Hello FS experts,
I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were all stored in .md files. So I changed all of them into .txt, ran recon-all -make (to start from where it left off?), and now it seems to be working.
Below is the output in the terminal when the error occurred (for the ASegStatsLUT.txt case)
CTABreadASCII(/Applications/freesurfer/ASegStatsLUT.txt): could not open file
Computing euler number
orig.nofix lheno = -28, rheno = -16
orig.nofix lhholes = 15, rhholes = 9
Loading mri/aseg.mgz
No such file or directory
ERROR: reading /Applications/freesurfer/ASegStatsLUT.txt
Darwin S-Yui-MacBook.local 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64
recon-all -s yuna exited with ERRORS at Mon Jun 5 22:20:13 KST 2017
I want to ask if I'm doing this correctly, if it's okay to change the format to .txt and run recon-all -make.
Best, Yuna.
p.s. I posted a question on the list one or two days ago and for some reason I wasn't able to reply through the archive with the e-mail address I was using, so I wasn't able to thank you guys for your help.
Now I'm posting with a new e-mail address, and I wanted to thank you for your replies!
Do you have read permission to that file?
On 6/6/17 3:45 AM, 곽유나 wrote:
Hello FS experts,
I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were all stored in .md files. So I changed all of them into .txt, ran recon-all -make (to start from where it left off?), and now it seems to be working.
Below is the output in the terminal when the error occurred (for the ASegStatsLUT.txt case)
CTABreadASCII(/Applications/freesurfer/ASegStatsLUT.txt): could not open file
Computing euler number
orig.nofix lheno = -28, rheno = -16
orig.nofix lhholes = 15, rhholes = 9
Loading mri/aseg.mgz
No such file or directory
ERROR: reading /Applications/freesurfer/ASegStatsLUT.txt
Darwin S-Yui-MacBook.local 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64
recon-all -s yuna exited with ERRORS at Mon Jun 5 22:20:13 KST 2017
I want to ask if I'm doing this correctly, if it's okay to change the format to .txt and run recon-all -make.
Best, Yuna.
p.s. I posted a question on the list one or two days ago and for some reason I wasn't able to reply through the archive with the e-mail address I was using, so I wasn't able to thank you guys for your help.
Now I'm posting with a new e-mail address, and I wanted to thank you for your replies!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yeah I do, I have a read & write permission to that file.
On Tue, Jun 6, 2017 at 11:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Do you have read permission to that file?
On 6/6/17 3:45 AM, 곽유나 wrote:
Hello FS experts,
I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were all stored in .md files. So I changed all of them into .txt, ran recon-all -make (to start from where it left off?), and now it seems to be working.
Below is the output in the terminal when the error occurred (for the ASegStatsLUT.txt case)
CTABreadASCII(/Applications/freesurfer/ASegStatsLUT.txt): could not open file
Computing euler number
orig.nofix lheno = -28, rheno = -16
orig.nofix lhholes = 15, rhholes = 9
Loading mri/aseg.mgz
No such file or directory
ERROR: reading /Applications/freesurfer/ASegStatsLUT.txt
Darwin S-Yui-MacBook.local 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64
recon-all -s yuna exited with ERRORS at Mon Jun 5 22:20:13 KST 2017
I want to ask if I'm doing this correctly, if it's okay to change the format to .txt and run recon-all -make.
Best, Yuna.
p.s. I posted a question on the list one or two days ago and for some reason I wasn't able to reply through the archive with the e-mail address I was using, so I wasn't able to thank you guys for your help.
Now I'm posting with a new e-mail address, and I wanted to thank you for your replies!
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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@nmr.mgh.harvard.edu
-
Douglas Greve -
곽유나