Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autorecon2 and autorecon3 Best, Paul
On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > it depends on how many connections there are > > On Fri, 19 May 2017, miracle ozzoude wrote: > > Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of >> recon-all stage from autorecon2. >> Best, >> Paul >> >> On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> yes, or try rerunning watershed with different parameters. YOu >> don't have to remove the entire skull that was left - just the >> connection between it and wm >> On Fri, 19 May 2017, miracle ozzoude wrote: >> >> Hello Bruce, Yes, the skull is still attached. >> Should I remove the skull for >> all the slices and re-run it again? >> Best, >> Paul >> >> On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Paul >> >> you need to look at the rh.orig.nofix and >> rh.inflated.nofix. >> Typically something big is wrong like skull >> attached to brain or >> something >> >> cheers >> Bruce >> >> >> On Fri, 19 May 2017, miracle ozzoude wrote: >> >> Hello Freesurfer expert, While running >> recon-all on >> one of my subjects, the >> pipeline got stuck during the "fix >> topology rh" >> stage for almost 12hrs. How >> do I diagnosis the problem and fix it? I >> have >> attached the recon-all.log >> file. Thank you >> Best, >> Paul >> >> >> _______________________________________________ >> 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 >> >> >> 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 > > > 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. > >
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