On Feb 14, 2017, at 12:39 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Juhyoung
First, can you please paste this kind of thing as text into your email instead of taking snapshots? That makes things easier for us.
Second, why are you telling recon-all not to do the inflation with -noinflate2? That is why it can't find the inflated surface.
cheers
Bruce
On Mon, 13 Feb 2017, Juhyoung Ryu wrote: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.
JuhyoungOn 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,
JuhyoungOn 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.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= <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.edu_fswiki_DownloadAndInstall&d=DwIFAw&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tbfGn9PX8Y7JNwBmOKbl0cqEDAJdta1JKDch4R2RH-Q&s=IZpj2AG9on5kqVAJyeidyZ75SJP8XLstoGw15-oiJMk&e= <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.
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