Hi Ilana, Nick kindly helped me addressing this issue in one of my subjects. In my case the brainmask had some cortex stripped from the top and the failure had stemmed from there. I would suggest that you also check your brainmask.mgz and see if the skull stripping was successful there. If that is the case you can correct it by adjusting the watershed value (increase it). Please check this link:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nasim On Feb 18, 2011, at 3:34 PM, Ilana Hairston wrote: > what does "old topo fixer" mean? > thanks > ilana > > On 15 February 2011 09:55, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Nasim, > > can you tar and gzip the entire subject dir and send it to us? I'll try > to track it down. In the mean time if you just rerun with the old topo > fixer it should work. Nick can post the appropriate flags > > cheers > Bruce > On Tue, 15 Feb > 2011, Nasim Maleki wrote: > > > Hello, > > > > I'm facing the same problem for one of my subjects. Is there a general > > solution for this problem or would you solve this problem on a case by case > > basis? I saw posts from others with the same problem. > > > > Thanks for your help, > > Nasim > > On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote: > > > >> Hi Jennifer, > >> > >> if you put this on our drop site we'll take a look. > >> > >> cheers > >> Bruce > >> > >> > >> On Mon, 29 Nov 2010, Jennifer Addicks wrote: > >> > >>> Hello, > >>> > >>> I have completed cortical reconstructions for 79 of 80 scans without > >>> error. However, the recon for one participant exited during topology > >>> correction with the following error message: > >>> > >>> ERROR: _FindFacePath: could not find path! > >>> Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel > >>> Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; > >>> root:xnu-1228.15.4~1/RELEASE_I386 i386 > >>> > >>> recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010 > >>> > >>> This error has been posted to the archive previously but the solution > >>> does not seem to accompany it. Any help would be appreciated. > >>> > >>> Thanks, > >>> Jennifer > >>> _______________________________________________ > >>> 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 > >> > > > > > > > > > _______________________________________________ > 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. > > > > > -- > ******************************* > peligro! flaca pero mala! > ****************************** >
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