me suggestions for >> solving this problem. >> >> Thank you, >> Aziz. >> >> >> >> ___ >> 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. >> >> >> >> >> -- >> >> Aziz Nanthaamornphong, Ph.D., >> Chair of Master of Science Program in Information Technology >> Department of ICT >> Faculty of Technology and Environment >> Prince of Songkla University, Phuket Campus >> +66 7627 6716 (v) >> http://research.te.psu.ac.th/aziz >> >> >> > ___ > 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. > > -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz ___ 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] Cannot allocate memory error
Hi Aziz it will be in the subject's surf dir. You can visualize it via: freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz without other files. Best Regards, Aziz. On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl wrote: Hi Aziz yes, you ran out of RAM. That said, a defect with 66K vertices is pretty big - more than 1/3 of a typical surface. You should check to make sure nothing big is wrong (hemis attached, skull left around, etc). Look at the inflated.nofix surface and it should be obvious what the defect is cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages CORRECTING DEFECT 46 (vertices=66623, convex hull=8931) Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation Cannot allocate memory Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux I am not sure if this problem came from the insufficient memory on my computer. Otherwise, please let me suggestions for solving this problem. Thank you, Aziz. ___ 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz ___ 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] Cannot allocate memory error
Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz without other files. Best Regards, Aziz. On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl wrote: > Hi Aziz > > yes, you ran out of RAM. That said, a defect with 66K vertices is pretty > big - more than 1/3 of a typical surface. You should check to make sure > nothing big is wrong (hemis attached, skull left around, etc). Look at > the inflated.nofix surface and it should be obvious what the defect is > > cheers > Bruce > > On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: > > Hi experts, >> >> I ran the command >> >> $recon-all -all -subjid 0696 >> >> I have got these error messages >> >> CORRECTING DEFECT 46 (vertices=66623, convex hull=8931) >> Excessive topologic defect encountered: could not allocate 322592700 edges >> for retessellation >> Cannot allocate memory >> >> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 >> 20:41:14 >> UTC 2012 i686 i686 i386 GNU/Linux >> >> I am not sure if this problem came from the insufficient memory on my >> computer. Otherwise, please let me suggestions for solving this problem. >> >> Thank you, >> Aziz. >> >> >> > ___ > 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. > > -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz ___ 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] Cannot allocate memory error
Hi Aziz yes, you ran out of RAM. That said, a defect with 66K vertices is pretty big - more than 1/3 of a typical surface. You should check to make sure nothing big is wrong (hemis attached, skull left around, etc). Look at the inflated.nofix surface and it should be obvious what the defect is cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages CORRECTING DEFECT 46 (vertices=66623, convex hull=8931) Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation Cannot allocate memory Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux I am not sure if this problem came from the insufficient memory on my computer. Otherwise, please let me suggestions for solving this problem. Thank you, Aziz. ___ 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] Cannot allocate memory error
Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages *CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)* *Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation* *Cannot allocate memory* *Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux* I am not sure if this problem came from the insufficient memory on my computer. Otherwise, please let me suggestions for solving this problem. Thank you, Aziz. ___ 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.
