Hi Jon I'm not sure what this means, but -make all is the thing to do in this case.
cheers Bruce On Wed, 6 Feb 2013, Jonathan Holt wrote: > Just had a cluster of computers lock up, unfortunately resulting in several > freesurfer jobs terminating prior to completion. It's possible I may have a > ton of this same error come tomorrow. Two questions > > 1) is there a way to tell if a surface is out of date without starting up > tkmedit? > > 2) last time I ran -make all, the command line disappeared until the job > completed. This never happens when I run recon-all with autorecon2&3. Anyway > to avoid this? > > jon > On Feb 1, 2013, at 1:28 PM, Jonathan Holt wrote: > >> OK, good deal! The first time I ran recon-all it exited with errors. That >> must be the issue. >> >> thanks, >> jon >> >>> >>>> Hi Jon >>>> >>>> that means that one of the surfaces is out of date, usually because you >>>> edited and reran but not to completion. Try running >>>> >>>> recon-all -s <subject> -make all >>>> >>>> cheers >>>> Bruce >>>> >>>> p.s. ignore the "can't find file" thing. It really means it tried to read >>>> it, but found it wasn't the same topology as the other surface and that's >>>> what it is complaining about >>>> >>>> On Fri, 1 Feb 2013, >>>> Jonathan Holt wrote: >>>> >>>>> Experts, >>>>> >>>>> Having an issue with this error. It's complaining about rh.pial not >>>>> matching rh.white, indicates there's no such file or directory and that >>>>> mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I >>>>> tried loading rh.pial manually, but upon loading it immediately removes >>>>> every surface on the LH. Wasn't an issue before I ran recon-all. Worth >>>>> noting this brain was generated from a particularly low contrast MRI >>>>> scan, and freesurfer had trouble generating correct surfaces from the get >>>>> go. >>>>> >>>>> Jon >>>>> >>>>> _______________________________________________ >>>>> 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. >>>> >>>> >>>> >>> >> > > > _______________________________________________ > 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
