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1) is there a way to tell if a surface is out of date without starting up tkmedit? 2) last time I ran -make all, the command line disappeared until the job completed.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 that means that one of the surfaces is out of date, usually because you 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
