I checked version of recon-all script using 'recon-all -version’ command and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed.
Juhyoung
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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