Hi freesurfer experts, Thank you for all your help.
So, I’m re-running freesurfer using version 6, But I got one error message after i type command like this: recon-all -s "$subjID" -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats
And error message like this:
I’m trying to find this error using freesurfer_v6 in the mail archive, but I couldn’t find the same thing. Could you explain this error?
Thanks in advance for any help. Juhyoung
On Feb 10, 2017, at 4:54 AM, Douglas Merkitch Douglas_Merkitch@rush.edu wrote:
The same thing happened to me on my mac when I changed the FREESURFER_HOME variable in the terminal, but not in the .bashrc file that I source when the terminal opens.
Hope this helps!
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center
On Feb 9, 2017, at 1:49 PM, zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu wrote:
Hello Juhyoung,
If its complaining about "RB_all_2008-03-26.gca" then something must have happened where you still have portions of the old freesurfer installed, or your mixing versions because Freesurfer v6 has no mention of RB_all_2008-03-26.gca. Please try completely removing the /Applications/freesurfer directory and reinstalling v6.0.
If this doesnt work please email me the exact command and error output.
Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer', which I installed freesurfer v6. I attached recon-all.log file below. I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c' in log file.
Is there anything to check more?
Thank you, Juhyoung
On Feb 9, 2017, at 12:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in your path?
And can you email the list so others can answer?
thanks Bruce
On Thu, 9 Feb 2017, Juhyoung Ryu wrote:
Hi Bruce, I installed FREESURFER with version 6.0 for your recommendation and I got an error: mri_em_register: could not open GCA /Applications/freesurfer/average/RB_all_2008-03-26.gca. That file not exist in 'average' folder, and there is one similar file: RB_all_2016-05-10.vc700.gca Do you think I should drop that file manually from FREESURFER v5.2? Thank you in advance,Juhyoung
Begin forwarded message:From: Juhyoung Ryu <jh67753737@gmail.com mailto:jh67753737@gmail.com> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0 Date: February 8, 2017 at 11:01:23 AM GMT+9 To: Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Hi Zeke and Bruce, Thank you very much for your help. I'll try it now and share the results. Thanks! Juhyoung.
On Feb 8, 2017, at 8:13 AM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote:Hello Juhyoung, I noticed from the recon-all.log files that you are using freesurfer v5.2. It was revealed that this version had issues regarding systematic white surface contraction and placement of the pial surface extending too far: https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2013-2DMay_029581.html&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=a958-NuaRasmvxPlNYQGH7Xxuni1ja2_K-IPFKTdb38&e= I would recommend processing these subjects with version 6.0 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.... https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=IZpj2AG9on5kqVAJyeidyZ75SJP8XLstoGw15-oiJMk&e= -Zeke On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
Hi FS developers, I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in _only 14 subjects._ Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also. I'd appreciate if you might help me. Juhyoung. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=MDwfHSTvfNLB1hGA3uqMR34lhPdwNmIGoO2KJZWZQCY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=MDwfHSTvfNLB1hGA3uqMR34lhPdwNmIGoO2KJZWZQCY&e=>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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=uU6KntzMpj5JM5tZY5-gdtSUO9jaucky-Rh0zhfG0kY&e= . 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.
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