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.
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.
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 fischl@nmr.mgh.harvard.edu 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.
Hi Aziz
it will be in the subject's surf dir. You can visualize it via:
freeview -f $SUBJECTS_DIR/<subject id>/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 fischl@nmr.mgh.harvard.edu 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
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 fischl@nmr.mgh.harvard.edu wrote:
Hi Aziz
it will be in the subject's surf dir. You can visualize it via:
freeview -f $SUBJECTS_DIR/<subject id>/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 <fischl@nmr.mgh.harvard.edu
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.
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 fischl@nmr.mgh.harvard.edu wrote: Hi Aziz
it will be in the subject's surf dir. You can visualize it via: freeview -f $SUBJECTS_DIR/<subject id>/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 <fischl@nmr.mgh.harvard.edu> 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@nmr.mgh.harvard.edu
-
Aziz Nanthaamornphong -
Bruce Fischl