On Feb 9, 2017, at 1:02 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

What does

which recon-all

return?

On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu <jh67753737@gmail.com> wrote:

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

<recon-all.log>

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://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
I would recommend processing these subjects with version 6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-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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