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, zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@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 <fis...@nmr.mgh.harvard.edu<mailto:fis...@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 <jh67753...@gmail.com<mailto:jh67753...@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 <zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@nmr.mgh.harvard.edu>> Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@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 <zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@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. _______________________________________________ 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= The information in this e-mail is intended only for the person to whom it is addressed. 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