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
Description: Binary data
> On Feb 9, 2017, at 12:38 PM, Bruce Fischl <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> >> 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> >> Cc: Bruce Fischl <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> 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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> The information in this e-mail is intended only for the person >> to whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
