Hi Bruce, In fact T1.mgz is ok, but the skull stripping failed and seemed to have taken only the jawbone and the neck.
Best regards, Matthieu 2015-12-09 16:16 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Matthieu > > you need to track backwards and see where the problem started. Why is the > norm warped? Actaully, it shouldn't be warped, although it might be > truncated if the skull stripping failed. > > > cheers > Bruce > On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > > Hi Bruce, >> >> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). >> >> Is this bug fixed in the v6 beta release ? >> >> If this is the case : >> 1) Would you advise me to try on the v6 ? >> 2) Should I so relaunch all recon-all process on my subjects computed >> with v5.3 and work only with the v6 beta ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 15:55 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Matthieu >> >> this might be a bug that is fixed in 6.0. Can you cehck the input to >> mri_cc (norm.mgz) and make sure it is not empty? In older versions >> if the >> skull stripping failed and generated an empty >> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. >> >> cheers >> Bruce >> >> On Wed, 9 Dec 2015, >> Matthieu Vanhoutte wrote: >> >> > Dear FS epxerts, >> > >> > I have launched a recon-all process on a subject. Unfortunately, >> I tried two times but the process get stucked at >> the same step >> > without error. >> > >> > Please found the recon-all.log associated attached to this mail. >> > >> > Thanks in advance for helping ! >> > >> > Best regards, >> > Matthieu >> > >> > >> _______________________________________________ >> 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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