do you mean they finished with an error? If so, what was it? On Fri, 8 Feb 2013, 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 1) is there a way to tell if a surface is out of date without starting up 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 that means that one of the surfaces is out of date, usually because you 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
