Hi Bruce, Do you have an idea of how to solve this problem of skull stripping (below) ?
Best regards, Matthieu 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > 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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