so they might have finished properly if you hadn't done so? Try running -make all again. In theory it's only supposed to reru what is needed.
Bruce On Fri, 8 Feb 2013, Jonathan Holt wrote: > No, the computers they were running on had to be rebooted before they > finished. > On Feb 8, 2013, at 1:19 PM, Jonathan Holt wrote: > >> Basically, I had a bunch of recon-all's terminate without finishing. Do I >> need to run recon-all -s <subjid> -make all, or can I run as usual? >> >> jon >> On Feb 6, 2013, at 9:35 PM, 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 1) is there a way to tell if a surface is out of date without starting up 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 that means that one of the surfaces is out of date, usually because you 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 >> >> > > > _______________________________________________ > 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
