Hi Nick, Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore.
Cheers, Ed On 9 May 2012, at 18:53, Nick Schmansky wrote: > can you send the recon-all.log file? does it say why the > lh.orig_corrected file wasnt created? > > On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote: >> Hi, >> >> I'm using the version of recon-all that Nick provided >> at April 17 to be able to run nu_correct prior to the >> Talairach stage. (I'm on a Mac, OSX 10.6, version >> v5.1.0). The command given was >> >> recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ >> -clean-tal -s subject. >> >> recon-all stopped and issued the following error: >> >> cp: ../surf/lh.orig_corrected: No such file or directory. >> >> Note that I included the option -no-wsgcaatlas to get >> a better skullstripping because in the default mode >> the skulltripping was bad. With this option it looks >> good. >> I got the above error regularly for other subjects as well >> and by including the -no-wsgcaatlas option recon-all >> finished without error, except for the present case. >> >> Cheers, >> Ed >> _______________________________________________ >> 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
