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 <fis...@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
<fis...@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.
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--
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
_______________________________________________
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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.
