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> >> 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. >>> Ill 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. >>> >>> Id 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
