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 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>
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>
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>
Cc: Bruce Fischl <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> 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=
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=
-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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